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###
### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL rhdf5filters
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* 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:    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 11.4.0-1ubuntu1~22.04) 11.4.0’
make -C zstd
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/zstd'
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/debug.c -o common/debug.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/entropy_common.c -o common/entropy_common.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/error_private.c -o common/error_private.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/fse_decompress.c -o common/fse_decompress.o
gcc -g -O2 -Wall -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 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/threading.c -o common/threading.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/xxhash.c -o common/xxhash.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c common/zstd_common.c -o common/zstd_common.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/fse_compress.c -o compress/fse_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/hist.c -o compress/hist.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/huf_compress.c -o compress/huf_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -g -O2 -Wall -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 -Wall -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 -Wall -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 -Wall -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 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -g -O2 -Wall -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DZSTD_DISABLE_ASM -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -g -O2 -Wall -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 -Wall -fpic -shared H5Zzstd.c -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" \
libzstd.a -L/usr/local/lib -o libH5Zzstd.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/zstd'
make -C blosc
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-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 of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
 1013 |         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 of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare]
 1095 |           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]
  567 | static void ComputeTable() {
      |             ^~~~~~~~~~~~
g++ -std=gnu++17 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++17 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++17 -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.4
make[2]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.9.4'
gcc -g -O2 -Wall -fpic -c lz4.c
gcc -g -O2 -Wall -fpic -c lz4hc.c
make[2]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc/lib/lz4-1.9.4'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.20.1'
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c bitshuffle-avx2.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c shuffle-avx2.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c bitshuffle-sse2.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c shuffle-sse2.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c bitshuffle-generic.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c shuffle-generic.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -DSHUFFLE_SSE2_ENABLED -DSHUFFLE_AVX2_ENABLED -c shuffle.c
In file included from shuffle.c:12:
shuffle-generic.h:61:13: warning: ‘unshuffle_generic_inline’ defined but not used [-Wunused-function]
   61 | 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]
   32 | static void shuffle_generic_inline(const size_t type_size,
      |             ^~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c blosclz.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c blosc.c
gcc -g -O2 -Wall -fpic -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd -msse2 -mavx2 -c fastcopy.c
make[2]: Leaving directory '/home/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/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 -Wall -fpic -c -o H5Zblosc.o H5Zblosc.c \
-I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -I./lib/blosc-1.20.1
H5Zblosc.c: In function ‘H5Z_filter_blosc’:
H5Zblosc.c:96:10: warning: unused variable ‘errmsg’ [-Wunused-variable]
   96 |     char errmsg[256];
      |          ^~~~~~
g++ -std=gnu++17 -g -O2 -Wall -fpic -L/usr/local/lib -shared -o libH5Zblosc.so H5Zblosc.o \
libblosc.a ../zstd/libzstd.a -lz
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/blosc'
make -C bzip2
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/bzip2'
make -C bzip2-1.0.8
make[2]: Entering directory '/home/biocbuild/bbs-3.17-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-3.17-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -g -O2 -Wall -fpic -shared H5Zbzip2.c -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" \
-I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a -L/usr/local/lib -o libH5Zbz2.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/bzip2'
make -C lzf
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/lzf'
make -C lzf
make[2]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -Wall -fpic -c lzf_c.c
gcc -g -O2 -Wall -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 '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -Wall -fpic -shared H5Zlzf.c -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" \
-I./lzf/ ./lzf/liblzf.a -L/usr/local/lib -o libH5Zlzf.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/rhdf5filters/src/lzf'
mkdir -p "/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp bzip2/libH5Zbz2.so "/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp blosc/libH5Zblosc.so "/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp lzf/libH5Zlzf.so "/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp zstd/libH5Zzstd.so "/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -I"/home/biocbuild/bbs-3.17-bioc/R/site-library/Rhdf5lib/include" -I'/home/biocbuild/bbs-3.17-bioc/R/site-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-3.17-bioc/R/lib -L/usr/local/lib -o rhdf5filters.so rhdf5filters.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-bioc/R/site-library/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)