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###
### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL rhdf5filters
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* 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 Bioc build machine
configure: configuring BZIP2 filter...
configure: compiling bundled bzip2 library
configure: configuring the Zstd filter...
configure: compiling bundled Zstd library
configure: configuring the BLOSC filter...
configure: compiling bundled BLOSC library
checking whether C compiler accepts -msse2... no
configure: Bioc build machine; disabling MAVX2
configure: configuring the VBZ filter
machine=aarch64
CPU_ARCH=arm64
VBZ_FLAGS=-D__ARM_NEON__
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 (GCC) 10.3.1’
make -C zstd
make[1]: Entering directory '/home/biocbuild/bbs-3.19-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/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" \
-I. -Icommon ../zstd/libzstd.a -L/usr/local/lib -o libH5Zzstd.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/zstd'
make -C blosc
make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/home/biocbuild/bbs-3.19-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/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -c snappy-c.cc
g++ -std=gnu++17 -g -O2 -Wall -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -c snappy-sinksource.cc
g++ -std=gnu++17 -g -O2 -Wall -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.4
make[2]: Entering directory '/home/biocbuild/bbs-3.19-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-3.19-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-3.19-bioc/meat/rhdf5filters/src/blosc/lib/blosc-1.20.1'
gcc -g -O2 -Wall -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd   -c bitshuffle-generic.c
gcc -g -O2 -Wall -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd   -c shuffle-generic.c
gcc -g -O2 -Wall -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd     -c shuffle.c
shuffle.c: In function ‘get_shuffle_implementation’:
shuffle.c:316:22: warning: unused variable ‘cpu_features’ [-Wunused-variable]
  316 |   blosc_cpu_features cpu_features = blosc_get_cpu_features();
      |                      ^~~~~~~~~~~~
In file included from shuffle.c:12:
At top level:
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/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd   -c blosclz.c
gcc -g -O2 -Wall -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd   -c blosc.c
gcc -g -O2 -Wall -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -I../lz4-1.9.4 -I../snappy-1.1.1 -I../../../zstd   -c fastcopy.c
make[2]: Leaving directory '/home/biocbuild/bbs-3.19-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
g++ -std=gnu++17 -g -O2 -Wall -fPIC -shared -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" H5Zblosc.cpp \
-L/usr/local/lib -I./lib/blosc-1.20.1 ./libblosc.a ../zstd/libzstd.a -lz -o libH5Zblosc.so 
make[1]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/blosc'
make -C bzip2
make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/bzip2'
make -C bzip2-1.0.8
make[2]: Entering directory '/home/biocbuild/bbs-3.19-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-3.19-bioc/meat/rhdf5filters/src/bzip2/bzip2-1.0.8'
gcc -g -O2 -Wall -fPIC -shared H5Zbzip2.c -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" \
-Ibzip2-1.0.8 bzip2-1.0.8/libbz2.a -L/usr/local/lib -o libH5Zbz2.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/bzip2'
make -C lzf
make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/lzf'
make -C lzf
make[2]: Entering directory '/home/biocbuild/bbs-3.19-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-3.19-bioc/meat/rhdf5filters/src/lzf/lzf'
gcc -g -O2 -Wall -fPIC -shared H5Zlzf.c -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" \
-I./lzf/ ./lzf/liblzf.a -L/usr/local/lib -o libH5Zlzf.so
make[1]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/lzf'
make -C vbz
make[1]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/vbz'
make -C third_party/streamvbyte
make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/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 '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/vbz/third_party/streamvbyte'
make -C vbz
make[2]: Entering directory '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/vbz/vbz'
g++ -std=gnu++17 -g -O2 -Wall -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -D__ARM_NEON__ -c vbz.cpp -o vbz.o
g++ -std=gnu++17 -g -O2 -Wall -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -D__ARM_NEON__ -c v0/vbz_streamvbyte.cpp -o v0/vbz_streamvbyte.o
g++ -std=gnu++17 -g -O2 -Wall -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -I../third_party/streamvbyte/include/ -I../third_party/ -I../../zstd/ -D__ARM_NEON__ -c v1/vbz_streamvbyte.cpp -o v1/vbz_streamvbyte.o
make[2]: Leaving directory '/home/biocbuild/bbs-3.19-bioc/meat/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 -Wall -fPIC -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/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 '/home/biocbuild/bbs-3.19-bioc/meat/rhdf5filters/src/vbz'
mkdir -p "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp bzip2/libH5Zbz2.so blosc/libH5Zblosc.so lzf/libH5Zlzf.so zstd/libH5Zzstd.so vbz/libH5Zvbz.so "/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG -I/usr/local/include -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/Rhdf5lib/include" -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o rhdf5filters.so rhdf5filters.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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)