############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL rhdf5filters ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'rhdf5filters' ... ** using staged installation ** libs Warning: this package has a non-empty 'configure.win' file, so building only the main architecture using C compiler: 'gcc.exe (GCC) 12.2.0' `R CMD config MAKE` -C zstd make[1]: Entering directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/zstd' gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/debug.c -o common/debug.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/entropy_common.c -o common/entropy_common.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/error_private.c -o common/error_private.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/fse_decompress.c -o common/fse_decompress.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/pool.c -o common/pool.o -o common/pool.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/threading.c -o common/threading.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/xxhash.c -o common/xxhash.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/zstd_common.c -o common/zstd_common.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/fse_compress.c -o compress/fse_compress.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/hist.c -o compress/hist.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/huf_compress.c -o compress/huf_compress.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress.c -o compress/zstd_compress.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_fast.c -o compress/zstd_fast.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_lazy.c -o compress/zstd_lazy.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_ldm.c -o compress/zstd_ldm.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_opt.c -o compress/zstd_opt.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/huf_decompress.c -o decompress/huf_decompress.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o gcc -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o gcc -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 -shared H5Zzstd.c -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" \ libzstd.a -o libH5Zzstd.so make[1]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/zstd' `R CMD config MAKE` -C blosc make[1]: Entering directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc' `R CMD config MAKE` -C lib/snappy-1.1.1 make[2]: Entering directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1' g++ -std=gnu++17 -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -c snappy.cc g++ -std=gnu++17 -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -c snappy-c.cc g++ -std=gnu++17 -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -c snappy-sinksource.cc g++ -std=gnu++17 -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -c snappy-stubs-internal.cc make[2]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1' `R CMD config MAKE` -C lib/lz4-1.9.4 make[2]: Entering directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.9.4' gcc -c lz4.c gcc -c lz4hc.c make[2]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.9.4' `R CMD config MAKE` -C lib/blosc-1.20.1 all make[2]: Entering directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.20.1' gcc -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -c bitshuffle-generic.c bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_byte_elem_remainder': bitshuffle-generic.c:40:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 40 | } | ^ bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_byte_elem_scal': bitshuffle-generic.c:48:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 48 | } | ^ bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bit_byte_remainder': bitshuffle-generic.c:85:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 85 | } | ^ bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_elem': bitshuffle-generic.c:109:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 109 | } | ^ bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bitrow_eight': bitshuffle-generic.c:121:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 121 | } | ^ bitshuffle-generic.c: In function 'blosc_internal_bshuf_trans_bit_elem_scal': bitshuffle-generic.c:139:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 139 | } | ^ bitshuffle-generic.c: In function 'blosc_internal_bshuf_shuffle_bit_eightelem_scal': bitshuffle-generic.c:204:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 204 | } | ^ bitshuffle-generic.c: In function 'blosc_internal_bshuf_untrans_bit_elem_scal': bitshuffle-generic.c:220:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 220 | } | ^ gcc -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -c shuffle-generic.c shuffle-generic.c: In function 'blosc_internal_shuffle_generic': shuffle-generic.c:17:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 17 | } | ^ shuffle-generic.c: In function 'blosc_internal_unshuffle_generic': shuffle-generic.c:25:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 25 | } | ^ gcc -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -c shuffle.c shuffle.c: In function 'blosc_internal_shuffle': shuffle.c:390:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 390 | } | ^ shuffle.c: In function 'blosc_internal_unshuffle': shuffle.c:403:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 403 | } | ^ shuffle.c: In function 'blosc_internal_bitshuffle': shuffle.c:430:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 430 | } | ^ shuffle.c: In function 'blosc_internal_bitunshuffle': shuffle.c:457:1: warning: visibility attribute not supported in this configuration; ignored [-Wattributes] 457 | } | ^ gcc -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -c blosclz.c gcc -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -c blosc.c gcc -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -c fastcopy.c make[2]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.20.1' rm -f libblosc.a ar cq libblosc.a lib/blosc-1.20.1/blosc.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/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 -c -o H5Zblosc.o H5Zblosc.c \ -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I./lib/blosc-1.20.1 g++ -std=gnu++17 -shared -o libH5Zblosc.so H5Zblosc.o \ libblosc.a ../zstd/libzstd.a -lz make[1]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc' `R CMD config MAKE` -C bzip2 make[1]: Entering directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/bzip2' `R CMD config MAKE` -C bzip2-1.0.8 make[2]: Entering directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8' gcc -D_FILE_OFFSET_BITS=64 -c blocksort.c gcc -D_FILE_OFFSET_BITS=64 -c huffman.c gcc -D_FILE_OFFSET_BITS=64 -c crctable.c gcc -D_FILE_OFFSET_BITS=64 -c randtable.c gcc -D_FILE_OFFSET_BITS=64 -c compress.c gcc -D_FILE_OFFSET_BITS=64 -c decompress.c gcc -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 make[2]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8' gcc -shared H5Zbzip2.c -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" \ -I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a -o libH5Zbz2.so make[1]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/bzip2' `R CMD config MAKE` -C lzf make[1]: Entering directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/lzf' `R CMD config MAKE` -C lzf make[2]: Entering directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/lzf/lzf' gcc -c lzf_c.c gcc -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 '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/lzf/lzf' gcc -shared H5Zlzf.c -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" \ -I./lzf/ ./lzf/liblzf.a -o libH5Zlzf.so make[1]: Leaving directory '/f/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/lzf' mkdir -p "F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64/" cp blosc/libH5Zblosc.so "F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64//libH5Zblosc.dll" cp bzip2/libH5Zbz2.so "F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64//libH5Zbz2.dll" cp lzf/libH5Zlzf.so "F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64//libH5Zlzf.dll" cp zstd/libH5Zzstd.so "F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/x64//libH5Zzstd.dll" gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -lpthread -I"F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include" -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rhdf5lib/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rhdf5filters.c -o rhdf5filters.o gcc -shared -s -static-libgcc -o rhdf5filters.dll tmp.def rhdf5filters.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rhdf5filters)