[ Started: 2023-04-20 00:08:16 CEST ] [ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.17" [3] "/home/omnipath/local/R/4.3" "/opt/R-beta/lib/R/library" Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 RC (2023-04-13 r84266) Old packages: 'rhdf5filters', 'vctrs' trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/rhdf5filters_1.11.3.tar.gz' Content type 'application/x-gzip' length 2959850 bytes (2.8 MB) ================================================== downloaded 2.8 MB trying URL 'https://cloud.r-project.org/src/contrib/vctrs_0.6.2.tar.gz' Content type 'application/x-gzip' length 964633 bytes (942 KB) ================================================== downloaded 942 KB * installing *source* package ‘rhdf5filters’ ... ** using staged installation configuring the BLOSC filter... x86_CPU=true checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether C compiler accepts -msse2... yes checking whether C compiler accepts -mavx2... yes checking for gcc __builtin_cpu_init function... (cached) true checking for x86 sse2 instruction support... yes checking for x86 avx2 instruction support... yes configure: creating ./config.status config.status: creating src/blosc/lib/blosc-1.20.1/Makefile config.status: creating src/blosc/Makefile configure: BZIP2_LIB=bzip2/libH5Zbz2.so configure: BLOSC_LIB=blosc/libH5Zblosc.so configure: LZF_LIB=lzf/libH5Zlzf.so configure: VBZ_LIB=vbz/libH5Zvbz.so configure: ZSTD_LIB=zstd/libH5Zzstd.so configure: creating ./config.status config.status: creating src/blosc/lib/blosc-1.20.1/Makefile config.status: creating src/blosc/Makefile config.status: creating src/Makevars ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ make -C zstd make[1]: Entering directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/zstd' gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/debug.c -o common/debug.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/entropy_common.c -o common/entropy_common.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/error_private.c -o common/error_private.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/fse_decompress.c -o common/fse_decompress.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/pool.c -o common/pool.o -o common/pool.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/threading.c -o common/threading.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/xxhash.c -o common/xxhash.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/zstd_common.c -o common/zstd_common.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/fse_compress.c -o compress/fse_compress.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/hist.c -o compress/hist.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/huf_compress.c -o compress/huf_compress.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress.c -o compress/zstd_compress.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_fast.c -o compress/zstd_fast.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_lazy.c -o compress/zstd_lazy.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_ldm.c -o compress/zstd_ldm.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_opt.c -o compress/zstd_opt.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/huf_decompress.c -o decompress/huf_decompress.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o gcc -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o rm -f libzstd.a ar cq libzstd.a common/debug.o common/entropy_common.o common/error_private.o common/fse_decompress.o common/pool.o common/threading.o common/xxhash.o common/zstd_common.o compress/fse_compress.o compress/hist.o compress/huf_compress.o compress/zstd_compress.o compress/zstd_compress_literals.o compress/zstd_compress_sequences.o compress/zstd_compress_superblock.o compress/zstd_double_fast.o compress/zstd_fast.o compress/zstd_lazy.o compress/zstd_ldm.o compress/zstd_opt.o compress/zstdmt_compress.o decompress/huf_decompress.o decompress/zstd_ddict.o decompress/zstd_decompress.o decompress/zstd_decompress_block.o ranlib libzstd.a gcc -g -O2 -fpic -shared H5Zzstd.c -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" \ libzstd.a -L/usr/local/lib -o libH5Zzstd.so make[1]: Leaving directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/zstd' make -C blosc make[1]: Entering directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/blosc' make -C lib/snappy-1.1.1 make[2]: Entering directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/blosc/lib/snappy-1.1.1' g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -c snappy.cc g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -c snappy-c.cc g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -c snappy-sinksource.cc g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -c snappy-stubs-internal.cc make[2]: Leaving directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/blosc/lib/snappy-1.1.1' make -C lib/lz4-1.9.4 make[2]: Entering directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/blosc/lib/lz4-1.9.4' gcc -g -O2 -fpic -c lz4.c gcc -g -O2 -fpic -c lz4hc.c make[2]: Leaving directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/blosc/lib/lz4-1.9.4' make -C lib/blosc-1.20.1 all make[2]: Entering directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/blosc/lib/blosc-1.20.1' gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c bitshuffle-avx2.c gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c shuffle-avx2.c gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c bitshuffle-sse2.c gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c shuffle-sse2.c gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c bitshuffle-generic.c gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c shuffle-generic.c gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED -c shuffle.c gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c blosclz.c gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c blosc.c gcc -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2 -mavx2 -c fastcopy.c make[2]: Leaving directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/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 gcc -g -O2 -fpic -c -o H5Zblosc.o H5Zblosc.c \ -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I./lib/blosc-1.20.1 g++ -std=gnu++17 -g -O2 -fpic -L/usr/local/lib -shared -o libH5Zblosc.so H5Zblosc.o \ libblosc.a ../zstd/libzstd.a -lz make[1]: Leaving directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/blosc' make -C bzip2 make[1]: Entering directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/bzip2' make -C bzip2-1.0.8 make[2]: Entering directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/bzip2/bzip2-1.0.8' gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c blocksort.c gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c huffman.c gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c crctable.c gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c randtable.c gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c compress.c gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c decompress.c gcc -g -O2 -fpic -D_FILE_OFFSET_BITS=64 -c bzlib.c rm -f libbz2.a ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o ranlib libbz2.a make[2]: Leaving directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/bzip2/bzip2-1.0.8' gcc -g -O2 -fpic -shared H5Zbzip2.c -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" \ -I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a -L/usr/local/lib -o libH5Zbz2.so make[1]: Leaving directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/bzip2' make -C lzf make[1]: Entering directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/lzf' make -C lzf make[2]: Entering directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/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/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/lzf/lzf' gcc -g -O2 -fpic -shared H5Zlzf.c -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" \ -I./lzf/ ./lzf/liblzf.a -L/usr/local/lib -o libH5Zlzf.so make[1]: Leaving directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/lzf' make -C vbz make[1]: Entering directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/vbz' make -C third_party/streamvbyte make[2]: Entering directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/vbz/third_party/streamvbyte' gcc -g -O2 -fpic -Iinclude -c ./src/streamvbyte_decode.c gcc -g -O2 -fpic -Iinclude -c ./src/streamvbyte_encode.c gcc -g -O2 -fpic -Iinclude -c ./src/streamvbytedelta_decode.c gcc -g -O2 -fpic -Iinclude -c ./src/streamvbytedelta_encode.c gcc -g -O2 -fpic -Iinclude -c ./src/streamvbyte_0124_encode.c gcc -g -O2 -fpic -Iinclude -c ./src/streamvbyte_0124_decode.c gcc -g -O2 -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/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/vbz/third_party/streamvbyte' make -C vbz make[2]: Entering directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/vbz/vbz' g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -c vbz.cpp -o vbz.o g++ -std=gnu++17 -g -O2 -fpic -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -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/4.3-3.17/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -c v1/vbz_streamvbyte.cpp -o v1/vbz_streamvbyte.o make[2]: Leaving directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/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/4.3-3.17/Rhdf5lib/include" -shared vbz_plugin.cpp \ libvbz.a -L/usr/local/lib ../zstd/libzstd.a third_party/streamvbyte/libstreamvbyte.a -o libH5Zvbz.so make[1]: Leaving directory '/tmp/RtmpPFUY3o/R.INSTALL2678354b72f86f/rhdf5filters/src/vbz' mkdir -p "/home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" cp bzip2/libH5Zbz2.so "/home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" cp blosc/libH5Zblosc.so "/home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" cp lzf/libH5Zlzf.so "/home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" cp vbz/libH5Zvbz.so "/home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" cp zstd/libH5Zzstd.so "/home/omnipath/local/R/4.3-3.17/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I/usr/local/include -I"/home/omnipath/local/R/4.3-3.17/Rhdf5lib/include" -I'/home/omnipath/local/R/4.3-3.17/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/4.3-3.17/00LOCK-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 ‘vctrs’ ... ** package ‘vctrs’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c altrep-rle.c -o altrep-rle.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c altrep.c -o altrep.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c arg-counter.c -o arg-counter.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c arg.c -o arg.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c assert.c -o assert.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c bind.c -o bind.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c c-unchop.c -o c-unchop.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c c.c -o c.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c callables.c -o callables.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cast-bare.c -o cast-bare.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cast-dispatch.c -o cast-dispatch.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cast.c -o cast.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c compare.c -o compare.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c complete.c -o complete.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c conditions.c -o conditions.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c dictionary.c -o dictionary.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c dim.c -o dim.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c empty.c -o empty.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c equal.c -o equal.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c expand.c -o expand.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fields.c -o fields.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c fill.c -o fill.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c globals.c -o globals.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c group.c -o group.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c growable.c -o growable.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c hash.c -o hash.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c init.c -o init.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c interval.c -o interval.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c match-joint.c -o match-joint.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c match.c -o match.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c missing.c -o missing.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c names.c -o names.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c order-collate.c -o order-collate.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c order-groups.c -o order-groups.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c order-sortedness.c -o order-sortedness.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c order-truelength.c -o order-truelength.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c order.c -o order.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c poly-op.c -o poly-op.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c proxy-restore.c -o proxy-restore.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c proxy.c -o proxy.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ptype-common.c -o ptype-common.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ptype.c -o ptype.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ptype2-dispatch.c -o ptype2-dispatch.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c ptype2.c -o ptype2.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c rank.c -o rank.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c rep.c -o rep.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c rlang-dev.c -o rlang-dev.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c rlang.c -o rlang.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c runs.c -o runs.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c set.c -o set.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c shape.c -o shape.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c size-common.c -o size-common.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c size.c -o size.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c slice-array.c -o slice-array.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c slice-assign-array.c -o slice-assign-array.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c slice-assign.c -o slice-assign.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c slice-chop.c -o slice-chop.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c slice-interleave.c -o slice-interleave.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c slice.c -o slice.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c split.c -o split.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c subscript-loc.c -o subscript-loc.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c subscript.c -o subscript.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c translate.c -o translate.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type-data-frame.c -o type-data-frame.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type-date-time.c -o type-date-time.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type-factor.c -o type-factor.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type-info.c -o type-info.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type-integer64.c -o type-integer64.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c type-tibble.c -o type-tibble.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c typeof2-s3.c -o typeof2-s3.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c typeof2.c -o typeof2.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c unspecified.c -o unspecified.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c utils-dispatch.c -o utils-dispatch.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c utils.c -o utils.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vctrs-core.c -o vctrs-core.o gcc -I"/opt/R-beta/lib/R/include" -DNDEBUG -I./rlang -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c version.c -o version.o gcc -shared -L/usr/local/lib -o vctrs.so altrep-rle.o altrep.o arg-counter.o arg.o assert.o bind.o c-unchop.o c.o callables.o cast-bare.o cast-dispatch.o cast.o compare.o complete.o conditions.o dictionary.o dim.o empty.o equal.o expand.o fields.o fill.o globals.o group.o growable.o hash.o init.o interval.o match-joint.o match.o missing.o names.o order-collate.o order-groups.o order-sortedness.o order-truelength.o order.o poly-op.o proxy-restore.o proxy.o ptype-common.o ptype.o ptype2-dispatch.o ptype2.o rank.o rep.o rlang-dev.o rlang.o runs.o set.o shape.o size-common.o size.o slice-array.o slice-assign-array.o slice-assign.o slice-chop.o slice-interleave.o slice.o split.o subscript-loc.o subscript.o translate.o type-data-frame.o type-date-time.o type-factor.o type-info.o type-integer64.o type-tibble.o typeof2-s3.o typeof2.o unspecified.o utils-dispatch.o utils.o vctrs-core.o version.o installing to /home/omnipath/local/R/4.3-3.17/00LOCK-vctrs/00new/vctrs/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 (vctrs) The downloaded source packages are in ‘/tmp/Rtmpe3BKDk/downloaded_packages’ Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 RC (2023-04-13 r84266) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 17 packages not available: BiocManager, yaml, rmarkdown, knitr, bookdown, sessioninfo, testthat, covr, RefManageR, rjson, tidyr, tibble, dplyr, igraph, lpSolve, stringr, readr [ Finished: 2023-04-20 00:09:25 CEST ]