Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:55:34 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE rhdf5filters PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1483/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
rhdf5filters 1.0.1 Mike Smith
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | [ OK ] | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK |
Package: rhdf5filters |
Version: 1.0.1 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL rhdf5filters |
StartedAt: 2020-10-16 16:07:51 -0400 (Fri, 16 Oct 2020) |
EndedAt: 2020-10-16 16:08:33 -0400 (Fri, 16 Oct 2020) |
EllapsedTime: 42.8 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL rhdf5filters ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’ * installing *source* package ‘rhdf5filters’ ... ** using staged installation configuring the BLOSC filter... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether C compiler accepts -msse2... yes checking for gcc __builtin_cpu_init function... yes checking for x86 sse2 instruction support... yes checking whether C compiler accepts -mavx2... yes checking for x86 avx2 instruction support... yes configure: creating ./config.status config.status: creating src/blosc/lib/blosc-1.16.3/Makefile config.status: creating src/blosc/Makefile configure: HDF5_INCLUDE=/src configure: BZIP2_LIB=bzip2/libH5Zbz2.so configure: BLOSC_LIB=blosc/libH5Zblosc.so configure: creating ./config.status config.status: creating src/blosc/lib/blosc-1.16.3/Makefile config.status: creating src/blosc/Makefile config.status: creating src/Makevars ** libs make -C blosc make[1]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc' make -C lib/snappy-1.1.1 make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1' g++ -std=gnu++11 -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -c snappy.cc snappy.cc: In member function ‘bool snappy::SnappyIOVecWriter::Append(const char*, size_t)’: snappy.cc:1013:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (curr_iov_index_ + 1 >= output_iov_count_) { ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ snappy.cc: In member function ‘bool snappy::SnappyIOVecWriter::AppendFromSelf(size_t, size_t)’: snappy.cc:1095:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (curr_iov_index_ + 1 >= output_iov_count_) { ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ snappy.cc: At global scope: snappy.cc:567:13: warning: ‘void snappy::ComputeTable()’ defined but not used [-Wunused-function] static void ComputeTable() { ^~~~~~~~~~~~ g++ -std=gnu++11 -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -c snappy-c.cc g++ -std=gnu++11 -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -c snappy-sinksource.cc g++ -std=gnu++11 -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -c snappy-stubs-internal.cc make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1' make -C lib/lz4-1.8.3 make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.8.3' gcc -g -O2 -Wall -fpic -c lz4.c gcc -g -O2 -Wall -fpic -c lz4hc.c make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.8.3' make -C lib/zstd-1.3.8 make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/zstd-1.3.8' gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress.c -o compress/zstd_compress.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_fast.c -o compress/zstd_fast.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_lazy.c -o compress/zstd_lazy.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_ldm.c -o compress/zstd_ldm.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_opt.c -o compress/zstd_opt.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/huf_decompress.c -o decompress/huf_decompress.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/zstd-1.3.8' make -C lib/blosc-1.16.3 all make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.16.3' gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c bitshuffle-avx2.c gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c shuffle-avx2.c gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c bitshuffle-sse2.c gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c shuffle-sse2.c gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c bitshuffle-generic.c gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c shuffle-generic.c gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED -c shuffle.c In file included from shuffle.c:11:0: shuffle-generic.h:61:13: warning: ‘unshuffle_generic_inline’ defined but not used [-Wunused-function] static void unshuffle_generic_inline(const size_t type_size, ^~~~~~~~~~~~~~~~~~~~~~~~ shuffle-generic.h:32:13: warning: ‘shuffle_generic_inline’ defined but not used [-Wunused-function] static void shuffle_generic_inline(const size_t type_size, ^~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c blosclz.c blosclz.c:219:17: warning: ‘get_match_32’ defined but not used [-Wunused-function] static uint8_t *get_match_32(uint8_t *ip, const uint8_t *ip_bound, const uint8_t *ref) { ^~~~~~~~~~~~ blosclz.c:173:17: warning: ‘get_match’ defined but not used [-Wunused-function] static uint8_t *get_match(uint8_t *ip, const uint8_t *ip_bound, const uint8_t *ref) { ^~~~~~~~~ gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c blosc.c gcc -g -O2 -Wall -fpic -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I../lz4-1.8.3 -I../snappy-1.1.1 -I../zstd-1.3.8 -msse2 -mavx2 -c fastcopy.c make[2]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.16.3' rm -f libblosc.a ar cq libblosc.a lib/blosc-1.16.3/bitshuffle-avx2.o lib/blosc-1.16.3/blosc.o lib/blosc-1.16.3/shuffle-avx2.o lib/blosc-1.16.3/shuffle-sse2.o lib/blosc-1.16.3/bitshuffle-generic.o lib/blosc-1.16.3/blosclz.o lib/blosc-1.16.3/shuffle.o lib/blosc-1.16.3/bitshuffle-sse2.o lib/blosc-1.16.3/fastcopy.o lib/blosc-1.16.3/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/lz4-1.8.3/lz4.o lib/lz4-1.8.3/lz4hc.o lib/zstd-1.3.8/common/debug.o lib/zstd-1.3.8/common/entropy_common.o lib/zstd-1.3.8/common/error_private.o lib/zstd-1.3.8/common/fse_decompress.o lib/zstd-1.3.8/common/pool.o lib/zstd-1.3.8/common/threading.o lib/zstd-1.3.8/common/xxhash.o lib/zstd-1.3.8/common/zstd_common.o lib/zstd-1.3.8/compress/fse_compress.o lib/zstd-1.3.8/compress/hist.o lib/zstd-1.3.8/compress/huf_compress.o lib/zstd-1.3.8/compress/zstd_compress.o lib/zstd-1.3.8/compress/zstd_double_fast.o lib/zstd-1.3.8/compress/zstd_fast.o lib/zstd-1.3.8/compress/zstd_lazy.o lib/zstd-1.3.8/compress/zstd_ldm.o lib/zstd-1.3.8/compress/zstd_opt.o lib/zstd-1.3.8/compress/zstdmt_compress.o lib/zstd-1.3.8/decompress/huf_decompress.o lib/zstd-1.3.8/decompress/zstd_ddict.o lib/zstd-1.3.8/decompress/zstd_decompress.o lib/zstd-1.3.8/decompress/zstd_decompress_block.o ranlib libblosc.a gcc -fpic -c -o H5Zblosc.o H5Zblosc.c \ -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I./lib/blosc-1.16.3 g++ -std=gnu++11 -g -O2 -Wall -fpic -L/usr/local/lib -shared -o libH5Zblosc.so H5Zblosc.o \ libblosc.a -lz make[1]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/blosc' make -C bzip2 make[1]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/bzip2' make -C bzip2-1.0.8 make[2]: Entering directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8' gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c blocksort.c gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c huffman.c gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c crctable.c gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c randtable.c gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c compress.c gcc -g -O2 -Wall -fpic -D_FILE_OFFSET_BITS=64 -c decompress.c gcc -g -O2 -Wall -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 '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8' gcc -g -O2 -Wall -fpic -shared H5Zbzip2.c -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" \ -I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a -o libH5Zbz2.so make[1]: Leaving directory '/home/biocbuild/bbs-3.11-bioc/meat/rhdf5filters/src/bzip2' mkdir -p "/home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/" cp bzip2/libH5Zbz2.so /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/ cp blosc/libH5Zblosc.so /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/ gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include" -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -g -O2 -Wall -fpic -g -O2 -Wall -c rhdf5filters.c -o rhdf5filters.o gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o rhdf5filters.so rhdf5filters.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-rhdf5filters/00new/rhdf5filters/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 (rhdf5filters)