[ Started: 2024-08-16 02:06:39 CEST ] [ dorothea v1.7.4 for BioC-3.20 from https://github.com/saezlab/dorothea@master (1461fb7 2024-02-24 12:55:48) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.20" [3] "/home/omnipath/local/R/4.4" "/usr/lib/R/library" 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.20 (BiocManager 1.30.23), R 4.4.1 (2024-06-14) Old packages: 'MatrixGenerics', 'rhdf5filters', 'Rhdf5lib', 'sparseMatrixStats', 'viper' trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/MatrixGenerics_1.17.0.tar.gz' Content type 'application/x-gzip' length 31687 bytes (30 KB) ================================================== downloaded 30 KB trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/rhdf5filters_1.17.0.tar.gz' Content type 'application/x-gzip' length 1179898 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/Rhdf5lib_1.27.0.tar.gz' Content type 'application/x-gzip' length 12062855 bytes (11.5 MB) ================================================== downloaded 11.5 MB trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/sparseMatrixStats_1.17.2.tar.gz' Content type 'application/x-gzip' length 706493 bytes (689 KB) ================================================== downloaded 689 KB trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/viper_1.39.0.tar.gz' Content type 'application/x-gzip' length 318584 bytes (311 KB) ================================================== downloaded 311 KB * installing *source* package ‘MatrixGenerics’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowAlls’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAlls’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowAnyNAs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAnyNAs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowAnys’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAnys’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowAvgsPerColSet’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colAvgsPerRowSet’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCollapse’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCollapse’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCounts’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCounts’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCummaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCummaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCummins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCummins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCumprods’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCumprods’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowCumsums’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colCumsums’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowIQRDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colIQRDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowIQRs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colIQRs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowLogSumExps’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colLogSumExps’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMadDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMadDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMaxs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMeans2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMeans2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowMins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colMins’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowOrderStats’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colOrderStats’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowProds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colProds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowQuantiles’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colQuantiles’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowRanges’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colRanges’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowRanks’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colRanks’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowSdDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colSdDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowSums2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colSums2’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowTabulates’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colTabulates’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowVarDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colVarDiffs’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowVars’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colVars’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedMads’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedMeans’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedMeans’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedMedians’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedSds’ in package ‘MatrixGenerics’ Creating a new generic function for ‘rowWeightedVars’ in package ‘MatrixGenerics’ Creating a new generic function for ‘colWeightedVars’ in package ‘MatrixGenerics’ ** 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 ‘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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed COMPILER = gcc checking whether C compiler accepts -w... yes checking whether to use -Wl,-rpath setting... yes 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 ON_BUILDER=false ON_BUILDER=false checking for szlib.h... no checking for libaec.h... no checking for curl/curl.h... yes checking for openssl/evp.h... yes checking for openssl/hmac.h... yes checking for openssl/sha.h... yes checking for curl_global_init in -lcurl... yes checking for EVP_sha256 in -lcrypto... yes S3_VFD=--enable-ros3-vfd configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gunzip -dc hdf5small_cxx_hl_1.10.7.tar.gz | tar xf -; cd hdf5/libaec-1.0.4/build; \ ../configure --with-pic --enable-shared=no --prefix=/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --libdir=/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib \ CC='gcc' CXX='g++ -std=gnu++17' \ CPPFLAGS='' \ CFLAGS='-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic' \ AR='ar' RANLIB='ranlib'; \ make; \ make install checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking how to print strings... printf 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 gcc understands -c and -o together... yes checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/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 how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop 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 dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... gawk checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no 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... yes 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 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 whether the -Werror option is usable... yes checking for simple visibility declarations... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... gcc3 checking whether to enable maintainer-specific portions of Makefiles... yes checking for gcc option to accept ISO C99... none needed checking for ANSI C header files... (cached) yes checking whether byte ordering is bigendian... no checking for inline... inline checking for int64_t... yes checking for size_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for uint8_t... yes checking for inline... (cached) inline checking for C/C++ restrict keyword... __restrict checking for memset... yes checking for strstr... yes checking for snprintf... yes checking whether __builtin_clzll is declared... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config/config.h config.status: executing libtool commands config.status: executing depfiles commands make[1]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build' Making all in src make[2]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -MT aec.o -MD -MP -MF .deps/aec.Tpo -c -o aec.o ../../src/aec.c mv -f .deps/aec.Tpo .deps/aec.Po /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -MT encode.lo -MD -MP -MF .deps/encode.Tpo -c -o encode.lo ../../src/encode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -MT encode.lo -MD -MP -MF .deps/encode.Tpo -c ../../src/encode.c -fPIC -DPIC -o encode.o mv -f .deps/encode.Tpo .deps/encode.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -MT encode_accessors.lo -MD -MP -MF .deps/encode_accessors.Tpo -c -o encode_accessors.lo ../../src/encode_accessors.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -MT encode_accessors.lo -MD -MP -MF .deps/encode_accessors.Tpo -c ../../src/encode_accessors.c -fPIC -DPIC -o encode_accessors.o mv -f .deps/encode_accessors.Tpo .deps/encode_accessors.Plo /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -MT decode.lo -MD -MP -MF .deps/decode.Tpo -c -o decode.lo ../../src/decode.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -MT decode.lo -MD -MP -MF .deps/decode.Tpo -c ../../src/decode.c -fPIC -DPIC -o decode.o mv -f .deps/decode.Tpo .deps/decode.Plo /bin/bash ../libtool --tag=CC --mode=link gcc -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -version-info 0:10:0 -no-undefined -o libaec.la -rpath /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib encode.lo encode_accessors.lo decode.lo libtool: link: ar cr .libs/libaec.a encode.o encode_accessors.o decode.o libtool: link: ranlib .libs/libaec.a libtool: link: ( cd ".libs" && rm -f "libaec.la" && ln -s "../libaec.la" "libaec.la" ) /bin/bash ../libtool --tag=CC --mode=link gcc -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -o aec aec.o libaec.la libtool: link: gcc -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -o aec aec.o ./.libs/libaec.a gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -MT utime.o -MD -MP -MF .deps/utime.Tpo -c -o utime.o ../../src/utime.c mv -f .deps/utime.Tpo .deps/utime.Po /bin/bash ../libtool --tag=CC --mode=link gcc -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -o utime utime.o libtool: link: gcc -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -o utime utime.o /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -MT sz_compat.lo -MD -MP -MF .deps/sz_compat.Tpo -c -o sz_compat.lo ../../src/sz_compat.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -I../config -DBUILDING_LIBAEC -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -MT sz_compat.lo -MD -MP -MF .deps/sz_compat.Tpo -c ../../src/sz_compat.c -fPIC -DPIC -o sz_compat.o mv -f .deps/sz_compat.Tpo .deps/sz_compat.Plo /bin/bash ../libtool --tag=CC --mode=link gcc -fvisibility=hidden -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic -version-info 2:1:0 -no-undefined -o libsz.la -rpath /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib sz_compat.lo libaec.la libtool: link: ar cr .libs/libsz.a sz_compat.o libtool: link: ranlib .libs/libsz.a libtool: link: ( cd ".libs" && rm -f "libsz.la" && ln -s "../libsz.la" "libsz.la" ) make[2]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' make[2]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[1]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[1]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build' Making install in src make[2]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' make[3]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' /usr/bin/mkdir -p '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib' /bin/bash ../libtool --mode=install /usr/bin/install -c libaec.la libsz.la '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib' libtool: install: /usr/bin/install -c .libs/libaec.lai /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.la libtool: install: /usr/bin/install -c .libs/libsz.lai /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.la libtool: install: /usr/bin/install -c .libs/libaec.a /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a libtool: install: chmod 644 /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a libtool: install: ranlib /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libaec.a libtool: install: /usr/bin/install -c .libs/libsz.a /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a libtool: install: chmod 644 /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a libtool: install: ranlib /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib/libsz.a libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/sbin" ldconfig -n /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib ---------------------------------------------------------------------- Libraries have been installed in: /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/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. ---------------------------------------------------------------------- /usr/bin/mkdir -p '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c aec '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin' libtool: install: /usr/bin/install -c aec /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/bin/aec /usr/bin/mkdir -p '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include' /usr/bin/install -c -m 644 ../../src/libaec.h ../../src/szlib.h '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include' /usr/bin/mkdir -p '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1' /usr/bin/install -c -m 644 ../../src/aec.1 '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/share/man/man1' make[3]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' make[2]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/src' make[2]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[3]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[2]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build' make[1]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build' cd hdf5; \ ./configure --with-pic --enable-shared=no --enable-cxx --enable-hl \ --enable-tests=no --enable-tools=no \ --with-szlib=/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip --with-zlib=yes \ --enable-ros3-vfd \ --enable-sharedlib-rpath \ CC='gcc' CXX='g++ -std=gnu++17' \ CPPFLAGS='' \ CFLAGS='-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -w -fpic' \ CXXFLAGS='-w -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic' \ AR='ar' RANLIB='ranlib' \ LDFLAGS='-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro'; \ make lib checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free 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suppressed checking for custom examples path definition... ${prefix}/share/hdf5_examples checking for custom plugin default path definition... /usr/local/hdf5/lib/plugin checking whether exception handling functions is checked during data conversions... yes checking whether data accuracy is guaranteed during data conversions... yes checking if the machine has window style path name... no checking if using special algorithm to convert long double to (unsigned) long values... no checking if using special algorithm to convert (unsigned) long to long double values... no checking if correctly converting long double to (unsigned) long long values... yes checking if correctly converting (unsigned) long long to long double values... yes checking if the system is IBM ppc64le and cannot correctly convert some long double values... no checking additional programs should be built... no checking if deprecated public symbols are available... yes checking which version of public symbols to use by default... v110 checking whether to perform strict file format checks... no checking for pread... yes checking 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: Fri Aug 16 02:07:19 CEST 2024 Configured by: omnipath@saezlab Host system: x86_64-pc-linux-gnu Uname information: Linux saezlab 6.0.0-1008-oem #8-Ubuntu SMP PREEMPT_DYNAMIC Wed Nov 16 17:31:27 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux Byte sex: little-endian Installation point: /tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/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: -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro H5_LDFLAGS: AM_LDFLAGS: -L/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/lib 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: -I/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/libaec-1.0.4/build/szip/include C Flags: -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -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++17 C++ Flags: -w -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -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/RtmpKnuniv/R.INSTALL4bd18e6c54b4/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/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/src' make[3]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro | \ 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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro | \ 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/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/src' make[2]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/src' make[2]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/c++' make[3]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/c++' make[3]: Nothing to be done for 'build-lib'. make[3]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/c++' + cd src + make lib make[3]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/c++/src' make[4]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/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/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/c++/src' make[3]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/c++/src' make[2]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/c++' make[2]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl' make[3]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl' make[3]: Nothing to be done for 'build-lib'. make[3]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl' + cd src + make lib make[3]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl/src' make[4]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/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/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl/src' make[3]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl/src' + cd c++ + make lib make[3]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl/c++' make[4]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl/c++' make[4]: Nothing to be done for 'build-lib'. make[4]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl/c++' + cd src + make lib make[4]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl/c++/src' make[5]: Entering directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl/c++/src' CXX H5PacketTable.lo CXXLD libhdf5_hl_cpp.la make[5]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl/c++/src' make[4]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl/c++/src' make[3]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl/c++' make[2]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5/hl' make[1]: Leaving directory '/tmp/RtmpKnuniv/R.INSTALL4bd18e6c54b4/Rhdf5lib/src/hdf5' mkdir -p "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src"/*.h "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/c++/src"/*.h "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/src"/*.h "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/c++/src"/*.h "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src"/libhdf5.settings "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" mkdir -p "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/src/.libs/libhdf5.a" "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp hdf5/libaec-1.0.4/build/szip/lib/libsz.a "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp hdf5/libaec-1.0.4/build/szip/lib/libaec.a "/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" gcc -I"/usr/share/R/include" -DNDEBUG -I"/home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Rhdf5lib.c -o Rhdf5lib.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o Rhdf5lib.so Rhdf5lib.o /home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a /home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a /home/omnipath/local/R/4.4-3.20/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libaec.a -lz -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-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 ‘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 ‘rhdf5filters’ ... ** 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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed configure: is NOT Bioc build machine configure: configuring BZIP2 filter... 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 bzlib.h... yes checking for BZ2_bzDecompressInit in -lbz2... yes configure: Using system bzip2 library configure: configuring the Zstd filter... checking for zstd.h... yes checking for ZSTD_decompress in -lzstd... yes configure: Using system Zstd library configure: configuring the BLOSC filter... checking for blosc.h... no configure: compiling bundled BLOSC library 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: configuring the VBZ filter checking whether C compiler accepts -mavx... yes checking for x86 avx instruction support... yes configure: creating ./config.status config.status: creating src/bzip2/Makefile config.status: creating src/zstd/Makefile config.status: creating src/blosc/lib/blosc-1.20.1/Makefile config.status: creating src/blosc/Makefile config.status: creating src/vbz/Makefile config.status: creating src/vbz/vbz/Makefile config.status: creating src/vbz/third_party/streamvbyte/Makefile config.status: creating src/Makevars ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ make -C zstd make[1]: Entering directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/zstd' gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -shared H5Zzstd.c -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" \ -lzstd -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o libH5Zzstd.so make[1]: Leaving directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/zstd' make -C blosc make[1]: Entering directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/blosc' make -C lib/snappy-1.1.1 make[2]: Entering directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/blosc/lib/snappy-1.1.1' g++ -std=gnu++17 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -c snappy.cc g++ -std=gnu++17 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -c snappy-c.cc g++ -std=gnu++17 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -c snappy-sinksource.cc g++ -std=gnu++17 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -c snappy-stubs-internal.cc make[2]: Leaving directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/blosc/lib/snappy-1.1.1' make -C lib/lz4-1.9.4 make[2]: Entering directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/blosc/lib/lz4-1.9.4' gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -c lz4.c gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -c lz4hc.c make[2]: Leaving directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/blosc/lib/lz4-1.9.4' make -C lib/blosc-1.20.1 all make[2]: Entering directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/blosc/lib/blosc-1.20.1' gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c bitshuffle-avx2.c gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c shuffle-avx2.c gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c bitshuffle-sse2.c gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c shuffle-sse2.c gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c bitshuffle-generic.c gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c shuffle-generic.c gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED -c shuffle.c gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c blosclz.c gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c blosc.c gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c fastcopy.c make[2]: Leaving directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/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/lz4-1.9.4/lz4.o lib/lz4-1.9.4/lz4hc.o ranlib libblosc.a g++ -std=gnu++17 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -shared -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" H5Zblosc.cpp \ -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -I./lib/blosc-1.20.1 ./libblosc.a -lzstd -lz -o libH5Zblosc.so make[1]: Leaving directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/blosc' make -C bzip2 make[1]: Entering directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/bzip2' gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -shared H5Zbzip2.c -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" \ -lbz2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o libH5Zbz2.so make[1]: Leaving directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/bzip2' make -C lzf make[1]: Entering directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/lzf' make -C lzf make[2]: Entering directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/lzf/lzf' gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -c lzf_c.c gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -c lzf_d.c rm -f liblzf.a ar cq liblzf.a lzf_c.o lzf_d.o ranlib liblzf.a make[2]: Leaving directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/lzf/lzf' gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -shared H5Zlzf.c -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" \ -I./lzf/ ./lzf/liblzf.a -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o libH5Zlzf.so make[1]: Leaving directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/lzf' make -C vbz make[1]: Entering directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/vbz' make -C third_party/streamvbyte make[2]: Entering directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/vbz/third_party/streamvbyte' gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbyte_decode.c gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbyte_encode.c gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbytedelta_decode.c gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbytedelta_encode.c gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbyte_0124_encode.c gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbyte_0124_decode.c gcc -std=gnu99 -fpic -Iinclude -c ./src/streamvbyte_zigzag.c rm -f libstreamvbyte.a ar cq libstreamvbyte.a streamvbyte_decode.o streamvbyte_encode.o streamvbytedelta_decode.o streamvbytedelta_encode.o streamvbyte_0124_encode.o streamvbyte_0124_decode.o streamvbyte_zigzag.o ranlib libstreamvbyte.a make[2]: Leaving directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/vbz/third_party/streamvbyte' make -C vbz make[2]: Entering directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/vbz/vbz' g++ -std=gnu++17 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -mssse3 -c vbz.cpp -o vbz.o g++ -std=gnu++17 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -mssse3 -c v0/vbz_streamvbyte.cpp -o v0/vbz_streamvbyte.o g++ -std=gnu++17 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -mssse3 -c v1/vbz_streamvbyte.cpp -o v1/vbz_streamvbyte.o make[2]: Leaving directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/vbz/vbz' rm -f libvbz.a ar cq libvbz.a vbz/vbz.o vbz/v0/vbz_streamvbyte.o vbz/v1/vbz_streamvbyte.o ranlib libvbz.a g++ -std=gnu++17 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -shared vbz_plugin.cpp \ libvbz.a -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -lzstd third_party/streamvbyte/libstreamvbyte.a -o libH5Zvbz.so make[1]: Leaving directory '/tmp/RtmpOr7J1z/R.INSTALL50a61223515fd/rhdf5filters/src/vbz' mkdir -p "/home/omnipath/local/R/4.4-3.20/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" cp bzip2/libH5Zbz2.so blosc/libH5Zblosc.so lzf/libH5Zlzf.so zstd/libH5Zzstd.so vbz/libH5Zvbz.so "/home/omnipath/local/R/4.4-3.20/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" gcc -I"/usr/share/R/include" -DNDEBUG -I"/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include" -I'/home/omnipath/local/R/4.4-3.20/Rhdf5lib/include' -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c rhdf5filters.c -o rhdf5filters.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -o rhdf5filters.so rhdf5filters.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.4-3.20/00LOCK-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 ‘sparseMatrixStats’ ... ** package ‘sparseMatrixStats’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ using C++11 g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c SparseMatrixView.cpp -o SparseMatrixView.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c methods.cpp -o methods.o g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.20/Rcpp/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c row_methods.cpp -o row_methods.o g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -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/4.4-3.20/00LOCK-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) The downloaded source packages are in ‘/tmp/RtmpLTv0G4/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.20 (BiocManager 1.30.23), R 4.4.1 (2024-06-14) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' XVector (NA -> 0.42.0) [CRAN] SparseArray (NA -> 1.2.4 ) [CRAN] S4Arrays (NA -> 1.2.1 ) [CRAN] IRanges (NA -> 2.36.0) [CRAN] S4Vectors (NA -> 0.40.2) [CRAN] GenomeInfoDb (NA -> 1.38.8) [CRAN] DelayedArray (NA -> 0.28.0) [CRAN] GenomicRa... (NA -> 1.54.1) [CRAN] Summarize... (NA -> 1.32.0) [CRAN] SingleCel... (NA -> 1.24.0) [CRAN] Skipping 9 packages ahead of CRAN: zlibbioc, MatrixGenerics, BiocGenerics, GenomeInfoDbData, Biobase, viper, BiocStyle, decoupleR, bcellViper Installing 10 packages: XVector, SparseArray, S4Arrays, IRanges, S4Vectors, GenomeInfoDb, DelayedArray, GenomicRanges, SummarizedExperiment, SingleCellExperiment trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/XVector_0.42.0.tar.gz' Content type 'application/gzip' length 67825 bytes (66 KB) ================================================== downloaded 66 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SparseArray_1.2.4.tar.gz' Content type 'application/gzip' length 367778 bytes (359 KB) ================================================== downloaded 359 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/S4Arrays_1.2.1.tar.gz' Content type 'application/gzip' length 282089 bytes (275 KB) ================================================== downloaded 275 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/IRanges_2.36.0.tar.gz' Content type 'application/gzip' length 481055 bytes (469 KB) ================================================== downloaded 469 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/S4Vectors_0.40.2.tar.gz' Content type 'application/gzip' length 838187 bytes (818 KB) ================================================== downloaded 818 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomeInfoDb_1.38.8.tar.gz' Content type 'application/gzip' length 3581806 bytes (3.4 MB) ================================================== downloaded 3.4 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/DelayedArray_0.28.0.tar.gz' Content type 'application/gzip' length 624166 bytes (609 KB) ================================================== downloaded 609 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GenomicRanges_1.54.1.tar.gz' Content type 'application/gzip' length 1140246 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SummarizedExperiment_1.32.0.tar.gz' Content type 'application/gzip' length 686052 bytes (669 KB) ================================================== downloaded 669 KB trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SingleCellExperiment_1.24.0.tar.gz' Content type 'application/gzip' length 985002 bytes (961 KB) ================================================== downloaded 961 KB * installing *source* package ‘S4Vectors’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c AEbufs.c -o AEbufs.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c DataFrame_class.c -o DataFrame_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Hits_class.c -o Hits_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c LLint_class.c -o LLint_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c List_class.c -o List_class.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-EawLoD/r-base-4.4.1=/usr/src/r-base-4.4.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c Rle_class.c -o Rle_class.o Rle_class.c: In function ‘_subset_Rle_by_ranges’: Rle_class.c:1136:17: error: format not a string literal and no format arguments [-Werror=format-security] 1136 | error(errmsg); | ^~~~~ Rle_class.c: In function ‘_subset_Rle_by_positions’: Rle_class.c:1161:17: error: format not a string literal and no format arguments [-Werror=format-security] 1161 | error(errmsg); | ^~~~~ Rle_class.c: In function ‘Rle_extract_range’: Rle_class.c:1190:17: error: format not a string literal and no format arguments [-Werror=format-security] 1190 | error(errmsg); | ^~~~~ cc1: some warnings being treated as errors make: *** [/usr/lib/R/etc/Makeconf:195: Rle_class.o] Error 1 ERROR: compilation failed for package ‘S4Vectors’ * removing ‘/home/omnipath/local/R/4.4-3.20/S4Vectors’ ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’ * removing ‘/home/omnipath/local/R/4.4-3.20/IRanges’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘XVector’ * removing ‘/home/omnipath/local/R/4.4-3.20/XVector’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘S4Arrays’ * removing ‘/home/omnipath/local/R/4.4-3.20/S4Arrays’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘GenomeInfoDb’ * removing ‘/home/omnipath/local/R/4.4-3.20/GenomeInfoDb’ ERROR: dependencies ‘S4Vectors’, ‘S4Arrays’, ‘IRanges’, ‘XVector’ are not available for package ‘SparseArray’ * removing ‘/home/omnipath/local/R/4.4-3.20/SparseArray’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘XVector’ are not available for package ‘GenomicRanges’ * removing ‘/home/omnipath/local/R/4.4-3.20/GenomicRanges’ ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘S4Arrays’, ‘SparseArray’ are not available for package ‘DelayedArray’ * removing ‘/home/omnipath/local/R/4.4-3.20/DelayedArray’ ERROR: dependencies ‘GenomicRanges’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘S4Arrays’, ‘DelayedArray’ are not available for package ‘SummarizedExperiment’ * removing ‘/home/omnipath/local/R/4.4-3.20/SummarizedExperiment’ ERROR: dependencies ‘SummarizedExperiment’, ‘S4Vectors’, ‘GenomicRanges’, ‘DelayedArray’ are not available for package ‘SingleCellExperiment’ * removing ‘/home/omnipath/local/R/4.4-3.20/SingleCellExperiment’ The downloaded source packages are in ‘/tmp/RtmpLTv0G4/downloaded_packages’ Warning messages: 1: In i.p(...) : installation of package ‘S4Vectors’ had non-zero exit status 2: In i.p(...) : installation of package ‘IRanges’ had non-zero exit status 3: In i.p(...) : installation of package ‘XVector’ had non-zero exit status 4: In i.p(...) : installation of package ‘S4Arrays’ had non-zero exit status 5: In i.p(...) : installation of package ‘GenomeInfoDb’ had non-zero exit status 6: In i.p(...) : installation of package ‘SparseArray’ had non-zero exit status 7: In i.p(...) : installation of package ‘GenomicRanges’ had non-zero exit status 8: In i.p(...) : installation of package ‘DelayedArray’ had non-zero exit status 9: In i.p(...) : installation of package ‘SummarizedExperiment’ had non-zero exit status 10: In i.p(...) : installation of package ‘SingleCellExperiment’ had non-zero exit status [ Finished: 2024-08-16 02:11:30 CEST ]