[ Started: 2022-11-03 01:01:18 CET ] [ CARNIVAL v2.7.2 for BioC-3.16 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.2-3.16" [3] "/home/omnipath/local/R/4.2" "/usr/lib/R/library" 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.1 (2022-06-23) Old packages: 'annotate', 'AnnotationDbi', 'AUCell', 'beachmat', 'Biobase', 'BiocCheck', 'BiocFileCache', 'BiocGenerics', 'BiocNeighbors', 'BiocParallel', 'BiocSingular', 'BiocStyle', 'biocViews', 'biomaRt', 'BioNet', 'Biostrings', 'BiRewire', 'bluster', 'bslib', 'callr', 'CARNIVAL', 'CellNOptR', 'CNORdt', 'CNORfeeder', 'CNORfuzzy', 'CNORode', 'ComplexHeatmap', 'cosmosR', 'decoupleR', 'DelayedArray', 'DelayedMatrixStats', 'DESeq2', 'edgeR', 'fgsea', 'genefilter', 'geneplotter', 'GenomeInfoDb', 'GenomicRanges', 'graph', 'GSEABase', 'GSVA', 'HDF5Array', 'IRanges', 'KEGGREST', 'limma', 'marray', 'MatrixGenerics', 'metapod', 'mistyR', 'piano', 'progeny', 'qvalue', 'RBGL', 'Rgraphviz', 'rhdf5', 'rhdf5filters', 'Rhdf5lib', 'S4Vectors', 'ScaledMatrix', 'scater', 'scran', 'scuttle', 'SingleCellExperiment', 'sparseMatrixStats', 'SummarizedExperiment', 'supraHex', 'viper', 'wppi', 'XVector', 'zlibbioc' also installing the dependency ‘nloptr’ trying URL 'https://cloud.r-project.org/src/contrib/nloptr_2.0.3.tar.gz' Content type 'application/x-gzip' length 2219877 bytes (2.1 MB) ================================================== downloaded 2.1 MB trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/annotate_1.76.0.tar.gz' Content type 'application/x-gzip' length 1473810 bytes (1.4 MB) ================================================== downloaded 1.4 MB trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/AnnotationDbi_1.60.0.tar.gz' Content type 'application/x-gzip' length 4328584 bytes (4.1 MB) 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================================================== downloaded 916 KB trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/sparseMatrixStats_1.10.0.tar.gz' Content type 'application/x-gzip' length 702076 bytes (685 KB) ================================================== downloaded 685 KB trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/SummarizedExperiment_1.28.0.tar.gz' Content type 'application/x-gzip' length 1526682 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/supraHex_1.36.0.tar.gz' Content type 'application/x-gzip' length 5066419 bytes (4.8 MB) ================================================== downloaded 4.8 MB trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/viper_1.32.0.tar.gz' Content type 'application/x-gzip' length 314961 bytes (307 KB) ================================================== downloaded 307 KB trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/wppi_1.6.0.tar.gz' Content type 'application/x-gzip' length 662021 bytes (646 KB) ================================================== downloaded 646 KB trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/XVector_0.38.0.tar.gz' Content type 'application/x-gzip' length 67821 bytes (66 KB) ================================================== downloaded 66 KB trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/zlibbioc_1.44.0.tar.gz' Content type 'application/x-gzip' length 214256 bytes (209 KB) ================================================== downloaded 209 KB * installing *source* package ‘nloptr’ ... ** package ‘nloptr’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++14 accepts -g... yes checking for g++ -std=gnu++14 option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -std=gnu++14 -E checking whether the compiler supports GNU C++... (cached) yes checking whether g++ -std=gnu++14 accepts -g... (cached) yes checking for g++ -std=gnu++14 option to enable C++11 features... (cached) none needed checking for pkg-config... /usr/bin/pkg-config checking if pkg-config knows NLopt... no checking for cmake... no ------------------ CMAKE NOT FOUND -------------------- CMake was not found on the PATH. Please install CMake: - sudo yum install cmake (Fedora/CentOS; inside a terminal) - sudo apt install cmake (Debian/Ubuntu; inside a terminal). - sudo pacman -S cmake (Arch Linux; inside a terminal). - sudo brew install cmake (MacOS; inside a terminal with Homebrew) - sudo port install cmake (MacOS; inside a terminal with MacPorts) Alternatively install CMake from: ------------------------------------------------------- ERROR: configuration failed for package ‘nloptr’ * removing ‘/home/omnipath/local/R/4.2-3.16/nloptr’ * installing *source* package ‘BiocFileCache’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocFileCache) * installing *source* package ‘BiocGenerics’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘aperm’ in package ‘BiocGenerics’ Creating a new generic function for ‘append’ in package ‘BiocGenerics’ Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’ Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’ Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’ Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’ Creating a new generic function for ‘eval’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’ Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’ Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’ Creating a new generic function for ‘Find’ in package ‘BiocGenerics’ Creating a new generic function for ‘Map’ in package ‘BiocGenerics’ Creating a new generic function for ‘Position’ in package ‘BiocGenerics’ Creating a new generic function for ‘get’ in package ‘BiocGenerics’ Creating a new generic function for ‘mget’ in package ‘BiocGenerics’ Creating a new generic function for ‘grep’ in package ‘BiocGenerics’ Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’ Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’ Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘match’ in package ‘BiocGenerics’ Creating a new generic function for ‘order’ in package ‘BiocGenerics’ Creating a new generic function for ‘paste’ in package ‘BiocGenerics’ Creating a new generic function for ‘rank’ in package ‘BiocGenerics’ Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’ Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’ Creating a new generic function for ‘union’ in package ‘BiocGenerics’ Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’ Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’ Creating a new generic function for ‘sort’ in package ‘BiocGenerics’ Creating a new generic function for ‘table’ in package ‘BiocGenerics’ Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’ Creating a new generic function for ‘unique’ in package ‘BiocGenerics’ Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’ Creating a new generic function for ‘var’ in package ‘BiocGenerics’ Creating a new generic function for ‘sd’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’ Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’ Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’ Creating a new generic function for ‘mad’ in package ‘BiocGenerics’ Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’ Creating a new generic function for ‘basename’ in package ‘BiocGenerics’ Creating a new generic function for ‘dirname’ in package ‘BiocGenerics’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocGenerics) * installing *source* package ‘BiocParallel’ ... ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for shm_open in -lrt... yes configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -I'/home/omnipath/local/R/4.2-3.16/cpp11/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ipcmutex.cpp -o ipcmutex.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o BiocParallel.so cpp11.o ipcmutex.o -lrt -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-BiocParallel/00new/BiocParallel/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocParallel) * installing *source* package ‘BiocStyle’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocStyle) * installing *source* package ‘BiRewire’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c BiRewire.c -o BiRewire.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c interface.c -o interface.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o BiRewire.so BiRewire.o interface.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-BiRewire/00new/BiRewire/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiRewire) * installing *source* package ‘bslib’ ... ** package ‘bslib’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bslib) * installing *source* package ‘callr’ ... ** package ‘callr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (callr) * installing *source* package ‘CARNIVAL’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CARNIVAL) * installing *source* package ‘decoupleR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (decoupleR) * installing *source* package ‘limma’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c normexp.c -o normexp.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c weighted_lowess.c -o weighted_lowess.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o limma.so init.o normexp.o weighted_lowess.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-limma/00new/limma/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (limma) * installing *source* package ‘MatrixGenerics’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MatrixGenerics) * installing *source* package ‘metapod’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c combine_group.cpp -o combine_group.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c combine_parallel.cpp -o combine_parallel.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c count_direction.cpp -o count_direction.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c summarize_direction.cpp -o summarize_direction.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o metapod.so RcppExports.o combine_group.o combine_parallel.o count_direction.o summarize_direction.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-metapod/00new/metapod/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (metapod) * installing *source* package ‘mistyR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mistyR) * installing *source* package ‘qvalue’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (qvalue) * installing *source* package ‘Rhdf5lib’ ... ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether we are using the GNU C++ compiler... yes checking whether g++ -std=gnu++14 accepts -g... yes COMPILER = gcc checking whether C compiler accepts -w... yes checking whether to use -Wl,-rpath setting... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for zlib.h... yes checking szlib.h usability... yes checking 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--enable-cxx --enable-hl \ --enable-tests=no --enable-tools=no \ --with-szlib=yes --with-zlib=yes \ --enable-ros3-vfd \ --enable-sharedlib-rpath \ CC='gcc' CXX='g++ -std=gnu++14' \ CPPFLAGS='' \ CFLAGS='-g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -w -fpic' \ CXXFLAGS='-w -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic'; \ make lib checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... 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for pwrite... yes checking whether to use pread/pwrite instead of read/write in certain VFDs... yes checking whether to have library information embedded in the executables... yes checking if alignment restrictions are strictly enforced... no configure: creating ./config.lt config.lt: creating libtool checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating src/libhdf5.settings config.status: creating Makefile config.status: creating src/Makefile config.status: creating utils/Makefile config.status: creating utils/mirror_vfd/Makefile config.status: creating bin/h5cc config.status: creating bin/Makefile config.status: creating c++/Makefile config.status: creating c++/src/Makefile config.status: creating c++/src/h5c++ config.status: creating hl/Makefile config.status: creating hl/src/Makefile config.status: creating hl/c++/Makefile config.status: creating hl/c++/src/Makefile config.status: creating src/H5config.h config.status: executing pubconf commands creating src/H5pubconf.h Post process src/libhdf5.settings config.status: executing depfiles commands config.status: executing libtool commands config.status: executing .classes commands SUMMARY OF THE HDF5 CONFIGURATION ================================= General Information: ------------------- HDF5 Version: 1.10.7 Configured on: Thu Nov 3 01:03:18 CET 2022 Configured by: omnipath@saezlab Host system: x86_64-unknown-linux-gnu Uname information: Linux saezlab 5.14.0-1051-oem #58-Ubuntu SMP Fri Aug 26 05:50:00 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Byte sex: little-endian Installation point: /tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hdf5 Compiling Options: ------------------ Build Mode: production Debugging Symbols: no Asserts: no Profiling: no Optimization Level: high Linking Options: ---------------- Libraries: static Statically Linked Executables: LDFLAGS: H5_LDFLAGS: AM_LDFLAGS: Extra libraries: -lcrypto -lcurl -lsz -laec -lz -ldl -lm Archiver: ar AR_FLAGS: cr Ranlib: ranlib Languages: ---------- C: yes C Compiler: /usr/bin/gcc CPPFLAGS: H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: C Flags: -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -w -fpic H5 C Flags: -std=c99 -Wno-c++-compat -Wno-format-nonliteral -Wshadow -Wundef -Wwrite-strings -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wno-jump-misses-init -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3 -Werror=bad-function-cast -Werror=declaration-after-statement -Werror=implicit-function-declaration -Werror=missing-declarations -Werror=missing-prototypes -Werror=nested-externs -Werror=old-style-definition -Werror=packed -Werror=pointer-sign -Werror=pointer-to-int-cast -Werror=redundant-decls -Werror=strict-prototypes -Werror=switch -Wunused-function -Wformat -Werror=incompatible-pointer-types -Werror=shadow -Wcast-function-type -Wmaybe-uninitialized AM C Flags: Shared C Library: no Static C Library: yes Fortran: no C++: yes C++ Compiler: /usr/bin/g++ -std=gnu++14 C++ Flags: -w -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic H5 C++ Flags: -Wall -Wconversion -Wctor-dtor-privacy -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-format-nonliteral -Wnon-virtual-dtor -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -O3 -Wcast-align -Wmissing-declarations -Werror=packed -Werror=redundant-decls -Werror=switch -Wunused-but-set-variable -Werror=unused-function -Werror=unused-variable -Wunused-parameter -Werror=shadow AM C++ Flags: Shared C++ Library: no Static C++ Library: yes Java: no Features: --------- Parallel HDF5: no Parallel Filtered Dataset Writes: no Large Parallel I/O: no High-level library: yes Build HDF5 Tests: no Build HDF5 Tools: no Threadsafety: no Default API mapping: v110 With deprecated public symbols: yes I/O filters (external): deflate(zlib),szip(encoder) MPE: no Direct VFD: no Mirror VFD: no (Read-Only) S3 VFD: yes (Read-Only) HDFS VFD: no dmalloc: no Packages w/ extra debug output: none API tracing: no Using memory checker: no Memory allocation sanity checks: no Function stack tracing: no Use file locking: best-effort Strict file format checks: no Optimization instrumentation: no make[1]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5' for d in src . c++ hl; do \ if test $d != .; then \ (cd $d && make lib) || exit 1; \ fi; \ done make[2]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/src' make[3]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/src' CC H5.lo CC H5checksum.lo CC H5dbg.lo CC H5system.lo CC H5timer.lo CC H5trace.lo CC H5A.lo CC H5Abtree2.lo CC H5Adense.lo CC H5Adeprec.lo CC H5Aint.lo CC H5Atest.lo CC H5AC.lo CC H5ACdbg.lo CC H5ACproxy_entry.lo CC H5B.lo CC H5Bcache.lo CC H5Bdbg.lo CC H5B2.lo CC H5B2cache.lo CC H5B2dbg.lo CC H5B2hdr.lo CC H5B2int.lo CC H5B2internal.lo CC H5B2leaf.lo CC H5B2stat.lo CC H5B2test.lo CC H5C.lo CC H5Cdbg.lo CC H5Cepoch.lo CC H5Cimage.lo CC H5Clog.lo CC H5Clog_json.lo CC H5Clog_trace.lo CC H5Cprefetched.lo CC H5Cquery.lo CC H5Ctag.lo CC H5Ctest.lo CC H5CS.lo CC H5CX.lo CC H5D.lo CC H5Dbtree.lo CC H5Dbtree2.lo CC H5Dchunk.lo CC H5Dcompact.lo CC H5Dcontig.lo CC H5Ddbg.lo CC H5Ddeprec.lo CC H5Dearray.lo CC H5Defl.lo CC H5Dfarray.lo CC H5Dfill.lo CC H5Dint.lo CC H5Dio.lo CC H5Dlayout.lo CC H5Dnone.lo CC H5Doh.lo CC H5Dscatgath.lo CC H5Dselect.lo CC H5Dsingle.lo CC H5Dtest.lo CC H5Dvirtual.lo CC H5E.lo CC H5Edeprec.lo CC H5Eint.lo CC H5EA.lo CC H5EAcache.lo CC H5EAdbg.lo CC H5EAdblkpage.lo CC H5EAdblock.lo CC H5EAhdr.lo CC H5EAiblock.lo CC H5EAint.lo CC H5EAsblock.lo CC H5EAstat.lo CC H5EAtest.lo CC H5F.lo CC H5Faccum.lo CC H5Fcwfs.lo CC H5Fdbg.lo CC H5Fdeprec.lo CC H5Fefc.lo CC H5Ffake.lo CC H5Fint.lo CC H5Fio.lo CC H5Fmount.lo CC H5Fquery.lo CC H5Fsfile.lo CC H5Fspace.lo CC H5Fsuper.lo CC H5Fsuper_cache.lo CC H5Ftest.lo CC H5FA.lo CC H5FAcache.lo CC H5FAdbg.lo CC H5FAdblock.lo CC H5FAdblkpage.lo CC H5FAhdr.lo CC H5FAint.lo CC H5FAstat.lo CC H5FAtest.lo CC H5FD.lo CC H5FDcore.lo CC H5FDfamily.lo CC H5FDhdfs.lo CC H5FDint.lo CC H5FDlog.lo CC H5FDmulti.lo CC H5FDsec2.lo CC H5FDspace.lo CC H5FDsplitter.lo CC H5FDstdio.lo CC H5FDtest.lo CC H5FL.lo CC H5FO.lo CC H5FS.lo CC H5FScache.lo CC H5FSdbg.lo CC H5FSint.lo CC H5FSsection.lo CC H5FSstat.lo CC H5FStest.lo CC H5G.lo CC H5Gbtree2.lo CC H5Gcache.lo CC H5Gcompact.lo CC H5Gdense.lo CC H5Gdeprec.lo CC H5Gent.lo CC H5Gint.lo CC H5Glink.lo CC H5Gloc.lo CC H5Gname.lo CC H5Gnode.lo CC H5Gobj.lo CC H5Goh.lo CC H5Groot.lo CC H5Gstab.lo CC H5Gtest.lo CC H5Gtraverse.lo CC H5HF.lo CC H5HFbtree2.lo CC H5HFcache.lo CC H5HFdbg.lo CC H5HFdblock.lo CC H5HFdtable.lo CC H5HFhdr.lo CC H5HFhuge.lo CC H5HFiblock.lo CC H5HFiter.lo CC H5HFman.lo CC H5HFsection.lo CC H5HFspace.lo CC H5HFstat.lo CC H5HFtest.lo CC H5HFtiny.lo CC H5HG.lo CC H5HGcache.lo CC H5HGdbg.lo CC H5HGquery.lo CC H5HL.lo CC H5HLcache.lo CC H5HLdbg.lo CC H5HLint.lo CC H5HLprfx.lo CC H5HLdblk.lo CC H5HP.lo CC H5I.lo CC H5Itest.lo CC H5L.lo CC H5Lexternal.lo CC H5make_libsettings.o CCLD H5make_libsettings LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \ sed -e 's/-L/:/g' -e 's/ //g'`" \ ./H5make_libsettings > H5lib_settings.c || \ (test $HDF5_Make_Ignore && echo "*** Error ignored") || \ (rm -f H5lib_settings.c ; exit 1) CC H5lib_settings.lo CC H5MF.lo CC H5MFaggr.lo CC H5MFdbg.lo CC H5MFsection.lo CC H5MM.lo CC H5MP.lo CC H5MPtest.lo CC H5O.lo CC H5Odeprec.lo CC H5Oainfo.lo CC H5Oalloc.lo CC H5Oattr.lo CC H5Oattribute.lo CC H5Obogus.lo CC H5Obtreek.lo CC H5Ocache.lo CC H5Ocache_image.lo CC H5Ochunk.lo CC H5Ocont.lo CC H5Ocopy.lo CC H5Odbg.lo CC H5Odrvinfo.lo CC H5Odtype.lo CC H5Oefl.lo CC H5Ofill.lo CC H5Oflush.lo CC H5Ofsinfo.lo CC H5Oginfo.lo CC H5Oint.lo CC H5Olayout.lo CC H5Olinfo.lo CC H5Olink.lo CC H5Omessage.lo CC H5Omtime.lo CC H5Oname.lo CC H5Onull.lo CC H5Opline.lo CC H5Orefcount.lo CC H5Osdspace.lo CC H5Oshared.lo CC H5Oshmesg.lo CC H5Ostab.lo CC H5Otest.lo CC H5Ounknown.lo CC H5P.lo CC H5Pacpl.lo CC H5Pdapl.lo CC H5Pdcpl.lo CC H5Pdeprec.lo CC H5Pdxpl.lo CC H5Pencdec.lo CC H5Pfapl.lo CC H5Pfcpl.lo CC H5Pfmpl.lo CC H5Pgcpl.lo CC H5Pint.lo CC H5Plapl.lo CC H5Plcpl.lo CC H5Pocpl.lo CC H5Pocpypl.lo CC H5Pstrcpl.lo CC H5Ptest.lo CC H5PB.lo CC H5PL.lo CC H5PLint.lo CC H5PLpath.lo CC H5PLplugin_cache.lo CC H5R.lo CC H5Rint.lo CC H5Rdeprec.lo CC H5UC.lo CC H5RS.lo CC H5S.lo CC H5Sall.lo CC H5Sdbg.lo CC H5Shyper.lo CC H5Snone.lo CC H5Spoint.lo CC H5Sselect.lo CC H5Stest.lo CC H5SL.lo CC H5SM.lo CC H5SMbtree2.lo CC H5SMcache.lo CC H5SMmessage.lo CC H5SMtest.lo CC H5ST.lo CC H5T.lo CC H5Tarray.lo CC H5Tbit.lo CC H5Tcommit.lo CC H5Tcompound.lo CC H5Tconv.lo CC H5Tcset.lo CC H5Tdbg.lo CC H5Tdeprec.lo CC H5Tenum.lo CC H5Tfields.lo CC H5Tfixed.lo CC H5Tfloat.lo CC H5detect.o CCLD H5detect LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \ sed -e 's/-L/:/g' -e 's/ //g'`" \ ./H5detect > H5Tinit.c || \ (test $HDF5_Make_Ignore && echo "*** Error ignored") || \ (rm -f H5Tinit.c ; exit 1) CC H5Tinit.lo CC H5Tnative.lo CC H5Toffset.lo CC H5Toh.lo CC H5Topaque.lo CC H5Torder.lo CC H5Tpad.lo CC H5Tprecis.lo CC H5Tstrpad.lo CC H5Tvisit.lo CC H5Tvlen.lo CC H5TS.lo CC H5VM.lo CC H5WB.lo CC H5Z.lo CC H5Zdeflate.lo CC H5Zfletcher32.lo CC H5Znbit.lo CC H5Zshuffle.lo CC H5Zscaleoffset.lo CC H5Zszip.lo CC H5Ztrans.lo CC H5FDros3.lo CC H5FDs3comms.lo CCLD libhdf5.la make[3]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/src' make[2]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/src' make[2]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/c++' make[3]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/c++' make[3]: Nothing to be done for 'build-lib'. make[3]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/c++' + cd src + make lib make[3]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/c++/src' make[4]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/c++/src' CXX H5Exception.lo CXX H5IdComponent.lo CXX H5DataSpace.lo CXX H5PropList.lo CXX H5Library.lo CXX H5FaccProp.lo CXX H5FcreatProp.lo CXX H5LcreatProp.lo CXX H5LaccProp.lo CXX H5DaccProp.lo CXX H5DxferProp.lo CXX H5DcreatProp.lo CXX H5Location.lo CXX H5AbstractDs.lo CXX H5Attribute.lo CXX H5Object.lo CXX H5OcreatProp.lo CXX H5DataType.lo CXX H5AtomType.lo CXX H5PredType.lo CXX H5EnumType.lo CXX H5IntType.lo CXX H5FloatType.lo CXX H5StrType.lo CXX H5ArrayType.lo CXX H5VarLenType.lo CXX H5CompType.lo CXX H5DataSet.lo CXX H5CommonFG.lo CXX H5Group.lo CXX H5File.lo CXXLD libhdf5_cpp.la make[4]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/c++/src' make[3]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/c++/src' make[2]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/c++' make[2]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl' make[3]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl' make[3]: Nothing to be done for 'build-lib'. make[3]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl' + cd src + make lib make[3]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl/src' make[4]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl/src' CC H5DO.lo CC H5DS.lo CC H5IM.lo CC H5LT.lo CC H5LTanalyze.lo CC H5LTparse.lo CC H5PT.lo CC H5TB.lo CC H5LD.lo CCLD libhdf5_hl.la make[4]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl/src' make[3]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl/src' + cd c++ + make lib make[3]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl/c++' make[4]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl/c++' make[4]: Nothing to be done for 'build-lib'. make[4]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl/c++' + cd src + make lib make[4]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl/c++/src' make[5]: Entering directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl/c++/src' CXX H5PacketTable.lo CXXLD libhdf5_hl_cpp.la libtool: warning: '/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libcurl.la' seems to be moved make[5]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl/c++/src' make[4]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl/c++/src' make[3]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl/c++' make[2]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5/hl' make[1]: Leaving directory '/tmp/Rtmp1bBoMx/R.INSTALL2872727cd09468/Rhdf5lib/src/hdf5' mkdir -p "/home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp ""hdf5/src"/"*.h "/home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp ""hdf5/c++/src"/"*.h "/home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp ""hdf5/hl/src"/"*.h "/home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp ""hdf5/hl/c++/src"/"*.h "/home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp ""hdf5/src"/"libhdf5.settings "/home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" mkdir -p "/home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp ""hdf5/src/.libs/libhdf5.a"" "/home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp ""hdf5/c++/src/.libs/libhdf5_cpp.a"" "/home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp ""hdf5/hl/src/.libs/libhdf5_hl.a"" "/home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp ""hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a"" "/home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" gcc -I"/usr/share/R/include" -DNDEBUG -I/home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rhdf5lib.c -o Rhdf5lib.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rhdf5lib.so Rhdf5lib.o /home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a -lsz -laec -lz -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rhdf5lib) * installing *source* package ‘supraHex’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (supraHex) * installing *source* package ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2022-11-03 01:05:54] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2022-11-03 01:05:54] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-11-03 01:05:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-11-03 01:05:54] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2022-11-03 01:05:54] [TRACE] [OmnipathR] Contains 1 files. [2022-11-03 01:05:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2022-11-03 01:05:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-11-03 01:05:54] [TRACE] [OmnipathR] Pandoc version: `2.5`. [2022-11-03 01:05:54] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2022-11-03 01:05:56] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-11-03 01:05:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-11-03 01:05:56] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2022-11-03 01:05:56] [TRACE] [OmnipathR] Contains 1 files. [2022-11-03 01:05:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2022-11-03 01:05:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-11-03 01:05:56] [TRACE] [OmnipathR] Pandoc version: `2.5`. [2022-11-03 01:05:56] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2022-11-03 01:05:58] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-11-03 01:05:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-11-03 01:05:58] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2022-11-03 01:05:58] [TRACE] [OmnipathR] Contains 1 files. [2022-11-03 01:05:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2022-11-03 01:05:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-11-03 01:05:58] [TRACE] [OmnipathR] Pandoc version: `2.5`. [2022-11-03 01:05:58] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) * installing *source* package ‘zlibbioc’ ... ** using staged installation configure: creating ./config.status config.status: creating src/Makevars ** libs mkdir -p "/home/omnipath/local/R/4.2-3.16/00LOCK-zlibbioc/00new/zlibbioc/include" gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_zlibbioc.c -o R_init_zlibbioc.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o zlibbioc.so R_init_zlibbioc.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-zlibbioc/00new/zlibbioc/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (zlibbioc) * installing *source* package ‘Biobase’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rinit.c -o Rinit.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c anyMissing.c -o anyMissing.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c envir.c -o envir.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c matchpt.c -o matchpt.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowMedians.c -o rowMedians.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sublist_extract.c -o sublist_extract.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-Biobase/00new/Biobase/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Biobase) * installing *source* package ‘edgeR’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_add_prior_count.cpp -o R_add_prior_count.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_ave_log_cpm.cpp -o R_ave_log_cpm.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_calculate_cpm.cpp -o R_calculate_cpm.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_check_poisson_bound.cpp -o R_check_poisson_bound.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_compute_apl.cpp -o R_compute_apl.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_compute_nbdev.cpp -o R_compute_nbdev.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_fit_levenberg.cpp -o R_fit_levenberg.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_fit_one_group.cpp -o R_fit_one_group.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_get_one_way_fitted.cpp -o R_get_one_way_fitted.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_initialize_levenberg.cpp -o R_initialize_levenberg.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_loess_by_col.cpp -o R_loess_by_col.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_simple_good_turing.cpp -o R_simple_good_turing.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c add_prior.cpp -o add_prior.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c adj_coxreid.cpp -o adj_coxreid.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fmm_spline.c -o fmm_spline.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c glm_levenberg.cpp -o glm_levenberg.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c glm_one_group.cpp -o glm_one_group.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.cpp -o init.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c interpolator.cpp -o interpolator.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nbdev.cpp -o nbdev.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c objects.cpp -o objects.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o edgeR.so R_add_prior_count.o R_ave_log_cpm.o R_calculate_cpm.o R_check_poisson_bound.o R_compute_apl.o R_compute_nbdev.o R_exact_test_by_deviance.o R_fit_levenberg.o R_fit_one_group.o R_get_one_way_fitted.o R_initialize_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_process_hairpin_reads.o R_simple_good_turing.o add_prior.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o nbdev.o objects.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-edgeR/00new/edgeR/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (edgeR) * installing *source* package ‘fgsea’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ScoreCalculation.cpp -o ScoreCalculation.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ScoreRuler.cpp -o ScoreRuler.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c esCalculation.cpp -o esCalculation.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fastGSEA.cpp -o fastGSEA.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fgseaMultilevel.cpp -o fgseaMultilevel.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c geseca.cpp -o geseca.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c util.cpp -o util.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-fgsea/00new/fgsea/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fgsea) * installing *source* package ‘graph’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c graph.c -o graph.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o graph.so graph.o -L/usr/lib/R/lib -lR mv graph.so BioC_graph.so installing to /home/omnipath/local/R/4.2-3.16/00LOCK-graph/00new/graph/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graph) * installing *source* package ‘marray’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (marray) * installing *source* package ‘rhdf5filters’ ... ** using staged installation configuring the BLOSC filter... x86_CPU=true checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether C compiler accepts -msse2... yes checking whether C compiler accepts -mavx2... yes checking for gcc __builtin_cpu_init function... (cached) true checking for x86 sse2 instruction support... yes checking for x86 avx2 instruction support... yes configure: creating ./config.status config.status: creating src/blosc/lib/blosc-1.20.1/Makefile config.status: creating src/blosc/Makefile configure: BZIP2_LIB=bzip2/libH5Zbz2.so configure: BLOSC_LIB=blosc/libH5Zblosc.so configure: LZF_LIB=lzf/libH5Zlzf.so configure: creating ./config.status config.status: creating src/blosc/lib/blosc-1.20.1/Makefile config.status: creating src/blosc/Makefile config.status: creating src/Makevars ** libs make -C blosc make[1]: Entering directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/blosc' make -C lib/snappy-1.1.1 make[2]: Entering directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/blosc/lib/snappy-1.1.1' g++ -std=gnu++14 -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -c snappy.cc g++ -std=gnu++14 -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -c snappy-c.cc g++ -std=gnu++14 -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -c snappy-sinksource.cc g++ -std=gnu++14 -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -c snappy-stubs-internal.cc make[2]: Leaving directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/blosc/lib/snappy-1.1.1' make -C lib/lz4-1.9.2 make[2]: Entering directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/blosc/lib/lz4-1.9.2' gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -c lz4.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -c lz4hc.c make[2]: Leaving directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/blosc/lib/lz4-1.9.2' make -C lib/zstd-1.4.5 make[2]: Entering directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/blosc/lib/zstd-1.4.5' gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress.c -o compress/zstd_compress.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_fast.c -o compress/zstd_fast.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_lazy.c -o compress/zstd_lazy.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_ldm.c -o compress/zstd_ldm.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_opt.c -o compress/zstd_opt.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/huf_decompress.c -o decompress/huf_decompress.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o make[2]: Leaving directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/blosc/lib/zstd-1.4.5' make -C lib/blosc-1.20.1 all make[2]: Entering directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/blosc/lib/blosc-1.20.1' gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c bitshuffle-avx2.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c shuffle-avx2.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c bitshuffle-sse2.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c shuffle-sse2.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c bitshuffle-generic.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c shuffle-generic.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED -c shuffle.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c blosclz.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c blosc.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c fastcopy.c make[2]: Leaving directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/blosc/lib/blosc-1.20.1' rm -f libblosc.a ar cq libblosc.a lib/blosc-1.20.1/bitshuffle-avx2.o lib/blosc-1.20.1/blosc.o lib/blosc-1.20.1/shuffle-avx2.o lib/blosc-1.20.1/shuffle-sse2.o lib/blosc-1.20.1/bitshuffle-generic.o lib/blosc-1.20.1/blosclz.o lib/blosc-1.20.1/shuffle.o lib/blosc-1.20.1/bitshuffle-sse2.o lib/blosc-1.20.1/fastcopy.o lib/blosc-1.20.1/shuffle-generic.o lib/snappy-1.1.1/snappy.o lib/snappy-1.1.1/snappy-c.o lib/snappy-1.1.1/snappy-sinksource.o lib/snappy-1.1.1/snappy-stubs-internal.o lib/lz4-1.9.2/lz4.o lib/lz4-1.9.2/lz4hc.o lib/zstd-1.4.5/common/debug.o lib/zstd-1.4.5/common/entropy_common.o lib/zstd-1.4.5/common/error_private.o lib/zstd-1.4.5/common/fse_decompress.o lib/zstd-1.4.5/common/pool.o lib/zstd-1.4.5/common/threading.o lib/zstd-1.4.5/common/xxhash.o lib/zstd-1.4.5/common/zstd_common.o lib/zstd-1.4.5/compress/fse_compress.o lib/zstd-1.4.5/compress/hist.o lib/zstd-1.4.5/compress/huf_compress.o lib/zstd-1.4.5/compress/zstd_compress.o lib/zstd-1.4.5/compress/zstd_compress_literals.o lib/zstd-1.4.5/compress/zstd_compress_sequences.o lib/zstd-1.4.5/compress/zstd_compress_superblock.o lib/zstd-1.4.5/compress/zstd_double_fast.o lib/zstd-1.4.5/compress/zstd_fast.o lib/zstd-1.4.5/compress/zstd_lazy.o lib/zstd-1.4.5/compress/zstd_ldm.o lib/zstd-1.4.5/compress/zstd_opt.o lib/zstd-1.4.5/compress/zstdmt_compress.o lib/zstd-1.4.5/decompress/huf_decompress.o lib/zstd-1.4.5/decompress/zstd_ddict.o lib/zstd-1.4.5/decompress/zstd_decompress.o lib/zstd-1.4.5/decompress/zstd_decompress_block.o ranlib libblosc.a gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -c -o H5Zblosc.o H5Zblosc.c \ -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -I./lib/blosc-1.20.1 g++ -std=gnu++14 -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -Wl,-Bsymbolic-functions -Wl,-z,relro -shared -o libH5Zblosc.so H5Zblosc.o \ libblosc.a -lz make[1]: Leaving directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/blosc' make -C bzip2 make[1]: Entering directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/bzip2' make -C bzip2-1.0.8 make[2]: Entering directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/bzip2/bzip2-1.0.8' gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -D_FILE_OFFSET_BITS=64 -c blocksort.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -D_FILE_OFFSET_BITS=64 -c huffman.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -D_FILE_OFFSET_BITS=64 -c crctable.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -D_FILE_OFFSET_BITS=64 -c randtable.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -D_FILE_OFFSET_BITS=64 -c compress.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -D_FILE_OFFSET_BITS=64 -c decompress.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -D_FILE_OFFSET_BITS=64 -c bzlib.c rm -f libbz2.a ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o ranlib libbz2.a make[2]: Leaving directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/bzip2/bzip2-1.0.8' gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -shared H5Zbzip2.c -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" \ -I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a -Wl,-Bsymbolic-functions -Wl,-z,relro -o libH5Zbz2.so make[1]: Leaving directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/bzip2' make -C lzf make[1]: Entering directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/lzf' make -C lzf make[2]: Entering directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/lzf/lzf' gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -c lzf_c.c gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -c lzf_d.c rm -f liblzf.a ar cq liblzf.a lzf_c.o lzf_d.o make[2]: Leaving directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/lzf/lzf' gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -shared H5Zlzf.c -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" \ -I./lzf/ ./lzf/liblzf.a -Wl,-Bsymbolic-functions -Wl,-z,relro -o libH5Zlzf.so make[1]: Leaving directory '/tmp/Rtmp7F3G7B/R.INSTALL28b70d3abaed4e/rhdf5filters/src/lzf' mkdir -p "/home/omnipath/local/R/4.2-3.16/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" cp bzip2/libH5Zbz2.so "/home/omnipath/local/R/4.2-3.16/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" cp blosc/libH5Zblosc.so "/home/omnipath/local/R/4.2-3.16/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" cp lzf/libH5Zlzf.so "/home/omnipath/local/R/4.2-3.16/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" gcc -I"/usr/share/R/include" -DNDEBUG -I"/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include" -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rhdf5filters.c -o rhdf5filters.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rhdf5filters.so rhdf5filters.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-rhdf5filters/00new/rhdf5filters/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rhdf5filters) * installing *source* package ‘S4Vectors’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c AEbufs.c -o AEbufs.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c DataFrame_class.c -o DataFrame_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Hits_class.c -o Hits_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c LLint_class.c -o LLint_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c List_class.c -o List_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rle_class.c -o Rle_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rle_utils.c -o Rle_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SEXP_utils.c -o SEXP_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SimpleList_class.c -o SimpleList_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c anyMissing.c -o anyMissing.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c character_utils.c -o character_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c eval_utils.c -o eval_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c hash_utils.c -o hash_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c integer_utils.c -o integer_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c logical_utils.c -o logical_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c map_ranges_to_runs.c -o map_ranges_to_runs.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c raw_utils.c -o raw_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c safe_arithm.c -o safe_arithm.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sort_utils.c -o sort_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c subsetting_utils.c -o subsetting_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vector_utils.c -o vector_utils.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-S4Vectors/00new/S4Vectors/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List” Creating a new generic function for ‘unname’ in package ‘S4Vectors’ Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’ Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’ Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"Hits","DFrame"’: no definition for class “DFrame” Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’ Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’ Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’ in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table” Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (S4Vectors) * installing *source* package ‘sparseMatrixStats’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SparseMatrixView.cpp -o SparseMatrixView.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c methods.cpp -o methods.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c row_methods.cpp -o row_methods.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o sparseMatrixStats.so RcppExports.o SparseMatrixView.o methods.o row_methods.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-sparseMatrixStats/00new/sparseMatrixStats/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sparseMatrixStats) * installing *source* package ‘BiocNeighbors’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c annoy.cpp -o annoy.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c build_annoy.cpp -o build_annoy.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c build_hnsw.cpp -o build_hnsw.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c build_vptree.cpp -o build_vptree.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c distances.cpp -o distances.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c exhaustive.cpp -o exhaustive.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c find_annoy.cpp -o find_annoy.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c find_exhaustive.cpp -o find_exhaustive.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c find_hnsw.cpp -o find_hnsw.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c find_kmknn.cpp -o find_kmknn.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c find_mutual_nns.cpp -o find_mutual_nns.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c find_vptree.cpp -o find_vptree.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c hnsw.cpp -o hnsw.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c kmknn.cpp -o kmknn.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c query_annoy.cpp -o query_annoy.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c query_exhaustive.cpp -o query_exhaustive.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c query_hnsw.cpp -o query_hnsw.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c query_kmknn.cpp -o query_kmknn.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c query_vptree.cpp -o query_vptree.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.cpp -o utils.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppHNSW/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vptree.cpp -o vptree.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o BiocNeighbors.so RcppExports.o annoy.o build_annoy.o build_hnsw.o build_vptree.o distances.o exhaustive.o find_annoy.o find_exhaustive.o find_hnsw.o find_kmknn.o find_mutual_nns.o find_vptree.o hnsw.o kmknn.o query_annoy.o query_exhaustive.o query_hnsw.o query_kmknn.o query_vptree.o utils.o vptree.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-BiocNeighbors/00new/BiocNeighbors/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocNeighbors) * installing *source* package ‘IRanges’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c CompressedList_class.c -o CompressedList_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Grouping_class.c -o Grouping_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c IPosRanges_comparison.c -o IPosRanges_comparison.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c IRanges_class.c -o IRanges_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c IRanges_constructor.c -o IRanges_constructor.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c NCList.c -o NCList.o NCList.c: In function ‘C_print_NCListAsINTSXP’: NCList.c:674:23: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 8 [-Wformat-overflow=] 674 | sprintf(format, "%c0%d%c", '%', max_digits, 'd'); | ^~ NCList.c:674:19: note: directive argument in the range [-2147483647, 2147483647] 674 | sprintf(format, "%c0%d%c", '%', max_digits, 'd'); | ^~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/share/R/include/Rinternals.h:39, from /usr/share/R/include/Rdefines.h:41, from /home/omnipath/local/R/4.2-3.16/S4Vectors/include/S4Vectors_defines.h:18, from ../inst/include/IRanges_defines.h:18, from IRanges.h:1, from NCList.c:5: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 15 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_IRanges.c -o R_init_IRanges.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Ranges_class.c -o Ranges_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RleViews_utils.c -o RleViews_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c coverage_methods.c -o coverage_methods.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c extractListFragments.c -o extractListFragments.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c inter_range_methods.c -o inter_range_methods.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-IRanges/00new/IRanges/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’ Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’ Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (IRanges) * installing *source* package ‘piano’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (piano) * installing *source* package ‘progeny’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (progeny) * installing *source* package ‘RBGL’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bbc.cpp -o bbc.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from bbc.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from bbc.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cliques.cpp -o cliques.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from cliques.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from cliques.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c clusteringCoef.cpp -o clusteringCoef.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from clusteringCoef.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from clusteringCoef.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dominatorTree.cpp -o dominatorTree.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from dominatorTree.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from dominatorTree.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c edmonds_optimum_branching.cpp -o edmonds_optimum_branching.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from edmonds_optimum_branching.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from edmonds_optimum_branching.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c hcs.cpp -o hcs.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from hcs.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from hcs.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c incrConnComp.cpp -o incrConnComp.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from incrConnComp.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from incrConnComp.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c interfaces.cpp -o interfaces.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from interfaces.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from interfaces.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c minST.cpp -o minST.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from minST.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from minST.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mincut.cpp -o mincut.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from mincut.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from mincut.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ordering.cpp -o ordering.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from ordering.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/mem_fn.hpp:25, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/mem_fn.hpp:22, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/bind.hpp:26, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/king_ordering.hpp:18, from ordering.cpp:9: /home/omnipath/local/R/4.2-3.16/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template T * get_pointer(std::auto_ptr const& p) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from ordering.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c planar.cpp -o planar.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from planar.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from planar.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c registerSigHandlers.cpp -o registerSigHandlers.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from registerSigHandlers.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from registerSigHandlers.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c shortestPath.cpp -o shortestPath.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from shortestPath.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from shortestPath.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sna.cpp -o sna.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from sna.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from sna.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c transitive_closure.cpp -o transitive_closure.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/mem_fn.hpp:25, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/mem_fn.hpp:22, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/bind.hpp:26, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /home/omnipath/local/R/4.2-3.16/BH/include/boost/get_pointer.hpp:48:40: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 48 | template T * get_pointer(std::auto_ptr const& p) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/get_pointer.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/mem_fn.hpp:25, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/mem_fn.hpp:22, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/bind.hpp:26, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/graph_concepts.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/depth_first_search.hpp:18, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/strong_components.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/get_pointer.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/mem_fn.hpp:25, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/mem_fn.hpp:22, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/bind.hpp:26, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/graph_concepts.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/depth_first_search.hpp:18, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/strong_components.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/get_pointer.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/mem_fn.hpp:25, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/mem_fn.hpp:22, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/bind.hpp:26, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/graph_concepts.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/depth_first_search.hpp:18, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/strong_components.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/get_pointer.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/mem_fn.hpp:25, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/mem_fn.hpp:22, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/bind.hpp:26, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/graph_concepts.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/depth_first_search.hpp:18, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/strong_components.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/get_pointer.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/mem_fn.hpp:25, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/mem_fn.hpp:22, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/bind.hpp:26, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/graph_concepts.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/depth_first_search.hpp:18, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/strong_components.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/get_pointer.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/mem_fn.hpp:25, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/mem_fn.hpp:22, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/bind.hpp:26, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/graph_concepts.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/depth_first_search.hpp:18, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/strong_components.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/get_pointer.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/mem_fn.hpp:25, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/mem_fn.hpp:22, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/bind.hpp:26, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/graph_concepts.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/depth_first_search.hpp:18, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/strong_components.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:17, from transitive_closure.cpp:16: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/get_pointer.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/mem_fn.hpp:25, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/mem_fn.hpp:22, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/bind.hpp:26, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:21, from transitive_closure.cpp:16: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/config/no_tr1/memory.hpp:21, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/get_pointer.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/mem_fn.hpp:25, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/mem_fn.hpp:22, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/bind/bind.hpp:26, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/transitive_closure.hpp:16, from transitive_closure.cpp:16: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/BH/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c wavefront.cpp -o wavefront.o In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:361:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 361 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:250:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 250 | template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:507:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 507 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:520:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 520 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:603:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 603 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:612:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 612 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:614:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 614 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /home/omnipath/local/R/4.2-3.16/BH/include/boost/scoped_ptr.hpp:13, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:38, from wavefront.cpp:1: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp: At global scope: /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/scoped_ptr.hpp:74:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 74 | explicit scoped_ptr( std::auto_ptr p ) BOOST_SP_NOEXCEPT : px( p.release() ) | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/detail/shared_count.hpp:27, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/vector_property_map.hpp:14, from /home/omnipath/local/R/4.2-3.16/BH/include/boost/property_map/property_map.hpp:606, from RBGL.hpp:17, from wavefront.cpp:1: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RBGL.so bbc.o cliques.o clusteringCoef.o dominatorTree.o edmonds_optimum_branching.o hcs.o incrConnComp.o interfaces.o minST.o mincut.o ordering.o planar.o registerSigHandlers.o shortestPath.o sna.o transitive_closure.o wavefront.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-RBGL/00new/RBGL/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RBGL) * installing *source* package ‘Rgraphviz’ ... ** using staged installation configure: Using bundled Graphviz. configure: Searching for the compilers specified by R. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking how to run the C preprocessor... gcc -E checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++14 accepts -g... yes checking for g++ -std=gnu++14 option to enable C++11 features... none needed 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(cached) yes checking tkInt.h usability... no checking tkInt.h presence... no checking for tkInt.h... no using /usr/lib/tkConfig.sh checking for connect... yes checking for gethostbyname... yes checking for main in -lXpm... no configure: WARNING: Optional Xpm library not available checking X11/Intrinsic.h usability... yes checking X11/Intrinsic.h presence... yes checking for X11/Intrinsic.h... yes checking for X11/Xaw/Text.h... no configure: WARNING: Optional Xaw library not available - missing headers checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for main in -lz... yes checking for deflateBound... no checking for GDK_PIXBUF... yes checking for GTK... no checking for GTKGL... no checking for GTKGLEXT... no checking for GLADE... no checking for qmake-qt4... no checking for qmake-qt3... no checking for qmake... no checking for sincos... yes checking if FILE struct contains _cnt... no checking if FILE struct contains _r... no checking if FILE struct contains _next... no checking if FILE struct contains _IO_read_end... yes checking if errno externs are declared... yes checking if getopt externs are declared... yes checking if intptr_t is declared... yes checking if assert needs __eprintf... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating lib/Makefile config.status: creating lib/cdt/Makefile config.status: creating lib/cdt/libcdt.pc config.status: creating lib/graph/Makefile config.status: creating lib/graph/libgraph.pc config.status: creating lib/rbtree/Makefile config.status: creating lib/pathplan/Makefile config.status: creating lib/pathplan/libpathplan.pc config.status: creating lib/dotgen/Makefile config.status: creating lib/neatogen/Makefile config.status: creating lib/fdpgen/Makefile config.status: creating lib/sparse/Makefile config.status: creating lib/sfdpgen/Makefile config.status: creating lib/osage/Makefile config.status: creating lib/circogen/Makefile config.status: creating lib/twopigen/Makefile config.status: creating lib/patchwork/Makefile config.status: creating lib/pack/Makefile config.status: creating lib/ortho/Makefile config.status: creating lib/common/Makefile config.status: creating lib/vpsc/Makefile config.status: creating lib/gvc/Makefile config.status: creating lib/gvc/libgvc.pc config.status: creating lib/xdot/Makefile config.status: creating lib/xdot/libxdot.pc config.status: creating plugin/Makefile config.status: creating plugin/core/Makefile config.status: creating plugin/dot_layout/Makefile config.status: creating plugin/neato_layout/Makefile config.status: creating graphviz.spec config.status: creating Doxyfile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands === configuring in libltdl (/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/libltdl) configure: running /bin/bash ./configure --disable-option-checking '--prefix=/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix' 'CC=gcc' 'CXX=g++ -std=gnu++14' 'CFLAGS=-g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2' 'LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro' '--libdir=/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib' '--includedir=/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include' '--with-cgraph=no' '--enable-swig=no' '--enable-static' '--disable-shared' '--with-pic' '--with-libgd=no' '--disable-ltdl' '--without-x' '--without-expat' '--without-devil' '--without-rsvg' '--without-ghostscript' '--without-visio' '--without-pangocairo' '--without-lasi' '--without-glitz' '--without-freetype2' '--without-fontconfig' '--without-rpat' '--without-glut' '--without-gts' '--without-png' '--without-tcl' '--without-jpeg' 'R_LIBS=/home/omnipath/local/R/4.2-3.16/00LOCK-Rgraphviz/00new:/home/omnipath/local/R/4.2-3.16:/home/omnipath/local/R/4.2-3.16:/home/omnipath/local/R/4.2' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for shl_load... no checking for shl_load in -ldld... no checking for dlopen... no checking for dlopen in -ldl... yes checking whether a program can dlopen itself... yes checking whether a statically linked program can dlopen itself... no checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking which extension is used for runtime loadable modules... .so checking which variable specifies run-time module search path... LD_LIBRARY_PATH checking for the default library search path... /lib64 /usr/lib64 /lib /usr/lib /opt/illumina/bsfs /usr/lib/x86_64-linux-gnu/libfakeroot /usr/local/lib /usr/local/lib/x86_64-linux-gnu /lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu /lib32 /usr/lib32 checking for library containing dlopen... -ldl checking for dlerror... yes checking for shl_load... (cached) no checking for shl_load in -ldld... (cached) no checking for dld_link in -ldld... no checking for _ prefix in compiled symbols... no checking whether deplibs are loaded by dlopen... yes checking for argz.h... yes checking for error_t... yes checking for argz_add... yes checking for argz_append... yes checking for argz_count... yes checking for argz_create_sep... yes checking for argz_insert... yes checking for argz_next... yes checking for argz_stringify... yes checking if argz actually works... yes checking whether libtool supports -dlopen/-dlpreopen... yes checking for unistd.h... (cached) yes checking for dl.h... no checking for sys/dl.h... no checking for dld.h... no checking for mach-o/dyld.h... no checking for dirent.h... yes checking for closedir... yes checking for opendir... yes checking for readdir... yes checking for strlcat... no checking for strlcpy... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands ---------------------------------------------------------------- graphviz-2.28.0 will be compiled with the following: options: cgraph: No (disabled by default - experimental) digcola: Yes expat: No (disabled) fontconfig: No (disabled) freetype: No (disabled) glut: No (disabled) gts: No (disabled) ipsepcola: No (disabled by default - C++ portability issues) ltdl: No (disabled) ortho: Yes png: No (disabled) jpeg: No (disabled) sfdp: Yes shared: No (disabled) static: Yes qt: No (qmake not found) commands: dot: Yes (always enabled) neato: Yes (always enabled) fdp: Yes (always enabled) circo: Yes (always enabled) twopi: Yes (always enabled) gvpr: Yes (always enabled) gvmap: Yes (always enabled) lefty: No (missing Xaw headers) smyrna: No (disabled by default - experimental) gvedit: No (qmake not found) plugin libraries: dot_layout: Yes (always enabled) neato_layout: Yes (always enabled) core: Yes (always enabled) devil: No (disabled) gd: No (disabled) gdiplus: No (disabled by default - Windows only) gdk_pixbuf: Yes ghostscript: No (disabled) glitz: No (disabled by default - incomplete) gtk: No (gtk library not available) lasi: No (disabled) ming: No (disabled by default - incomplete) pangocairo: No (disabled) quartz: No (disabled by default - Mac only) rsvg: No (disabled) visio: No (disabled by default - experimental) xlib: No (disabled or unavailable) language extensions: gv_sharp: No (swig not available) gv_go: No (disabled by default - experimental) gv_guile: No (swig not available) gv_io: No (disabled by default - no swig support yet) gv_java: No (swig not available) gv_lua: No (swig not available) gv_ocaml: No (swig not available) gv_perl: No (swig not available) gv_php: No (swig not available) gv_python: No (swig not available) gv_python23: No (disabled by default - for multiversion installs) gv_python24: No (disabled by default - for multiversion installs) gv_python25: No (disabled by default - for multiversion installs) gv_python26: No (disabled by default - for multiversion installs) gv_python27: No (disabled by default - for multiversion installs) gv_R: No (swig not available) gv_ruby: No (swig not available) gv_tcl: No (swig not available) tcldot: Yes tclpathplan: Yes gdtclft: No (gd not available) tkspline: Yes grep 'PACKAGE\|VERSION\|GVPLUGIN' config.h > graphviz_version.h make install-recursive make[1]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz' Making install in libltdl make[2]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/libltdl' make install-am make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/libltdl' /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c -o dlopen.lo `test -f 'loaders/dlopen.c' || echo './'`loaders/dlopen.c libtool: compile: gcc -DHAVE_CONFIG_H -I. "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT dlopen.lo -MD -MP -MF .deps/dlopen.Tpo -c loaders/dlopen.c -fPIC -DPIC -o dlopen.o mv -f .deps/dlopen.Tpo .deps/dlopen.Plo /bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -module -avoid-version -Wl,-Bsymbolic-functions -Wl,-z,relro -o dlopen.la dlopen.lo -ldl -ldl libtool: link: ar cru .libs/dlopen.a dlopen.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/dlopen.a libtool: link: ( cd ".libs" && rm -f "dlopen.la" && ln -s "../dlopen.la" "dlopen.la" ) /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c -o libltdlc_la-preopen.lo `test -f 'loaders/preopen.c' || echo './'`loaders/preopen.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT libltdlc_la-preopen.lo -MD -MP -MF .deps/libltdlc_la-preopen.Tpo -c loaders/preopen.c -fPIC -DPIC -o libltdlc_la-preopen.o mv -f .deps/libltdlc_la-preopen.Tpo .deps/libltdlc_la-preopen.Plo /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c -o libltdlc_la-lt__alloc.lo `test -f 'lt__alloc.c' || echo './'`lt__alloc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT libltdlc_la-lt__alloc.lo -MD -MP -MF .deps/libltdlc_la-lt__alloc.Tpo -c lt__alloc.c -fPIC -DPIC -o libltdlc_la-lt__alloc.o mv -f .deps/libltdlc_la-lt__alloc.Tpo .deps/libltdlc_la-lt__alloc.Plo /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c -o libltdlc_la-lt_dlloader.lo `test -f 'lt_dlloader.c' || echo './'`lt_dlloader.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT libltdlc_la-lt_dlloader.lo -MD -MP -MF .deps/libltdlc_la-lt_dlloader.Tpo -c lt_dlloader.c -fPIC -DPIC -o libltdlc_la-lt_dlloader.o mv -f .deps/libltdlc_la-lt_dlloader.Tpo .deps/libltdlc_la-lt_dlloader.Plo /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c -o libltdlc_la-lt_error.lo `test -f 'lt_error.c' || echo './'`lt_error.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT libltdlc_la-lt_error.lo -MD -MP -MF .deps/libltdlc_la-lt_error.Tpo -c lt_error.c -fPIC -DPIC -o libltdlc_la-lt_error.o mv -f .deps/libltdlc_la-lt_error.Tpo .deps/libltdlc_la-lt_error.Plo /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c -o libltdlc_la-ltdl.lo `test -f 'ltdl.c' || echo './'`ltdl.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT libltdlc_la-ltdl.lo -MD -MP -MF .deps/libltdlc_la-ltdl.Tpo -c ltdl.c -fPIC -DPIC -o libltdlc_la-ltdl.o mv -f .deps/libltdlc_la-ltdl.Tpo .deps/libltdlc_la-ltdl.Plo /bin/bash ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc -DLT_CONFIG_H='' -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c -o libltdlc_la-slist.lo `test -f 'slist.c' || echo './'`slist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -DLTDLOPEN=libltdlc "-DLT_CONFIG_H=" -DLTDL -I. -I. -Ilibltdl -I./libltdl -I./libltdl -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MT libltdlc_la-slist.lo -MD -MP -MF .deps/libltdlc_la-slist.Tpo -c slist.c -fPIC -DPIC -o libltdlc_la-slist.o mv -f .deps/libltdlc_la-slist.Tpo .deps/libltdlc_la-slist.Plo /bin/bash ./libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -no-undefined -dlpreopen dlopen.la -Wl,-Bsymbolic-functions -Wl,-z,relro -o libltdlc.la libltdlc_la-preopen.lo libltdlc_la-lt__alloc.lo libltdlc_la-lt_dlloader.lo libltdlc_la-lt_error.lo libltdlc_la-ltdl.lo libltdlc_la-slist.lo lt__strl.lo -ldl libtool: link: rm -f .libs/libltdlc.nm .libs/libltdlc.nmS .libs/libltdlc.nmT libtool: link: (cd .libs && gcc -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -fno-builtin -fPIC -DPIC "libltdlcS.c") libtool: link: rm -f ".libs/libltdlcS.c" ".libs/libltdlc.nm" ".libs/libltdlc.nmS" ".libs/libltdlc.nmT" libtool: link: (cd .libs/libltdlc.lax/dlopen.a && ar x "/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/libltdl/./.libs/dlopen.a") libtool: link: ar cru .libs/libltdlc.a libltdlc_la-preopen.o libltdlc_la-lt__alloc.o libltdlc_la-lt_dlloader.o libltdlc_la-lt_error.o libltdlc_la-ltdl.o libltdlc_la-slist.o lt__strl.o .libs/libltdlcS.o .libs/libltdlc.lax/dlopen.a/dlopen.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libltdlc.a libtool: link: rm -fr .libs/libltdlc.lax libtool: link: ( cd ".libs" && rm -f "libltdlc.la" && ln -s "../libltdlc.la" "libltdlc.la" ) make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/libltdl' make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/libltdl' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/libltdl' make[2]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/libltdl' Making install in lib make[2]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib' Making install in cdt make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/cdt' CC dtclose.lo CC dtdisc.lo dtdisc.c:13:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] 13 | static Void_t* dtmemory(dt, addr, size, disc) | ^~~~~~~~ CC dtextract.lo CC dtflatten.lo CC dthash.lo dthash.c:15:13: warning: function declaration isn't a prototype [-Wstrict-prototypes] 15 | static void dthtab(dt) | ^~~~~~ dthash.c:81:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] 81 | static Void_t* dthash(dt,obj,type) | ^~~~~~ dthash.c: In function 'dthash': dthash.c:306:6: warning: 'r' may be used uninitialized in this function [-Wmaybe-uninitialized] 306 | (*dt->memoryf)(dt,(Void_t*)r,0,disc); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC dtlist.lo dtlist.c:11:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] 11 | static Void_t* dtlist(dt, obj, type) | ^~~~~~ CC dtmethod.lo CC dtopen.lo CC dtrenew.lo CC dtrestore.lo CC dtsize.lo dtsize.c:11:12: warning: function declaration isn't a prototype [-Wstrict-prototypes] 11 | static int treecount(e) | ^~~~~~~~~ CC dtstat.lo dtstat.c:11:13: warning: function declaration isn't a prototype [-Wstrict-prototypes] 11 | static void dttstat(ds,root,depth,level) | ^~~~~~~ dtstat.c:31:13: warning: function declaration isn't a prototype [-Wstrict-prototypes] 31 | static void dthstat(data, ds, count) | ^~~~~~~ CC dtstrhash.lo CC dttree.lo dttree.c:14:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] 14 | static Void_t* dttree(dt,obj,type) | ^~~~~~ dttree.c: In function 'dttree': dttree.c:218:16: warning: 'me' may be used uninitialized in this function [-Wmaybe-uninitialized] 218 | root->right = link.left; CC dttreeset.lo dttreeset.c:11:18: warning: function declaration isn't a prototype [-Wstrict-prototypes] 11 | static Dtlink_t* treebalance(list, size) | ^~~~~~~~~~~ CC dtview.lo dtview.c:12:16: warning: function declaration isn't a prototype [-Wstrict-prototypes] 12 | static Void_t* dtvsearch(dt,obj,type) | ^~~~~~~~~ dtview.c: In function 'dtvsearch': dtview.c:20:12: warning: variable 'lk' set but not used [-Wunused-but-set-variable] 20 | int cmp, lk, sz, ky; | ^~ CC dtwalk.lo dtwalk.c: In function 'dtwalk': dtwalk.c:14:1: warning: function declaration isn't a prototype [-Wstrict-prototypes] 14 | int(* userf)(); | ^~~ CCLD libcdt.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libcdt_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/cdt' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libcdt.la '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libcdt.lai /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libcdt.la libtool: install: /usr/bin/install -c .libs/libcdt.a /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libcdt.a libtool: install: chmod 644 /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libcdt.a libtool: install: ranlib /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libcdt.a libtool: finish: PATH="/usr/bin:/bin:/sbin" ldconfig -n /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 cdt.3 '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man3' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 cdt.3.pdf '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libcdt.pc '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/pkgconfig' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 cdt.h '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/cdt' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/cdt' Making install in graph make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/graph' CC attribs.lo CC agxbuf.lo CC edge.lo CC graph.lo graph.c: In function 'agclose': graph.c:374:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 374 | if (g->attr) | ^~ graph.c:376:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 376 | if (g->didset) | ^~ CC graphio.lo CC lexer.lo lexer.c: In function 'scan_token': lexer.c:141:11: warning: comparison between pointer and zero character constant [-Wpointer-compare] 141 | if (p == '\0') | ^~ lexer.c:141:9: note: did you mean to dereference the pointer? 141 | if (p == '\0') | ^ lexer.c:147:12: warning: pointer targets in returning 'unsigned char *' from a function with return type 'char *' differ in signedness [-Wpointer-sign] 147 | return p; | ^ lexer.c: In function 'html_pair': lexer.c:322:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 322 | int rc, depth = 1; | ^~ In file included from lexer.c:20: lexer.c: In function 'aglex': agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ lexer.c:413:29: note: in expansion of macro 'agxbuse' 413 | aglval.str = agstrdup_html(agxbuse(&xb)); | ^~~~~~~ lexer.c:435:26: warning: pointer targets in passing argument 1 of 'scan_token' differ in signedness [-Wpointer-sign] 435 | LexPtr = scan_token(LexPtr, tbuf); | ^~~~~~ | | | char * lexer.c:136:40: note: expected 'unsigned char *' but argument is of type 'char *' 136 | static char *scan_token(unsigned char *p, unsigned char *token) | ~~~~~~~~~~~~~~~^ lexer.c:435:34: warning: pointer targets in passing argument 2 of 'scan_token' differ in signedness [-Wpointer-sign] 435 | LexPtr = scan_token(LexPtr, tbuf); | ^~~~ | | | char * lexer.c:136:58: note: expected 'unsigned char *' but argument is of type 'char *' 136 | static char *scan_token(unsigned char *p, unsigned char *token) | ~~~~~~~~~~~~~~~^~~~~ lexer.c: In function 'aglasterr': lexer.c:527:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] 527 | fread(buf, sizeof(char), len, agerrout); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC node.lo CC parser.lo CC refstr.lo CC trie.lo CCLD libgraph.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libgraph_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/graph' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libgraph.la '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libgraph.lai /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libgraph.la libtool: install: /usr/bin/install -c .libs/libgraph.a /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libgraph.a libtool: install: chmod 644 /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libgraph.a libtool: install: ranlib /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libgraph.a libtool: finish: PATH="/usr/bin:/bin:/sbin" ldconfig -n /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 graph.3 '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man3' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 graph.3.pdf '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libgraph.pc '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/pkgconfig' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 graph.h '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/graph' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/graph' Making install in pathplan make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/pathplan' CC cvt.lo cvt.c:276:13: warning: 'append_bezier' defined but not used [-Wunused-function] 276 | static void append_bezier(Ppoint_t * bezier) | ^~~~~~~~~~~~~ CC inpoly.lo CC route.lo CC shortest.lo CC shortestpth.lo CC solvers.lo CC triang.lo CC util.lo CC visibility.lo CCLD libpathplan.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libpathplan_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/pathplan' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libpathplan.la '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libpathplan.lai /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libpathplan.la libtool: install: /usr/bin/install -c .libs/libpathplan.a /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libpathplan.a libtool: install: chmod 644 /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libpathplan.a libtool: install: ranlib /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libpathplan.a libtool: finish: PATH="/usr/bin:/bin:/sbin" ldconfig -n /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 pathplan.3 '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man3' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 pathplan.3.pdf '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libpathplan.pc '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/pkgconfig' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 pathgeom.h pathplan.h '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/pathplan' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/pathplan' Making install in vpsc make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/vpsc' make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/vpsc' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/vpsc' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/vpsc' Making install in rbtree make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/rbtree' CC misc.lo CC red_black_tree.lo CC stack.lo CCLD librbtree_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/rbtree' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/rbtree' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/rbtree' Making install in ortho make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/ortho' CC fPQ.lo CC intset.lo CC maze.lo maze.c: In function 'mkMazeGraph': maze.c:325:20: warning: variable 'ncnt' set but not used [-Wunused-but-set-variable] 325 | int nsides, i, ncnt, maxdeg; | ^~~~ CC ortho.lo ortho.c: In function 'addLoop': ortho.c:461:9: warning: variable 'wt' set but not used [-Wunused-but-set-variable] 461 | double wt; | ^~ ortho.c: In function 'addNodeEdges': ortho.c:497:9: warning: variable 'wt' set but not used [-Wunused-but-set-variable] 497 | double wt; | ^~ ortho.c: In function 'orthoEdges': ortho.c:192:11: warning: 'prevbp.x' may be used uninitialized in this function [-Wmaybe-uninitialized] 192 | else if (prevbp.x > bp1.x) l1 = B_RIGHT; | ^ ortho.c:152:22: note: 'prevbp.x' was declared here 152 | pointf bp1, bp2, prevbp; /* bend points */ | ^~~~~~ ortho.c:179:11: warning: 'prevbp.y' may be used uninitialized in this function [-Wmaybe-uninitialized] 179 | else if (prevbp.y > bp1.y) l1 = B_UP; | ^ ortho.c:152:22: note: 'prevbp.y' was declared here 152 | pointf bp1, bp2, prevbp; /* bend points */ | ^~~~~~ ortho.c:1356:2: warning: 'ps' may be used uninitialized in this function [-Wmaybe-uninitialized] 1356 | freePS (ps); | ^~~~~~~~~~~ CC partition.lo partition.c: In function 'traverse_polygon': partition.c:328:7: warning: variable 'do_switch' set but not used [-Wunused-but-set-variable] 328 | int do_switch = FALSE; | ^~~~~~~~~ partition.c:327:7: warning: variable 'retval' set but not used [-Wunused-but-set-variable] 327 | int retval; | ^~~~~~ partition.c: In function 'partition': partition.c:731:9: warning: variable 'nt' set but not used [-Wunused-but-set-variable] 731 | int nt; | ^~ partition.c: In function 'make_new_monotone_poly': partition.c:274:5: warning: 'tq' may be used uninitialized in this function [-Wmaybe-uninitialized] 274 | q = vp1->vpos[iq]; | ~~^~~~~~~~~~~~~~~ partition.c:212:7: warning: 'tp' may be used uninitialized in this function [-Wmaybe-uninitialized] 212 | int tp, tq; | ^~ partition.c: In function 'monotonate_trapezoids': partition.c:665:10: warning: 'size' may be used uninitialized in this function [-Wmaybe-uninitialized] 665 | return size; | ^~~~ CC rawgraph.lo CC sgraph.lo CC trapezoid.lo trapezoid.c:22: warning: "__USE_ISOC99" redefined 22 | #define __USE_ISOC99 | In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/string.h:26, from trapezoid.c:19: /usr/include/features.h:336: note: this is the location of the previous definition 336 | # define __USE_ISOC99 1 | trapezoid.c:66:12: warning: function declaration isn't a prototype [-Wstrict-prototypes] 66 | static int newnode() | ^~~~~~~ trapezoid.c: In function 'add_segment': trapezoid.c:437:7: warning: variable 'tritop' set but not used [-Wunused-but-set-variable] 437 | int tritop = 0, tribot = 0, is_swapped; | ^~~~~~ trapezoid.c:996:3: warning: 'tlastr' may be used uninitialized in this function [-Wmaybe-uninitialized] 996 | merge_trapezoids(segnum, tfirstr, tlastr, S_RIGHT, tr, qs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ trapezoid.c:996:3: warning: 'tfirstr' may be used uninitialized in this function [-Wmaybe-uninitialized] CCLD libortho_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/ortho' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/ortho' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/ortho' Making install in sparse make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/sparse' CC SparseMatrix.lo SparseMatrix.c: In function 'SparseMatrix_import_binary': SparseMatrix.c:629:48: warning: variable 'iread' set but not used [-Wunused-but-set-variable] 629 | int m, n, nz, nzmax, type, format, property, iread; | ^~~~~ CC general.lo CC BinaryHeap.lo In file included from general.h:21, from BinaryHeap.h:17, from BinaryHeap.c:14: BinaryHeap.c: In function 'BinaryHeap_sanity_check': BinaryHeap.c:269:74: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 269 | for (i = 0; i < h->len + IntStack_get_length(h->id_stack); i++) assert(mask[i] =- 1); | ^~~~ CC IntStack.lo CCLD libsparse_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/sparse' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/sparse' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/sparse' Making install in patchwork make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/patchwork' CC patchwork.lo CC patchworkinit.lo CC tree_map.lo CCLD libpatchwork_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/patchwork' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/patchwork' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/patchwork' Making install in common make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/common' CC arrows.lo arrows.c: In function 'arrowOrthoClip': arrows.c:392:21: warning: 'hlen' may be used uninitialized in this function [-Wmaybe-uninitialized] 392 | else r.x = p.x - hlen; | ~~~~^~~~~~ CC colxlate.lo CC fontmetrics.lo CC args.lo CC memory.lo CC globals.lo CC htmllex.lo In file included from render.h:47, from htmllex.c:15: htmllex.c: In function 'error_context': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ htmllex.c:57:35: note: in expansion of macro 'agxbuse' 57 | agerr(AGPREV, "... %s ...\n", agxbuse(state.xb)); | ^~~~~~~ CC htmlparse.lo In file included from render.h:47, from ../../lib/common/htmlparse.y:16: ../../lib/common/htmlparse.y: In function 'appendFItemList': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ ../../lib/common/htmlparse.y:193:25: note: in expansion of macro 'agxbuse' 193 | fi->ti.str = strdup(agxbuse(ag)); | ^~~~~~~ In file included from render.h:47, from ../../lib/common/htmlparse.y:16: ../../lib/common/htmlparse.y: In function 'htmlparse': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ ../../lib/common/htmlparse.y:500:24: note: in expansion of macro 'agxbuse' 500 | if (nonSpace(agxbuse(HTMLstate.str))) { | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ ../../lib/common/htmlparse.y:511:24: note: in expansion of macro 'agxbuse' 511 | if (nonSpace(agxbuse(HTMLstate.str))) { | ^~~~~~~ CC htmltable.lo In file included from render.h:47, from htmltable.c:35: htmltable.c: In function 'initAnchor': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ htmltable.c:299:7: note: in expansion of macro 'agxbuse' 299 | id = agxbuse (&xb); | ^~~~~~~ htmltable.c: In function 'nameOf': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ htmltable.c:1665:12: note: in expansion of macro 'agxbuse' 1665 | return agxbuse(xb); | ^~~~~~~ CC input.lo input.c: In function 'dotneato_basename': input.c:136:5: warning: this 'while' clause does not guard... [-Wmisleading-indentation] 136 | while (*s) s++; s--; | ^~~~~ input.c:136:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'while' 136 | while (*s) s++; s--; | ^ In file included from render.h:47, from input.c:15: input.c: In function 'global_def': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ input.c:200:24: note: in expansion of macro 'agxbuse' 200 | sym = dclfun(NULL, agxbuse (xb), rhs); | ^~~~~~~ CC pointset.lo CC postproc.lo CC routespl.lo CC splines.lo CC psusershape.lo psusershape.c: In function 'user_init': psusershape.c:49:30: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 49 | int saw_bb, must_inline, rc; | ^~ In file included from render.h:47, from psusershape.c:20: psusershape.c: In function 'ps_string': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ psusershape.c:303:5: note: in expansion of macro 'agxbputc' 303 | agxbputc (&xb, RPAREN); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ psusershape.c:305:9: note: in expansion of macro 'agxbuse' 305 | s = agxbuse(&xb); | ^~~~~~~ psusershape.c:268:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 268 | int rc; | ^~ CC timing.lo CC labels.lo labels.c: In function 'xml_url_string': labels.c:561:21: warning: variable 'prev' set but not used [-Wunused-but-set-variable] 561 | char *p, *sub, *prev = NULL; | ^~~~ CC ns.lo CC shapes.lo CC utils.lo utils.c: In function 'chkPort': utils.c:690:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] 690 | else | ^~~~ utils.c:692:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' 692 | pt.name = s; | ^~ In file included from render.h:47, from utils.c:14: utils.c: In function 'clustNode': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c:950:5: note: in expansion of macro 'agxbputc' 950 | agxbputc(xb, ':'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ utils.c:954:29: note: in expansion of macro 'agxbuse' 954 | cn = agnode(agroot(cg), agxbuse(xb)); | ^~~~~~~ utils.c: In function 'scanEntity': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c:1359:5: note: in expansion of macro 'agxbputc' 1359 | agxbputc(xb, '&'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c:1369:5: note: in expansion of macro 'agxbputc' 1369 | agxbputc(xb, '#'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils.c:1371:5: note: in expansion of macro 'agxbputc' 1371 | agxbputc(xb, ';'); | ^~~~~~~~ utils.c: In function 'htmlEntityUTF8': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ utils.c:1515:18: note: in expansion of macro 'agxbuse' 1515 | ns = strdup (agxbuse(&xb)); | ^~~~~~~ utils.c:1456:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 1456 | int rc; | ^~ In file included from render.h:47, from utils.c:14: utils.c: In function 'latin1ToUTF8': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ utils.c:1555:18: note: in expansion of macro 'agxbuse' 1555 | ns = strdup (agxbuse(&xb)); | ^~~~~~~ utils.c:1531:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 1531 | int rc; | ^~ In file included from render.h:47, from utils.c:14: utils.c: In function 'utf8ToLatin1': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ utils.c:1587:18: note: in expansion of macro 'agxbuse' 1587 | ns = strdup (agxbuse(&xb)); | ^~~~~~~ utils.c:1573:9: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 1573 | int rc; | ^~ CC geom.lo CC output.lo In file included from render.h:47, from output.c:14: output.c: In function 'attach_attrs_and_arrows': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ output.c:350:22: note: in expansion of macro 'agxbuse' 350 | agset(n, "pos", agxbuse(&xb)); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ output.c:373:24: note: in expansion of macro 'agxbuse' 373 | agset(n, "rects", agxbuse(&xb)); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ output.c:391:4: note: in expansion of macro 'agxbputc' 391 | agxbputc(&xb, ' '); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ output.c:403:32: note: in expansion of macro 'agxbuse' 403 | agxset(n, N_vertices->index, agxbuse(&xb)); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ output.c:417:4: note: in expansion of macro 'agxbputc' 417 | agxbputc(&xb, ';'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ output.c:434:8: note: in expansion of macro 'agxbputc' 434 | agxbputc(&xb, ' '); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ output.c:440:19: note: in expansion of macro 'agxbuse' 440 | agset(e, "pos", agxbuse(&xb)); | ^~~~~~~ CC emit.lo In file included from render.h:47, from emit.c:25: emit.c: In function 'getObjId': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:212:2: note: in expansion of macro 'agxbputc' 212 | agxbputc (xb, '_'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ emit.c:218:12: note: in expansion of macro 'agxbuse' 218 | return agxbuse(xb); | ^~~~~~~ emit.c: In function 'emit_xdot': emit.c:941:11: warning: variable 'fontname' set but not used [-Wunused-but-set-variable] 941 | char* fontname; | ^~~~~~~~ emit.c:940:12: warning: variable 'fontsize' set but not used [-Wunused-but-set-variable] 940 | double fontsize; | ^~~~~~~~ In file included from render.h:47, from emit.c:25: emit.c: In function 'selectedlayer': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ emit.c:1152:22: note: in expansion of macro 'agxbuse' 1152 | w1 = w0 = strtok(agxbuse(&xb), gvc->layerDelims); | ^~~~~~~ emit.c: In function 'nodeIntersect': emit.c:2247:11: warning: variable 'target' set but not used [-Wunused-but-set-variable] 2247 | char* target; | ^~~~~~ emit.c:2246:11: warning: variable 'tooltip' set but not used [-Wunused-but-set-variable] 2246 | char* tooltip; | ^~~~~~~ emit.c: In function 'xdotBB': emit.c:2474:12: warning: variable 'sz' set but not used [-Wunused-but-set-variable] 2474 | pointf sz; | ^~ emit.c: In function 'style_token': emit.c:3262:16: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 3262 | int token, rc; | ^~ In file included from render.h:47, from emit.c:25: emit.c: In function 'parse_style': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:3356:3: note: in expansion of macro 'agxbputc' 3356 | agxbputc(&ps_xb, '\0'); /* terminate previous */ | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ emit.c:3359:22: note: in expansion of macro 'agxbuse' 3359 | agxbput(&ps_xb, agxbuse(&xb)); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:3360:6: note: in expansion of macro 'agxbputc' 3360 | agxbputc(&ps_xb, '\0'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ emit.c:3372:11: note: in expansion of macro 'agxbuse' 3372 | (void)agxbuse(&ps_xb); /* adds final '\0' to buffer */ | ^~~~~~~ emit.c: In function 'getObjId': emit.c:214:5: warning: 'pfx' may be used uninitialized in this function [-Wmaybe-uninitialized] 214 | agxbput (xb, pfx); | ^~~~~~~~~~~~~~~~~ emit.c: In function 'xdotBB': emit.c:2515:11: warning: 'fontname' may be used uninitialized in this function [-Wmaybe-uninitialized] 2515 | sz = textsize (g, op->para, fontname, fontsize); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:2515:11: warning: 'fontsize' may be used uninitialized in this function [-Wmaybe-uninitialized] emit.c: In function 'emit_edge': emit.c:1932:3: warning: 'bz.eflag' may be used uninitialized in this function [-Wmaybe-uninitialized] 1932 | arrow_gen(job, EMIT_HDRAW, bz.ep, bz.list[bz.size - 1], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1933 | arrowsize, penwidth, bz.eflag); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:1792:12: note: 'bz.eflag' was declared here 1792 | bezier bz; | ^~ emit.c:1921:3: warning: 'bz.sflag' may be used uninitialized in this function [-Wmaybe-uninitialized] 1921 | arrow_gen(job, EMIT_TDRAW, bz.sp, bz.list[0], | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1922 | arrowsize, penwidth, bz.sflag); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:1792:12: note: 'bz.sflag' was declared here 1792 | bezier bz; | ^~ emit.c:1932:47: warning: 'bz.size' may be used uninitialized in this function [-Wmaybe-uninitialized] 1932 | arrow_gen(job, EMIT_HDRAW, bz.ep, bz.list[bz.size - 1], | ~~^~~~~ emit.c:1792:12: note: 'bz.size' was declared here 1792 | bezier bz; | ^~ emit.c:1932:44: warning: 'bz.list' may be used uninitialized in this function [-Wmaybe-uninitialized] 1932 | arrow_gen(job, EMIT_HDRAW, bz.ep, bz.list[bz.size - 1], | ^ emit.c:1792:12: note: 'bz.list' was declared here 1792 | bezier bz; | ^~ emit.c:1776:10: warning: 'endcolor' may be used uninitialized in this function [-Wmaybe-uninitialized] 1776 | gvrender_set_fillcolor(job, endcolor); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emit.c:1723:11: note: 'endcolor' was declared here 1723 | char* endcolor; | ^~~~~~~~ emit.c:1746:19: warning: 'segs' may be used uninitialized in this function [-Wmaybe-uninitialized] 1746 | if (s == segs->segs) { | ~~~~^~~~~~ emit.c:1721:18: note: 'segs' was declared here 1721 | colorsegs_t* segs; | ^~~~ CCLD libcommon_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/common' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 arith.h geom.h color.h types.h textpara.h usershape.h '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/common' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/common' Making install in pack make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/pack' CC ccomps.lo CC pack.lo pack.c: In function 'putGraphs': pack.c:953:12: warning: 'pts' may be used uninitialized in this function [-Wmaybe-uninitialized] 953 | return pts; | ^~~ CCLD libpack_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/pack' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 pack.3 '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man3' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 pack.3.pdf '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 pack.h '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/pack' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/pack' Making install in xdot make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/xdot' CC xdot.lo xdot.c: In function 'sprintXDot': xdot.c:537:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 537 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xdot.c:538:21: note: in expansion of macro 'agxbputc' 538 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ xdot.c:606:16: note: in expansion of macro 'agxbuse' 606 | s = strdup(agxbuse(&xb)); | ^~~~~~~ CCLD libxdot.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libxdot_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/xdot' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libxdot.la '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libxdot.lai /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libxdot.la libtool: install: /usr/bin/install -c .libs/libxdot.a /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libxdot.a libtool: install: chmod 644 /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libxdot.a libtool: install: ranlib /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libxdot.a libtool: finish: PATH="/usr/bin:/bin:/sbin" ldconfig -n /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 xdot.3 '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man3' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 xdot.3.pdf '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libxdot.pc '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/pkgconfig' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 xdot.h '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/xdot' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/xdot' Making install in gvc make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/gvc' CC gvrender.lo CC gvlayout.lo CC gvdevice.lo In file included from ../../lib/common/types.h:18, from gvplugin_device.h:17, from gvdevice.c:55: gvdevice.c: In function 'gvfwrite': gvdevice.c:269:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 269 | assert(size = sizeof(char)); | ^~~~ CC gvloadimage.lo CC gvcontext.lo CC gvjobs.lo CC gvevent.lo CC gvplugin.lo In file included from gvplugin.c:23: gvplugin.c: In function 'gvplugin_list': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvplugin.c:392:3: note: in expansion of macro 'agxbputc' 392 | agxbputc(&xb,' '); agxbput(&xb, (*pnext)->typestr); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvplugin.c:393:3: note: in expansion of macro 'agxbputc' 393 | agxbputc(&xb,':'); agxbput(&xb, (*pnext)->package->name); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvplugin.c:410:3: note: in expansion of macro 'agxbputc' 410 | agxbputc(&xb,' '); agxbput(&xb, q); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvplugin.c:423:7: note: in expansion of macro 'agxbuse' 423 | bp = agxbuse(&xb); | ^~~~~~~ CC gvconfig.lo CC gvtextlayout.lo CC gvusershape.lo gvusershape.c: In function 'gvusershape_open': gvusershape.c:415:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 415 | if (!(us->data = (void*)find_user_shape(us->name))) | ^~ gvusershape.c:417:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 417 | free(us); | ^~~~ CC gvc.lo CCLD libgvc.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libgvc_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/gvc' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib' /bin/bash ../../libtool --mode=install /usr/bin/install -c libgvc.la '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib' libtool: install: /usr/bin/install -c .libs/libgvc.lai /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libgvc.la libtool: install: /usr/bin/install -c .libs/libgvc.a /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libgvc.a libtool: install: chmod 644 /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libgvc.a libtool: install: ranlib /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/libgvc.a libtool: finish: PATH="/usr/bin:/bin:/sbin" ldconfig -n /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib ---------------------------------------------------------------------- Libraries have been installed in: /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man3' /usr/bin/install -c -m 644 gvc.3 '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man3' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /usr/bin/install -c -m 644 gvc.3.pdf '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc/pdf' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/pkgconfig' /usr/bin/install -c -m 644 libgvc.pc '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/pkgconfig' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 gvc.h gvcext.h gvplugin.h gvcjob.h gvcommon.h gvplugin_render.h gvplugin_layout.h gvconfig.h gvplugin_textlayout.h gvplugin_device.h gvplugin_loadimage.h '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/gvc' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/gvc' Making install in circogen make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/circogen' CC circularinit.lo CC nodelist.lo CC block.lo CC edgelist.lo CC circular.lo CC deglist.lo CC blocktree.lo CC blockpath.lo CC circpos.lo circpos.c: In function 'doBlock': circpos.c:338:13: warning: 'midAngle' may be used uninitialized in this function [-Wmaybe-uninitialized] 338 | PSI(pi->n) = midAngle; circpos.c:264:39: note: 'midAngle' was declared here 264 | double mindistAngle, rotateAngle, midAngle; | ^~~~~~~~ CC nodeset.lo CCLD libcircogen_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/circogen' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/circogen' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/circogen' Making install in dotgen make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/dotgen' CC acyclic.lo CC class1.lo CC class2.lo CC cluster.lo CC compound.lo CC conc.lo CC decomp.lo CC fastgr.lo CC flat.lo CC dotinit.lo CC mincross.lo mincross.c: In function 'mincross.constprop': mincross.c:374:9: warning: 'sepIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] 374 | int sepIndex; | ^~~~~~~~ CC position.lo CC rank.lo CC sameport.lo CC dotsplines.lo dotsplines.c: In function 'makeLineEdge': dotsplines.c:1604:23: warning: right-hand operand of comma expression has no effect [-Wunused-value] 1604 | lp = ED_label(e)->pos, lp; | ^ dotsplines.c: In function 'completeregularpath': dotsplines.c:1866:9: warning: variable 'pn' set but not used [-Wunused-but-set-variable] 1866 | int pn; | ^~ dotsplines.c:1865:13: warning: variable 'pp' set but not used [-Wunused-but-set-variable] 1865 | pointf *pp; | ^~ dotsplines.c: In function 'makeSimpleFlatLabels': dotsplines.c:993:18: warning: 'lmaxx' may be used uninitialized in this function [-Wmaybe-uninitialized] 993 | points[5].x = lmaxx; | ~~~~~~~~~~~~^~~~~~~ dotsplines.c:997:18: warning: 'lminx' may be used uninitialized in this function [-Wmaybe-uninitialized] 997 | points[7].x = lminx; | ~~~~~~~~~~~~^~~~~~~ CC aspect.lo aspect.c: In function 'computeCombiAR': aspect.c:1614:12: warning: variable 'maxLayerIndex' set but not used [-Wunused-but-set-variable] 1614 | int i, maxLayerIndex; | ^~~~~~~~~~~~~ aspect.c: In function 'rank3': aspect.c:702:9: warning: 'maxLayerIndex' may be used uninitialized in this function [-Wmaybe-uninitialized] 702 | int maxLayerIndex; | ^~~~~~~~~~~~~ aspect.c:750:2: warning: 'nextMaxWidth' may be used uninitialized in this function [-Wmaybe-uninitialized] 749 | if (nextMaxWidth <= layerWidthInfo[maxLayerIndex].width / 4 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 750 | || nextMaxWidth >= layerWidthInfo[maxLayerIndex].width * 3 / 4) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aspect.c:703:12: note: 'nextMaxWidth' was declared here 703 | double nextMaxWidth; | ^~~~~~~~~~~~ CCLD libdotgen_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/dotgen' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/dotgen' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/dotgen' Making install in fdpgen make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/fdpgen' CC comp.lo CC dbg.lo CC grid.lo CC fdpinit.lo CC layout.lo CC tlayout.lo CC xlayout.lo CC clusteredges.lo CCLD libfdpgen_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/fdpgen' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/fdpgen' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/fdpgen' Making install in neatogen make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/neatogen' CC adjust.lo In file included from ../../lib/common/render.h:44, from neato.h:37, from adjust.c:19: adjust.c: In function 'getSizes': ../../lib/common/memory.h:39:30: warning: 'nedge_nodes' may be used uninitialized in this function [-Wmaybe-uninitialized] 39 | #define N_GNEW(n,t) (t*)gmalloc((n)*sizeof(t)) | ^~~~~~~ adjust.c:670:12: note: 'nedge_nodes' was declared here 670 | int i, nedge_nodes; | ^~~~~~~~~~~ adjust.c: In function 'removeOverlapWith': adjust.c:1045:9: warning: 'ret' may be used uninitialized in this function [-Wmaybe-uninitialized] 1045 | int ret; | ^~~ CC circuit.lo CC edges.lo CC geometry.lo CC heap.lo CC hedges.lo CC info.lo CC neatoinit.lo CC legal.lo CC lu.lo CC matinv.lo CC memory.lo CC poly.lo CC printvis.lo CC site.lo CC solve.lo CC neatosplines.lo neatosplines.c: In function 'makeObstacle': neatosplines.c:363:13: warning: variable 'desc' set but not used [-Wunused-but-set-variable] 363 | epsf_t *desc; | ^~~~ neatosplines.c: In function '_spline_edges': neatosplines.c:603:15: warning: unused variable 'rtr' [-Wunused-variable] 603 | router_t* rtr = 0; | ^~~ CC stuff.lo CC voronoi.lo voronoi.c: In function 'voronoi': voronoi.c:48:7: warning: 'newintstar.y' may be used uninitialized in this function [-Wmaybe-uninitialized] 45 | if (newsite != (struct Site *) NULL && (PQempty() | ~~~~~~~~~~ 46 | || newsite->coord.y < | ~~~~~~~~~~~~~~~~~~~~~ 47 | newintstar.y | ~~~~~~~~~~~~ 48 | || (newsite->coord.y == | ^~~~~~~~~~~~~~~~~~~~~~~ 49 | newintstar.y | ~~~~~~~~~~~~ 50 | && newsite->coord.x < | ~~~~~~~~~~~~~~~~~~~~~ 51 | newintstar.x))) { | ~~~~~~~~~~~~~~ CC stress.lo stress.c: In function 'mdsModel': stress.c:1383:12: warning: 'delta' may be used uninitialized in this function [-Wmaybe-uninitialized] 1383 | delta += abs(Dij[i*nG + j - shift] - graph[i].ewgts[e]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CC kkutils.lo CC matrix_ops.lo CC embed_graph.lo CC dijkstra.lo CC conjgrad.lo CC pca.lo CC closest.lo CC bfs.lo CC constraint.lo CC quad_prog_solve.lo CC smart_ini_x.lo CC constrained_majorization.lo CC opt_arrangement.lo CC overlap.lo CC call_tri.lo CC compute_hierarchy.lo CC delaunay.lo CC multispline.lo CCLD libneatogen_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/neatogen' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/neatogen' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/neatogen' Making install in twopigen make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/twopigen' CC twopiinit.lo CC circle.lo circle.c: In function 'circleLayout': circle.c:285:5: warning: 'delx' may be used uninitialized in this function [-Wmaybe-uninitialized] 285 | xf += delx; | ~~~^~~~~~~ circle.c:268:20: note: 'delx' was declared here 268 | double xf = 0, delx, d; | ^~~~ CCLD libtwopigen_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/twopigen' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/twopigen' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/twopigen' Making install in sfdpgen make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/sfdpgen' CC sfdpinit.lo CC spring_electrical.lo spring_electrical.c: In function 'rotate': spring_electrical.c:1850:8: warning: variable 'y' set but not used [-Wunused-but-set-variable] 1850 | real y[4], axis[2], center[2], x0, x1; | ^ CC LinkedList.lo CC sparse_solve.lo CC post_process.lo post_process.c: In function 'StressMajorizationSmoother2_new': post_process.c:110:36: warning: variable 'dd' set but not used [-Wunused-but-set-variable] 110 | real *avg_dist, diag_d, diag_w, *dd, dist, s = 0, stop = 0, sbot = 0; | ^~ post_process.c: In function 'StressMajorizationSmoother_smooth': post_process.c:578:102: warning: variable 'res' set but not used [-Wunused-but-set-variable] 578 | real *w, *dd, *d, *y = NULL, *x0 = NULL, *x00 = NULL, diag, diff = 1, *lambda = sm->lambda, maxit, res, alpha = 0., M = 0.; | ^~~ post_process.c:578:9: warning: variable 'w' set but not used [-Wunused-but-set-variable] 578 | real *w, *dd, *d, *y = NULL, *x0 = NULL, *x00 = NULL, diag, diff = 1, *lambda = sm->lambda, maxit, res, alpha = 0., M = 0.; | ^ post_process.c:577:32: warning: variable 'jw' set but not used [-Wunused-but-set-variable] 577 | int i, j, m, *id, *jd, *iw, *jw, idiag, flag = 0, iter = 0; | ^~ post_process.c:577:27: warning: variable 'iw' set but not used [-Wunused-but-set-variable] 577 | int i, j, m, *id, *jd, *iw, *jw, idiag, flag = 0, iter = 0; | ^~ post_process.c: In function 'TriangleSmoother_new': post_process.c:698:68: warning: variable 'jd' set but not used [-Wunused-but-set-variable] 698 | int i, j, k, m = A->m, *ia = A->ia, *ja = A->ja, *iw, *jw, *id, *jd, jdiag, nz; | ^~ post_process.c:698:63: warning: variable 'id' set but not used [-Wunused-but-set-variable] 698 | int i, j, k, m = A->m, *ia = A->ia, *ja = A->ja, *iw, *jw, *id, *jd, jdiag, nz; | ^~ CC stress_model.lo CC uniform_stress.lo uniform_stress.c: In function 'uniform_stress': uniform_stress.c:112:8: warning: variable 'res' set but not used [-Wunused-but-set-variable] 112 | real res; | ^~~ CC QuadTree.lo CC Multilevel.lo Multilevel.c: In function 'maximal_independent_vertex_set': Multilevel.c:87:30: warning: variable 'n' set but not used [-Wunused-but-set-variable] 87 | int i, ii, j, *ia, *ja, m, n, *p = NULL; | ^ Multilevel.c: In function 'maximal_independent_vertex_set_RS': Multilevel.c:138:57: warning: variable 'removed' set but not used [-Wunused-but-set-variable] 138 | int i, jj, ii, *p = NULL, j, k, *ia, *ja, m, n, gain, removed, nf = 0; | ^~~~~~~ Multilevel.c:138:48: warning: variable 'n' set but not used [-Wunused-but-set-variable] 138 | int i, jj, ii, *p = NULL, j, k, *ia, *ja, m, n, gain, removed, nf = 0; | ^ Multilevel.c: In function 'maximal_independent_edge_set_heavest_edge_pernode_leaves_first': Multilevel.c:327:30: warning: variable 'n' set but not used [-Wunused-but-set-variable] 327 | int i, ii, j, *ia, *ja, m, n, *p = NULL, q; | ^ Multilevel.c: In function 'maximal_independent_edge_set_heavest_edge_pernode_supernodes_first': Multilevel.c:502:30: warning: variable 'n' set but not used [-Wunused-but-set-variable] 502 | int i, ii, j, *ia, *ja, m, n, *p = NULL; | ^ Multilevel.c: In function 'maximal_independent_edge_set_heavest_cluster_pernode_leaves_first': Multilevel.c:646:30: warning: variable 'n' set but not used [-Wunused-but-set-variable] 646 | int i, ii, j, *ia, *ja, m, n, *p = NULL, q, iv; | ^ CC PriorityQueue.lo CCLD libsfdpgen_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/sfdpgen' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/sfdpgen' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/sfdpgen' Making install in osage make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/osage' CC osageinit.lo CCLD libosage_C.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/osage' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/osage' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib/osage' make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib' make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib' make[2]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/lib' Making install in plugin make[2]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin' Making install in core make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin/core' CC gvplugin_core.lo CC gvrender_core_dot.lo In file included from gvrender_core_dot.c:32: gvrender_core_dot.c: In function 'xdot_str': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvrender_core_dot.c:100:5: note: in expansion of macro 'agxbputc' 100 | agxbputc(xbufs[emit_state], ' '); | ^~~~~~~~ gvrender_core_dot.c: In function 'xdot_points': gvrender_core_dot.c:107:12: warning: variable 'rc' set but not used [-Wunused-but-set-variable] 107 | int i, rc; | ^~ In file included from gvrender_core_dot.c:32: gvrender_core_dot.c: In function 'xdot_style': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvrender_core_dot.c:162:13: note: in expansion of macro 'agxbputc' 162 | agxbputc(&xbuf, '('); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvrender_core_dot.c:166:21: note: in expansion of macro 'agxbputc' 166 | agxbputc(&xbuf, ','); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gvrender_core_dot.c:172:13: note: in expansion of macro 'agxbputc' 172 | agxbputc(&xbuf, ')'); | ^~~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:174:30: note: in expansion of macro 'agxbuse' 174 | xdot_str (job, "S ", agxbuse(&xbuf)); | ^~~~~~~ gvrender_core_dot.c: In function 'xdot_end_node': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:186:31: note: in expansion of macro 'agxbuse' 186 | agxset(n, xd->n_draw->index, agxbuse(xbufs[EMIT_NDRAW])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:192:33: note: in expansion of macro 'agxbuse' 192 | agxset(n, xd->n_l_draw->index, agxbuse(xbufs[EMIT_NLABEL])); | ^~~~~~~ gvrender_core_dot.c: In function 'xdot_end_edge': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:206:31: note: in expansion of macro 'agxbuse' 206 | agxset(e, xd->e_draw->index, agxbuse(xbufs[EMIT_EDRAW])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:212:31: note: in expansion of macro 'agxbuse' 212 | agxset(e, xd->t_draw->index, agxbuse(xbufs[EMIT_TDRAW])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:218:31: note: in expansion of macro 'agxbuse' 218 | agxset(e, xd->h_draw->index, agxbuse(xbufs[EMIT_HDRAW])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:224:32: note: in expansion of macro 'agxbuse' 224 | agxset(e, xd->e_l_draw->index,agxbuse(xbufs[EMIT_ELABEL])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:230:32: note: in expansion of macro 'agxbuse' 230 | agxset(e, xd->tl_draw->index, agxbuse(xbufs[EMIT_TLABEL])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:236:32: note: in expansion of macro 'agxbuse' 236 | agxset(e, xd->hl_draw->index, agxbuse(xbufs[EMIT_HLABEL])); | ^~~~~~~ gvrender_core_dot.c: In function 'xdot_end_cluster': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:289:42: note: in expansion of macro 'agxbuse' 289 | agxset(cluster_g, xd->g_draw->index, agxbuse(xbufs[EMIT_CDRAW])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:295:41: note: in expansion of macro 'agxbuse' 295 | agxset(cluster_g, xd->g_l_draw->index, agxbuse(xbufs[EMIT_CLABEL])); | ^~~~~~~ gvrender_core_dot.c: In function 'xdot_end_graph': ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:436:31: note: in expansion of macro 'agxbuse' 436 | agxset(g, xd->g_draw->index, agxbuse(xbufs[EMIT_GDRAW])); | ^~~~~~~ ../../lib/graph/agxbuf.h:68:11: warning: right-hand operand of comma expression has no effect [-Wunused-value] 68 | (int)(*(X)->ptr++ = ((unsigned char)C))) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../lib/graph/agxbuf.h:74:21: note: in expansion of macro 'agxbputc' 74 | #define agxbuse(X) (agxbputc(X,'\0'),(char*)((X)->ptr = (X)->buf)) | ^~~~~~~~ gvrender_core_dot.c:444:33: note: in expansion of macro 'agxbuse' 444 | agxset(g, xd->g_l_draw->index, agxbuse(xbufs[EMIT_GLABEL])); | ^~~~~~~ CC gvrender_core_fig.lo CC gvrender_core_map.lo CC gvrender_core_ps.lo CC gvrender_core_svg.lo CC gvrender_core_tk.lo gvrender_core_tk.c: In function 'tkgen_print_tags': gvrender_core_tk.c:58:18: warning: variable 'ObjId' set but not used [-Wunused-but-set-variable] 58 | unsigned int ObjId; | ^~~~~ gvrender_core_tk.c:57:21: warning: variable 'ObjPart' set but not used [-Wunused-but-set-variable] 57 | char *ObjType, *ObjPart; | ^~~~~~~ CC gvrender_core_vml.lo gvrender_core_vml.c: In function 'vml_ellipse': gvrender_core_vml.c:452:38: warning: variable 'bottom' set but not used [-Wunused-but-set-variable] 452 | double dx, dy, left, right, top, bottom; | ^~~~~~ gvrender_core_vml.c:452:26: warning: variable 'right' set but not used [-Wunused-but-set-variable] 452 | double dx, dy, left, right, top, bottom; | ^~~~~ CC gvloadimage_core.lo gvloadimage_core.c:19:22: warning: extra tokens at end of #include directive 19 | #include # for read() declaration | ^ CCLD libgvplugin_core_C.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libgvplugin_core.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin/core' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz' /bin/bash ../../libtool --mode=install /usr/bin/install -c libgvplugin_core.la '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz' libtool: install: /usr/bin/install -c .libs/libgvplugin_core.lai /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.la libtool: install: /usr/bin/install -c .libs/libgvplugin_core.a /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a libtool: install: chmod 644 /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a libtool: install: ranlib /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_core.a libtool: finish: PATH="/usr/bin:/bin:/sbin" ldconfig -n /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz ---------------------------------------------------------------------- Libraries have been installed in: /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin/core' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin/core' Making install in dot_layout make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin/dot_layout' CC gvplugin_dot_layout.lo CC gvlayout_dot_layout.lo CCLD libgvplugin_dot_layout_C.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libgvplugin_dot_layout.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin/dot_layout' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz' /bin/bash ../../libtool --mode=install /usr/bin/install -c libgvplugin_dot_layout.la '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz' libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.lai /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.la libtool: install: /usr/bin/install -c .libs/libgvplugin_dot_layout.a /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a libtool: install: chmod 644 /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a libtool: install: ranlib /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_dot_layout.a libtool: finish: PATH="/usr/bin:/bin:/sbin" ldconfig -n /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz ---------------------------------------------------------------------- Libraries have been installed in: /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin/dot_layout' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin/dot_layout' Making install in neato_layout make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin/neato_layout' CC gvplugin_neato_layout.lo CC gvlayout_neato_layout.lo CCLD libgvplugin_neato_layout_C.la ar: `u' modifier ignored since `D' is the default (see `U') CCLD libgvplugin_neato_layout.la ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin/neato_layout' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz' /bin/bash ../../libtool --mode=install /usr/bin/install -c libgvplugin_neato_layout.la '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz' libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.lai /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.la libtool: install: /usr/bin/install -c .libs/libgvplugin_neato_layout.a /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a libtool: install: chmod 644 /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a libtool: install: ranlib /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz/libgvplugin_neato_layout.a libtool: finish: PATH="/usr/bin:/bin:/sbin" ldconfig -n /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz ---------------------------------------------------------------------- Libraries have been installed in: /tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz If you ever happen to want to link against installed libraries in a given directory, LIBDIR, you must either use libtool, and specify the full pathname of the library, or use the `-LLIBDIR' flag during linking and do at least one of the following: - add LIBDIR to the `LD_LIBRARY_PATH' environment variable during execution - add LIBDIR to the `LD_RUN_PATH' environment variable during linking - use the `-Wl,-rpath -Wl,LIBDIR' linker flag - have your system administrator add LIBDIR to `/etc/ld.so.conf' See any operating system documentation about shared libraries for more information, such as the ld(1) and ld.so(8) manual pages. ---------------------------------------------------------------------- make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin/neato_layout' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin/neato_layout' make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin' make[4]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin' make[2]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz/plugin' make[2]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz' make[3]: Entering directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man7' /usr/bin/install -c -m 644 graphviz.7 '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/man/man7' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' /usr/bin/install -c -m 644 graphviz_version.h '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz' /bin/mkdir -p '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc' /usr/bin/install -c -m 644 AUTHORS COPYING ChangeLog NEWS cpl1.0.txt '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/share/graphviz/doc' make[3]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz' make[2]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz' make[1]: Leaving directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/graphviz' cp: -r not specified; omitting directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/graphviz' cp: -r not specified; omitting directory '/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/lib/pkgconfig' checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for zlib.h... yes checking for deflateBound in -lz... yes checking for library containing pow... -lm checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for whether compiler has bool... yes configure: Using the following compilation and linking flags for Rgraphviz configure: PKG_CFLAGS= -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz configure: PKG_LIBS=libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -lm configure: GVIZ_DEFS=-DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 configure: Compiling using Graphviz version: '2.28.0'. configure: Using bundled Graphviz: 'TRUE'. configure: creating ./config.status config.status: creating R/graphviz_build_version.R config.status: creating src/Makevars ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c LL_funcs.c -o LL_funcs.o gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rgraphviz.c -o Rgraphviz.o gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RgraphvizInit.c -o RgraphvizInit.o gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c agopen.c -o agopen.o gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c agread.c -o agread.o gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c agwrite.c -o agwrite.o gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bezier.c -o bezier.o gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c buildEdgeList.c -o buildEdgeList.o gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c buildNodeList.c -o buildNodeList.o gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c doLayout.c -o doLayout.o gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c graphvizVersion.c -o graphvizVersion.o gcc -I"/usr/share/R/include" -DNDEBUG -I/tmp/RtmpJmhIxh/R.INSTALL28bfa96ce0ada9/Rgraphviz/src/libunix/include/graphviz -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=28 -DGRAPHVIZ_STATIC -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o libxdot.a libgvplugin_dot_layout.a libgvplugin_neato_layout.a libgvplugin_core.a libgvc.a libpathplan.a libgraph.a libcdt.a -lz -lm -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-Rgraphviz/00new/Rgraphviz/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rgraphviz) * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5.c -o H5.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5A.c -o H5A.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5D.c -o H5D.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5E.c -o H5E.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5F.c -o H5F.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5G.c -o H5G.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5I.c -o H5I.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5L.c -o H5L.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5O.c -o H5O.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5P.c -o H5P.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5R.c -o H5R.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5S.c -o H5S.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5S_extras.c -o H5S_extras.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5T.c -o H5T.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5Z.c -o H5Z.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5constants.c -o H5constants.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c HandleList.cpp -o HandleList.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c HandleListWrap.c -o HandleListWrap.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bit64conversion.c -o bit64conversion.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c external_filters.c -o external_filters.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5dump.c -o h5dump.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5ls.c -o h5ls.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5testLock.c -o h5testLock.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c printdatatype.c -o printdatatype.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c wrap.c -o wrap.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5R.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /home/omnipath/local/R/4.2-3.16/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-rhdf5/00new/rhdf5/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rhdf5) * installing *source* package ‘viper’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (viper) * installing *source* package ‘biocViews’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biocViews) * installing *source* package ‘bluster’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c build_snn.cpp -o build_snn.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sum_neighbor_weights.cpp -o sum_neighbor_weights.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o bluster.so RcppExports.o build_snn.o sum_neighbor_weights.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-bluster/00new/bluster/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bluster) * installing *source* package ‘CellNOptR’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c simulatorT1.c -o simulatorT1.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c simulatorTN.c -o simulatorTN.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o CellNOptR.so simulatorT1.o simulatorTN.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-CellNOptR/00new/CellNOptR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CellNOptR) * installing *source* package ‘ComplexHeatmap’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ComplexHeatmap) * installing *source* package ‘DelayedArray’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_DelayedArray.c -o R_init_DelayedArray.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c abind.c -o abind.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c array_selection.c -o array_selection.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compress_atomic_vector.c -o compress_atomic_vector.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sparseMatrix_utils.c -o sparseMatrix_utils.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o abind.o array_selection.o compress_atomic_vector.o sparseMatrix_utils.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-DelayedArray/00new/DelayedArray/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowsum’ in package ‘DelayedArray’ Creating a new generic function for ‘apply’ in package ‘DelayedArray’ Creating a new generic function for ‘sweep’ in package ‘DelayedArray’ Creating a new generic function for ‘scale’ in package ‘DelayedArray’ Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’ Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DelayedArray) * installing *source* package ‘GenomeInfoDb’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomeInfoDb) * installing *source* package ‘XVector’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RDS_random_access.c -o RDS_random_access.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_XVector.c -o R_init_XVector.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SharedDouble_class.c -o SharedDouble_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SharedInteger_class.c -o SharedInteger_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SharedRaw_class.c -o SharedRaw_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SharedVector_class.c -o SharedVector_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XDouble_class.c -o XDouble_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XInteger_class.c -o XInteger_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XRawList_comparison.c -o XRawList_comparison.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XRaw_class.c -o XRaw_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XVectorList_class.c -o XVectorList_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XVector_class.c -o XVector_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c io_utils.c -o io_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c slice_methods.c -o slice_methods.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vector_copy.c -o vector_copy.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c view_summarization_methods.c -o view_summarization_methods.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-XVector/00new/XVector/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (XVector) * installing *source* package ‘beachmat’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o beachmat.so RcppExports.o fragment_sparse_rows.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-beachmat/00new/beachmat/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (beachmat) * installing *source* package ‘BiocCheck’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocCheck) * installing *source* package ‘Biostrings’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c BAB_class.c -o BAB_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c BitMatrix.c -o BitMatrix.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MIndex_class.c -o MIndex_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c PreprocessedTB_class.c -o PreprocessedTB_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_Biostrings.c -o R_init_Biostrings.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RoSeqs_utils.c -o RoSeqs_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SparseList_utils.c -o SparseList_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XStringSetList_class.c -o XStringSetList_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XStringSet_class.c -o XStringSet_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XString_class.c -o XString_class.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c XVector_stubs.c -o XVector_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c align_needwunsQS.c -o align_needwunsQS.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c align_utils.c -o align_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c find_palindromes.c -o find_palindromes.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gtestsim.c -o gtestsim.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c inject_code.c -o inject_code.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c letter_frequency.c -o letter_frequency.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lowlevel_matching.c -o lowlevel_matching.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_PWM.c -o match_PWM.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pattern.c -o match_pattern.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pattern_indels.c -o match_pattern_indels.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pattern_shiftor.c -o match_pattern_shiftor.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pdict.c -o match_pdict.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pdict_Twobit.c -o match_pdict_Twobit.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_pdict_utils.c -o match_pdict_utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c match_reporting.c -o match_reporting.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c matchprobes.c -o matchprobes.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pmatchPattern.c -o pmatchPattern.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_fasta_files.c -o read_fasta_files.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c read_fastq_files.c -o read_fastq_files.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceAt.c -o replaceAt.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c replace_letter_at.c -o replace_letter_at.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c strutils.c -o strutils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c translate.c -o translate.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c unstrsplit_methods.c -o unstrsplit_methods.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -I'/home/omnipath/local/R/4.2-3.16/XVector/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c xscat.c -o xscat.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-Biostrings/00new/Biostrings/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet” Creating a new generic function for ‘strsplit’ in package ‘Biostrings’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’ Creating a new generic function for ‘pattern’ in package ‘Biostrings’ Creating a new generic function for ‘offset’ in package ‘Biostrings’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Biostrings) * installing *source* package ‘CNORdt’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c simulatorDT.c -o simulatorDT.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o CNORdt.so simulatorDT.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-CNORdt/00new/CNORdt/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CNORdt) * installing *source* package ‘CNORfeeder’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CNORfeeder) * installing *source* package ‘CNORfuzzy’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c simulatorT1.c -o simulatorT1.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o CNORfuzzy.so simulatorT1.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-CNORfuzzy/00new/CNORfuzzy/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CNORfuzzy) * installing *source* package ‘CNORode’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c FG_transfer_function.c -o FG_transfer_function.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodea.c -o cvodea.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodea_io.c -o cvodea_io.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodes.c -o cvodes.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodes_band.c -o cvodes_band.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodes_bandpre.c -o cvodes_bandpre.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodes_bbdpre.c -o cvodes_bbdpre.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodes_dense.c -o cvodes_dense.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodes_diag.c -o cvodes_diag.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodes_direct.c -o cvodes_direct.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodes_io.c -o cvodes_io.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodes_spbcgs.c -o cvodes_spbcgs.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodes_spgmr.c -o cvodes_spgmr.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodes_spils.c -o cvodes_spils.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cvodes_sptfqmr.c -o cvodes_sptfqmr.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c decimal2binary.c -o decimal2binary.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c findStates.c -o findStates.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fnvector_serial.c -o fnvector_serial.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getAdjacencyMatrix.c -o getAdjacencyMatrix.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getNumBits.c -o getNumBits.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getNumInputs.c -o getNumInputs.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getStateIndex.c -o getStateIndex.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getTruthTables.c -o getTruthTables.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c get_count_bits.c -o get_count_bits.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c get_input_index.c -o get_input_index.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c get_support_truth_tables.c -o get_support_truth_tables.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c get_truth_tables_index.c -o get_truth_tables_index.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c hill_function.c -o hill_function.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c linear_transfer_function.c -o linear_transfer_function.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c normHill.c -o normHill.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c normHill_mod.c -o normHill_mod.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nvector_serial.c -o nvector_serial.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c printAdjMat.c -o printAdjMat.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c printInterMat.c -o printInterMat.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c printNminiTerms.c -o printNminiTerms.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c printTruthTables.c -o printTruthTables.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rhsODE.c -o rhsODE.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sim_logic_ode.c -o sim_logic_ode.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c simulateODE.c -o simulateODE.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sundials_band.c -o sundials_band.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sundials_dense.c -o sundials_dense.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sundials_direct.c -o sundials_direct.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sundials_iterative.c -o sundials_iterative.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sundials_math.c -o sundials_math.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sundials_nvector.c -o sundials_nvector.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sundials_spbcgs.c -o sundials_spbcgs.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sundials_spgmr.c -o sundials_spgmr.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sundials_sptfqmr.c -o sundials_sptfqmr.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o CNORode.so FG_transfer_function.o cvodea.o cvodea_io.o cvodes.o cvodes_band.o cvodes_bandpre.o cvodes_bbdpre.o cvodes_dense.o cvodes_diag.o cvodes_direct.o cvodes_io.o cvodes_spbcgs.o cvodes_spgmr.o cvodes_spils.o cvodes_sptfqmr.o decimal2binary.o findStates.o fnvector_serial.o getAdjacencyMatrix.o getNumBits.o getNumInputs.o getStateIndex.o getTruthTables.o get_count_bits.o get_input_index.o get_support_truth_tables.o get_truth_tables_index.o hill_function.o linear_transfer_function.o normHill.o normHill_mod.o nvector_serial.o printAdjMat.o printInterMat.o printNminiTerms.o printTruthTables.o rhsODE.o sim_logic_ode.o simulateODE.o sundials_band.o sundials_dense.o sundials_direct.o sundials_iterative.o sundials_math.o sundials_nvector.o sundials_spbcgs.o sundials_spgmr.o sundials_sptfqmr.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-CNORode/00new/CNORode/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CNORode) * installing *source* package ‘DelayedMatrixStats’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DelayedMatrixStats) * installing *source* package ‘GenomicRanges’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/IRanges/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c transcript_utils.c -o transcript_utils.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-GenomicRanges/00new/GenomicRanges/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GenomicRanges) * installing *source* package ‘HDF5Array’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5File.c -o H5File.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c global_errmsg_buf.c -o global_errmsg_buf.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c H5DSetDescriptor.c -o H5DSetDescriptor.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5dimscales.c -o h5dimscales.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c uaselection.c -o uaselection.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5mread_helpers.c -o h5mread_helpers.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5mread_startscounts.c -o h5mread_startscounts.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ChunkIterator.c -o ChunkIterator.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5mread_index.c -o h5mread_index.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5mread_sparse.c -o h5mread_sparse.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5mread.c -o h5mread.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c h5summarize.c -o h5summarize.o gcc -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/S4Vectors/include' -I'/home/omnipath/local/R/4.2-3.16/Rhdf5lib/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_init_HDF5Array.c -o R_init_HDF5Array.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o HDF5Array.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o /home/omnipath/local/R/4.2-3.16/Rhdf5lib/lib/libhdf5_hl.a /home/omnipath/local/R/4.2-3.16/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-HDF5Array/00new/HDF5Array/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (HDF5Array) * installing *source* package ‘ScaledMatrix’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ScaledMatrix) * installing *source* package ‘BiocSingular’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compute_scale.cpp -o compute_scale.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o BiocSingular.so RcppExports.o compute_scale.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-BiocSingular/00new/BiocSingular/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BiocSingular) * installing *source* package ‘KEGGREST’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (KEGGREST) * installing *source* package ‘SummarizedExperiment’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SummarizedExperiment) * installing *source* package ‘AnnotationDbi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’ Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’ Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (AnnotationDbi) * installing *source* package ‘SingleCellExperiment’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SingleCellExperiment) * installing *source* package ‘annotate’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (annotate) * installing *source* package ‘biomaRt’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biomaRt) * installing *source* package ‘BioNet’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BioNet) * installing *source* package ‘scuttle’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cumulative_prop.cpp -o cumulative_prop.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c downsample_counts.cpp -o downsample_counts.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fit_linear_model.cpp -o fit_linear_model.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pool_size_factors.cpp -o pool_size_factors.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sum_counts.cpp -o sum_counts.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.cpp -o utils.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o scuttle.so RcppExports.o cumulative_prop.o downsample_counts.o fit_linear_model.o pool_size_factors.o sum_counts.o utils.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-scuttle/00new/scuttle/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scuttle) * installing *source* package ‘genefilter’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c half_range_mode.cpp -o half_range_mode.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nd.c -o nd.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pAUC.c -o pAUC.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowPAUCs.c -o rowPAUCs.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rowttests.c -o rowttests.o gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -c ttest.f -o ttest.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-genefilter/00new/genefilter/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (genefilter) * installing *source* package ‘geneplotter’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (geneplotter) * installing *source* package ‘GSEABase’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GSEABase) * installing *source* package ‘scater’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scater) * installing *source* package ‘scran’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -I'/home/omnipath/local/R/4.2-3.16/dqrng/include' -I'/home/omnipath/local/R/4.2-3.16/scuttle/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -I'/home/omnipath/local/R/4.2-3.16/dqrng/include' -I'/home/omnipath/local/R/4.2-3.16/scuttle/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c choose_effect_size.cpp -o choose_effect_size.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -I'/home/omnipath/local/R/4.2-3.16/dqrng/include' -I'/home/omnipath/local/R/4.2-3.16/scuttle/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c combine_rho.cpp -o combine_rho.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -I'/home/omnipath/local/R/4.2-3.16/dqrng/include' -I'/home/omnipath/local/R/4.2-3.16/scuttle/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compute_blocked_stats.cpp -o compute_blocked_stats.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -I'/home/omnipath/local/R/4.2-3.16/dqrng/include' -I'/home/omnipath/local/R/4.2-3.16/scuttle/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compute_residual_stats.cpp -o compute_residual_stats.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -I'/home/omnipath/local/R/4.2-3.16/dqrng/include' -I'/home/omnipath/local/R/4.2-3.16/scuttle/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compute_rho_null.cpp -o compute_rho_null.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -I'/home/omnipath/local/R/4.2-3.16/dqrng/include' -I'/home/omnipath/local/R/4.2-3.16/scuttle/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cyclone_scores.cpp -o cyclone_scores.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -I'/home/omnipath/local/R/4.2-3.16/dqrng/include' -I'/home/omnipath/local/R/4.2-3.16/scuttle/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c overlap_exprs.cpp -o overlap_exprs.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/beachmat/include' -I'/home/omnipath/local/R/4.2-3.16/BH/include' -I'/home/omnipath/local/R/4.2-3.16/dqrng/include' -I'/home/omnipath/local/R/4.2-3.16/scuttle/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rand_custom.cpp -o rand_custom.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o scran.so RcppExports.o choose_effect_size.o combine_rho.o compute_blocked_stats.o compute_residual_stats.o compute_rho_null.o cyclone_scores.o overlap_exprs.o rand_custom.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-scran/00new/scran/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scran) * installing *source* package ‘AUCell’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (AUCell) * installing *source* package ‘cosmosR’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cosmosR) * installing *source* package ‘DESeq2’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppArmadillo/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c DESeq2.cpp -o DESeq2.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include' -I'/home/omnipath/local/R/4.2-3.16/RcppArmadillo/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o DESeq2.so DESeq2.o RcppExports.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-DESeq2/00new/DESeq2/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DESeq2) * installing *source* package ‘GSVA’ ... ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c kernel_estimation.c -o kernel_estimation.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ks_test.c -o ks_test.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-zYgbYq/r-base-4.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c register_cmethods.c -o register_cmethods.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-GSVA/00new/GSVA/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GSVA) The downloaded source packages are in ‘/tmp/Rtmpp0Dh9T/downloaded_packages’ Warning message: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘nloptr’ had non-zero exit status Skipping 2 packages ahead of CRAN: bslib, callr [ Finished: 2022-11-03 01:24:23 CET ]