[ Started: 2024-03-20 23:55:26 CET ] [ dorothea v1.7.4 for BioC-3.19 from https://github.com/saezlab/dorothea@master ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.19" [3] "/home/omnipath/local/R/4.4" "/opt/R-devel/lib/R/library" Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable) (2024-03-19 r86153) Old packages: 'AUCell', 'beachmat', 'BiocSingular', 'DelayedArray', 'DelayedMatrixStats', 'GenomicRanges', 'GSVA', 'HDF5Array', 'MatrixGenerics', 'OmnipathR', 'rhdf5', 'rhdf5filters', 'Rhdf5lib', 'S4Arrays', 'ScaledMatrix', 'SingleCellExperiment', 'SparseArray', 'sparseMatrixStats', 'SummarizedExperiment', 'viper' trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/AUCell_1.25.2.tar.gz' Content type 'application/x-gzip' length 1764092 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/beachmat_2.19.1.tar.gz' Content type 'application/x-gzip' length 512130 bytes (500 KB) ================================================== downloaded 500 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/BiocSingular_1.19.0.tar.gz' Content type 'application/x-gzip' length 614043 bytes (599 KB) ================================================== downloaded 599 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/DelayedArray_0.29.9.tar.gz' Content type 'application/x-gzip' length 633869 bytes (619 KB) ================================================== downloaded 619 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/DelayedMatrixStats_1.25.1.tar.gz' Content type 'application/x-gzip' length 270471 bytes (264 KB) ================================================== downloaded 264 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/GenomicRanges_1.55.4.tar.gz' Content type 'application/x-gzip' length 1140405 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/GSVA_1.51.6.tar.gz' Content type 'application/x-gzip' length 2356069 bytes (2.2 MB) ================================================== downloaded 2.2 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/HDF5Array_1.31.6.tar.gz' Content type 'application/x-gzip' length 8101044 bytes (7.7 MB) ================================================== downloaded 7.7 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/MatrixGenerics_1.15.0.tar.gz' Content type 'application/x-gzip' length 31188 bytes (30 KB) ================================================== downloaded 30 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/OmnipathR_3.11.2.tar.gz' Content type 'application/x-gzip' length 3014067 bytes (2.9 MB) ================================================== downloaded 2.9 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/rhdf5_2.47.6.tar.gz' Content type 'application/x-gzip' length 1273153 bytes (1.2 MB) ================================================== downloaded 1.2 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/rhdf5filters_1.15.4.tar.gz' Content type 'application/x-gzip' length 1180183 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/Rhdf5lib_1.25.1.tar.gz' Content type 'application/x-gzip' length 12057444 bytes (11.5 MB) ================================================== downloaded 11.5 MB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/S4Arrays_1.3.6.tar.gz' Content type 'application/x-gzip' length 282277 bytes (275 KB) ================================================== downloaded 275 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/ScaledMatrix_1.11.1.tar.gz' Content type 'application/x-gzip' length 313573 bytes (306 KB) ================================================== downloaded 306 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/SingleCellExperiment_1.25.0.tar.gz' Content type 'application/x-gzip' length 979303 bytes (956 KB) ================================================== downloaded 956 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/SparseArray_1.3.4.tar.gz' Content type 'application/x-gzip' length 367916 bytes (359 KB) ================================================== downloaded 359 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/sparseMatrixStats_1.15.0.tar.gz' Content type 'application/x-gzip' length 702899 bytes (686 KB) ================================================== downloaded 686 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/SummarizedExperiment_1.33.3.tar.gz' Content type 'application/x-gzip' length 688149 bytes (672 KB) ================================================== downloaded 672 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/viper_1.37.0.tar.gz' Content type 'application/x-gzip' length 318322 bytes (310 KB) ================================================== downloaded 310 KB * installing *source* package ‘GenomicRanges’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I/usr/local/include -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I/usr/local/include -fpic -g -O2 -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I/usr/local/include -fpic -g -O2 -c transcript_utils.c -o transcript_utils.o gcc -shared -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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 ‘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 ‘OmnipathR’ ... ** 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 [2024-03-20 23:56:07] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-03-20 23:56:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 23:56:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 23:56:07] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-20 23:56:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-20 23:56:07] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-20 23:56:07] [TRACE] [OmnipathR] Contains 1 files. [2024-03-20 23:56:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-20 23:56:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 23:56:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 23:56:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-20 23:56:07] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-20 23:56:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-20 23:56:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 23:56:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-20 23:56:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 23:56:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-20 23:56:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 23:56:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-20 23:56:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 23:56:07] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-03-20 23:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 23:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 23:56:08] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-03-20 23:56:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-20 23:56:08] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-03-20 23:56:08] [TRACE] [OmnipathR] Contains 1 files. [2024-03-20 23:56:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-20 23:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-20 23:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 23:56:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-03-20 23:56:08] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-03-20 23:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-20 23:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 23:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-20 23:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 23:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-20 23:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 23:56:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-20 23:56:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-20 23:56:08] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) * 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... yes checking for libaec.h... yes checking for SZ_BufftoBuffCompress in -lsz... yes checking for aec_buffer_encode in -lsz... yes 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 11.4.0-1ubuntu1~22.04) 11.4.0’ gunzip -dc hdf5small_cxx_hl_1.10.7.tar.gz | tar xf -; cd hdf5; \ ./configure --with-pic --enable-shared=no --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++17' \ CPPFLAGS='-I/usr/local/include' \ CFLAGS='-g -O2 -w -fpic' \ CXXFLAGS='-w -g -O2 -fpic' \ AR='ar' RANLIB='ranlib' \ LDFLAGS='-L/usr/local/lib'; \ make lib checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/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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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... 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 how to run the C++ preprocessor... g++ -std=gnu++17 -E checking for ld used by g++ -std=gnu++17... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ -std=gnu++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ -std=gnu++17 option to produce PIC... -fPIC -DPIC checking if g++ -std=gnu++17 PIC flag -fPIC -DPIC works... yes checking if g++ -std=gnu++17 static flag -static works... yes checking if g++ -std=gnu++17 supports -c -o file.o... yes checking if g++ -std=gnu++17 supports -c -o file.o... (cached) yes checking whether the g++ -std=gnu++17 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if we should install only statically linked executables... no checking if -Wl,-rpath should be used to link shared libs in nondefault directories... yes checking for ceil in -lm... yes checking for dlopen in -ldl... yes checking for egrep... (cached) /usr/bin/grep -E checking for sys/resource.h... yes checking for sys/time.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/ioctl.h... yes checking for sys/stat.h... (cached) yes checking for sys/socket.h... yes checking for sys/types.h... (cached) yes checking for sys/file.h... yes checking for stddef.h... yes checking for setjmp.h... yes checking for features.h... yes checking for dirent.h... yes checking for stdint.h... (cached) yes checking for stdbool.h... yes checking for netdb.h... yes checking for netinet/in.h... yes checking for arpa/inet.h... yes checking for io.h... no checking for winsock2.h... no checking for sys/timeb.h... yes checking for _FILE_OFFSET_BITS value needed for large files... no checking size of int8_t... 1 checking size of uint8_t... 1 checking size of int_least8_t... 1 checking size of uint_least8_t... 1 checking size of int_fast8_t... 1 checking size of uint_fast8_t... 1 checking size of int16_t... 2 checking size of uint16_t... 2 checking size of int_least16_t... 2 checking size of uint_least16_t... 2 checking size of int_fast16_t... 8 checking size of uint_fast16_t... 8 checking size of int32_t... 4 checking size of uint32_t... 4 checking size of int_least32_t... 4 checking size of uint_least32_t... 4 checking size of int_fast32_t... 8 checking size of uint_fast32_t... 8 checking size of int64_t... 8 checking size of uint64_t... 8 checking size of int_least64_t... 8 checking size of uint_least64_t... 8 checking size of int_fast64_t... 8 checking size of uint_fast64_t... 8 checking size of size_t... 8 checking size of ssize_t... 8 checking size of ptrdiff_t... 8 checking size of off_t... 8 checking size of bool... 1 checking size of time_t... 8 checking if dev_t is scalar... yes checking for dmalloc library... suppressed checking for zlib.h... yes checking for compress2 in -lz... yes checking for compress2... yes checking for szlib.h... yes checking for libaec.h... yes checking for aec_encode in -laec... yes checking for SZ_BufftoBuffCompress in -lsz... yes checking for szlib encoder... yes checking for thread safe support... no checking for gcc options needed to detect all undeclared functions... none needed checking whether CLOCK_MONOTONIC is declared... yes checking for tm_gmtoff in struct tm... yes checking for global timezone variable... yes checking for st_blocks in struct stat... no checking for _getvideoconfig... no checking for gettextinfo... no checking for GetConsoleScreenBufferInfo... no checking for getpwuid... yes checking for _scrsize... no checking for ioctl... yes checking for struct videoconfig... no checking for struct text_info... no checking for TIOCGWINSZ... yes checking for TIOCGETD... yes checking for library containing clock_gettime... none required checking for alarm... yes checking for clock_gettime... yes checking for difftime... yes checking for fcntl... yes checking for flock... yes checking for fork... yes checking for frexpf... yes checking for frexpl... yes checking for gethostname... yes checking for getrusage... yes checking for gettimeofday... yes checking for lstat... yes checking for rand_r... yes checking for random... yes checking for setsysinfo... no checking for signal... yes checking for longjmp... yes checking for setjmp... yes checking for siglongjmp... yes checking for sigsetjmp... no checking for sigprocmask... yes checking for snprintf... yes checking for srandom... yes checking for strdup... yes checking for symlink... yes checking for system... yes checking for strtoll... yes checking for strtoull... yes checking for tmpfile... yes checking for asprintf... yes checking for vasprintf... yes checking for vsnprintf... yes checking for waitpid... yes checking for roundf... yes checking for lroundf... yes checking for llroundf... yes checking for round... yes checking for lround... yes checking for llround... yes checking for an ANSI C-conforming const... yes checking if the compiler understands __inline__... yes checking if the compiler understands __inline... yes checking if the compiler understands inline... yes checking for __attribute__ extension... yes checking for __func__ extension... yes checking for __FUNCTION__ extension... yes checking for C99 designated initialization support... yes checking how to print long long... %ld and %lu checking enable debugging symbols... no checking enable asserts... no checking enable developer warnings... no checking profiling... no checking optimization level... high checking enable file locking... best-effort checking for internal debug output... none checking whether function stack tracking is enabled... no checking for API tracing... no checking whether a memory checking tool will be used... no checking whether internal memory allocation sanity checking is used... no checking for parallel support files... skipped checking whether O_DIRECT is declared... yes checking for posix_memalign... yes checking if the direct I/O virtual file driver (VFD) is enabled... no checking if the Mirror virtual file driver (VFD) is enabled... 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 checking if the Read-Only S3 virtual file driver (VFD) is enabled... yes checking for libhdfs... 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 /bin/mv creating src/H5pubconf.h mv2 one 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: Wed Mar 20 23:56:23 CET 2024 Configured by: omnipath@saezlab Host system: x86_64-unknown-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/RtmpiRLR2r/R.INSTALL9c6832c841e47/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: -L/usr/local/lib 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: -I/usr/local/include H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API AM_CPPFLAGS: C Flags: -g -O2 -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 -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/RtmpiRLR2r/R.INSTALL9c6832c841e47/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/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/src' make[3]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/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 -L/usr/local/lib | \ 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 -L/usr/local/lib | \ 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/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/src' make[2]: Leaving directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/src' make[2]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/c++' make[3]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/c++' make[3]: Nothing to be done for 'build-lib'. make[3]: Leaving directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/c++' + cd src + make lib make[3]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/c++/src' make[4]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/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/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/c++/src' make[3]: Leaving directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/c++/src' make[2]: Leaving directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/c++' make[2]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl' make[3]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl' make[3]: Nothing to be done for 'build-lib'. make[3]: Leaving directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl' + cd src + make lib make[3]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl/src' make[4]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/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/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl/src' make[3]: Leaving directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl/src' + cd c++ + make lib make[3]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl/c++' make[4]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl/c++' make[4]: Nothing to be done for 'build-lib'. make[4]: Leaving directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl/c++' + cd src + make lib make[4]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl/c++/src' make[5]: Entering directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl/c++/src' CXX H5PacketTable.lo CXXLD libhdf5_hl_cpp.la make[5]: Leaving directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl/c++/src' make[4]: Leaving directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl/c++/src' make[3]: Leaving directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl/c++' make[2]: Leaving directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5/hl' make[1]: Leaving directory '/tmp/RtmpiRLR2r/R.INSTALL9c6832c841e47/Rhdf5lib/src/hdf5' mkdir -p "/home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src"/*.h "/home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/c++/src"/*.h "/home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/src"/*.h "/home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/hl/c++/src"/*.h "/home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" cp "hdf5/src"/libhdf5.settings "/home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" mkdir -p "/home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/src/.libs/libhdf5.a" "/home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/" gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I"/home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -c Rhdf5lib.c -o Rhdf5lib.o gcc -shared -L/usr/local/lib -o Rhdf5lib.so Rhdf5lib.o /home/omnipath/local/R/4.4-3.19/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a -lsz -laec -lz installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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 ‘S4Arrays’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c R_init_S4Arrays.c -o R_init_S4Arrays.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c abind.c -o abind.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c array_selection.c -o array_selection.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c dim_tuning_utils.c -o dim_tuning_utils.o gcc -shared -L/usr/local/lib -o S4Arrays.so R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-S4Arrays/00new/S4Arrays/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘rowsum’ in package ‘S4Arrays’ Creating a new generic function for ‘abind’ in package ‘S4Arrays’ ** 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 (S4Arrays) * 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... yes checking for blosc_compress in -lblosc... yes configure: Using system BLOSC library 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 11.4.0-1ubuntu1~22.04) 11.4.0’ make -C zstd make[1]: Entering directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/zstd' gcc -g -O2 -fpic -shared H5Zzstd.c -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" \ -lzstd -L/usr/local/lib -o libH5Zzstd.so make[1]: Leaving directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/zstd' make -C blosc make[1]: Entering directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/blosc' g++ -std=gnu++17 -g -O2 -fpic -shared -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" H5Zblosc.cpp \ -L/usr/local/lib -lblosc -lzstd -lz -o libH5Zblosc.so make[1]: Leaving directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/blosc' make -C bzip2 make[1]: Entering directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/bzip2' gcc -g -O2 -fpic -shared H5Zbzip2.c -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" \ -lbz2 -L/usr/local/lib -o libH5Zbz2.so make[1]: Leaving directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/bzip2' make -C lzf make[1]: Entering directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/lzf' make -C lzf make[2]: Entering directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/lzf/lzf' gcc -g -O2 -fpic -c lzf_c.c gcc -g -O2 -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/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/lzf/lzf' gcc -g -O2 -fpic -shared H5Zlzf.c -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" \ -I./lzf/ ./lzf/liblzf.a -L/usr/local/lib -o libH5Zlzf.so make[1]: Leaving directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/lzf' make -C vbz make[1]: Entering directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/vbz' make -C third_party/streamvbyte make[2]: Entering directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/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/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/vbz/third_party/streamvbyte' make -C vbz make[2]: Entering directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/vbz/vbz' g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/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 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/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 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/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/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/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 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" -shared vbz_plugin.cpp \ libvbz.a -L/usr/local/lib -lzstd third_party/streamvbyte/libstreamvbyte.a -o libH5Zvbz.so make[1]: Leaving directory '/tmp/RtmpdGC7jv/R.INSTALLa04de1b4d8c18/rhdf5filters/src/vbz' mkdir -p "/home/omnipath/local/R/4.4-3.19/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" cp bzip2/libH5Zbz2.so blosc/libH5Zblosc.so lzf/libH5Zlzf.so zstd/libH5Zzstd.so vbz/libH5Zvbz.so "/home/omnipath/local/R/4.4-3.19/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -I"/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include" -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -g -O2 -fpic -g -O2 -c rhdf5filters.c -o rhdf5filters.o gcc -shared -L/usr/local/lib -o rhdf5filters.so rhdf5filters.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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 ‘SparseArray’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c R_init_SparseArray.c -o R_init_SparseArray.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c Rvector_summarization.c -o Rvector_summarization.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c Rvector_utils.c -o Rvector_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SBT_utils.c -o SBT_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_Ops_methods.c -o SparseArray_Ops_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_abind.c -o SparseArray_abind.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_aperm.c -o SparseArray_aperm.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_class.c -o SparseArray_class.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_subsetting.c -o SparseArray_subsetting.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseArray_summarization.c -o SparseArray_summarization.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c SparseMatrix_mult.c -o SparseMatrix_mult.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c XVector_stubs.c -o XVector_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c coerceVector2.c -o coerceVector2.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c leaf_vector_Arith.c -o leaf_vector_Arith.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c leaf_vector_Compare.c -o leaf_vector_Compare.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c leaf_vector_Logic.c -o leaf_vector_Logic.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c leaf_vector_dotprod.c -o leaf_vector_dotprod.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c leaf_vector_summarization.c -o leaf_vector_summarization.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c leaf_vector_utils.c -o leaf_vector_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c matrixStats_methods.c -o matrixStats_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c randomSparseArray.c -o randomSparseArray.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c readSparseCSV.c -o readSparseCSV.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c rowsum_methods.c -o rowsum_methods.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c sparseMatrix_utils.c -o sparseMatrix_utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fpic -g -O2 -c test.c -o test.o gcc -shared -L/usr/local/lib -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Complex_methods.o SparseArray_Math_methods.o SparseArray_Ops_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_class.o SparseArray_dim_tuning.o SparseArray_subassignment.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o XVector_stubs.o coerceVector2.o leaf_vector_Arith.o leaf_vector_Compare.o leaf_vector_Logic.o leaf_vector_dotprod.o leaf_vector_summarization.o leaf_vector_utils.o matrixStats_methods.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-SparseArray/00new/SparseArray/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 (SparseArray) * installing *source* package ‘sparseMatrixStats’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c SparseMatrixView.cpp -o SparseMatrixView.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c methods.cpp -o methods.o g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c row_methods.cpp -o row_methods.o g++ -std=gnu++11 -shared -L/usr/local/lib -o sparseMatrixStats.so RcppExports.o SparseMatrixView.o methods.o row_methods.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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 ‘DelayedArray’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c R_init_DelayedArray.c -o R_init_DelayedArray.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I/usr/local/include -fpic -g -O2 -c compress_atomic_vector.c -o compress_atomic_vector.o gcc -shared -L/usr/local/lib -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o compress_atomic_vector.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-DelayedArray/00new/DelayedArray/libs ** R ** inst ** byte-compile and prepare package for lazy loading 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 ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5.c -o H5.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5A.c -o H5A.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5D.c -o H5D.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5E.c -o H5E.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5F.c -o H5F.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5G.c -o H5G.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5I.c -o H5I.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5L.c -o H5L.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5O.c -o H5O.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5P.c -o H5P.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5R.c -o H5R.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5S.c -o H5S.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5S_extras.c -o H5S_extras.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5T.c -o H5T.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5T_extras.c -o H5T_extras.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5Z.c -o H5Z.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5constants.c -o H5constants.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c HandleList.cpp -o HandleList.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c HandleListWrap.c -o HandleListWrap.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c bit64conversion.c -o bit64conversion.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c external_filters.c -o external_filters.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5dump.c -o h5dump.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5ls.c -o h5ls.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5testLock.c -o h5testLock.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c printdatatype.c -o printdatatype.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c wrap.c -o wrap.o g++ -std=gnu++17 -shared -L/usr/local/lib -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 H5T_extras.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/4.4-3.19/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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 ‘beachmat’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++17 g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c delayed_isometric_binary.cpp -o delayed_isometric_binary.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c delayed_isometric_math.cpp -o delayed_isometric_math.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c delayed_isometric_unary.cpp -o delayed_isometric_unary.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c delayed_other.cpp -o delayed_other.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c dense_matrix.cpp -o dense_matrix.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c sparse_matrix.cpp -o sparse_matrix.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c tatami_utils.cpp -o tatami_utils.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c unknown_matrix.cpp -o unknown_matrix.o g++ -std=gnu++17 -shared -L/usr/local/lib -o beachmat.so RcppExports.o delayed_isometric_binary.o delayed_isometric_math.o delayed_isometric_unary.o delayed_other.o dense_matrix.o fragment_sparse_rows.o sparse_matrix.o tatami_utils.o unknown_matrix.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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 ‘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 ‘HDF5Array’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5File.c -o H5File.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c global_errmsg_buf.c -o global_errmsg_buf.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c H5DSetDescriptor.c -o H5DSetDescriptor.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5dimscales.c -o h5dimscales.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c uaselection.c -o uaselection.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5mread_helpers.c -o h5mread_helpers.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5mread_startscounts.c -o h5mread_startscounts.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c ChunkIterator.c -o ChunkIterator.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5mread_index.c -o h5mread_index.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5mread_sparse.c -o h5mread_sparse.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5mread.c -o h5mread.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c h5summarize.c -o h5summarize.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c R_init_HDF5Array.c -o R_init_HDF5Array.o gcc -shared -L/usr/local/lib -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/4.4-3.19/Rhdf5lib/lib/libhdf5_hl.a /home/omnipath/local/R/4.4-3.19/Rhdf5lib/lib/libhdf5.a -lcrypto -lcurl -lsz -laec -lz -ldl -lm installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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 ‘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 ‘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 ‘BiocSingular’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++17 g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/beachmat/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I'/home/omnipath/local/R/4.4-3.19/beachmat/include' -I/usr/local/include -fpic -g -O2 -c compute_scale.cpp -o compute_scale.o g++ -std=gnu++17 -shared -L/usr/local/lib -o BiocSingular.so RcppExports.o compute_scale.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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 ‘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 ‘GSVA’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c kernel_estimation.c -o kernel_estimation.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ks_test.c -o ks_test.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c register_cmethods.c -o register_cmethods.o gcc -shared -L/usr/local/lib -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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/RtmpCCiWSX/downloaded_packages’ Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable) (2024-03-19 r86153) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 19 packages ahead of CRAN: zlibbioc, XVector, SparseArray, S4Arrays, IRanges, S4Vectors, MatrixGenerics, BiocGenerics, GenomeInfoDb, DelayedArray, Biobase, GenomicRanges, SummarizedExperiment, SingleCellExperiment, viper, OmnipathR, BiocStyle, decoupleR, bcellViper [ Finished: 2024-03-21 00:06:41 CET ]