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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data Rarr
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* checking for file ‘Rarr/DESCRIPTION’ ... OK
* preparing ‘Rarr’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘Rarr’ ...
** using staged installation
NO_RLIB=
R_CPPFLAGS=-I/home/biocbuild/R/R-4.4.1/include
configure: is Bioc build machine
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: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/compression_tools/blosc/lib/blosc-1.20.1/Makefile
config.status: creating src/compression_tools/blosc/Makefile
config.status: creating src/compression_tools/blosc/lib/snappy-1.1.1/Makefile
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -g -O2 -Wall -fPIC  -g -O2  -Wall -c Rarr.c -o Rarr.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -g -O2 -Wall -fPIC  -g -O2  -Wall -c bit64_conversion.c -o bit64_conversion.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -g -O2 -Wall -fPIC  -g -O2  -Wall -c compress.c -o compress.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -g -O2 -Wall -fPIC  -g -O2  -Wall -c decompress.c -o decompress.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -g -O2 -Wall -fPIC  -g -O2  -Wall -c float16_conversion.c -o float16_conversion.o
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include   -g -O2 -Wall -fPIC  -g -O2  -Wall -c type_conversion.c -o type_conversion.o
make -C compression_tools/zstd
make[1]: Entering directory '/home/biocbuild/tmp/RtmpJRsFkM/Rbuild2a523734ebc6b5/Rarr/src/compression_tools/zstd'
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/debug.c -o common/debug.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/entropy_common.c -o common/entropy_common.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/error_private.c -o common/error_private.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/fse_decompress.c -o common/fse_decompress.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -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_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/threading.c -o common/threading.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/xxhash.c -o common/xxhash.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c common/zstd_common.c -o common/zstd_common.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/fse_compress.c -o compress/fse_compress.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/hist.c -o compress/hist.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/huf_compress.c -o compress/huf_compress.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -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_ -DNDEBUG -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_ -DNDEBUG -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_ -DNDEBUG -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_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -DZSTD_DISABLE_ASM -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -g -O2 -Wall -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -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
make[1]: Leaving directory '/home/biocbuild/tmp/RtmpJRsFkM/Rbuild2a523734ebc6b5/Rarr/src/compression_tools/zstd'
make -C compression_tools/blosc
make[1]: Entering directory '/home/biocbuild/tmp/RtmpJRsFkM/Rbuild2a523734ebc6b5/Rarr/src/compression_tools/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory '/home/biocbuild/tmp/RtmpJRsFkM/Rbuild2a523734ebc6b5/Rarr/src/compression_tools/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17 -g -O2 -Wall -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.4.1/include -DUSING_R  -c snappy.cc
snappy.cc: In member function 'bool snappy::SnappyIOVecWriter::Append(const char*, size_t)':
snappy.cc:1021:33: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare]
 1021 |         if (curr_iov_index_ + 1 >= output_iov_count_) {
      |             ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
snappy.cc: In member function 'bool snappy::SnappyIOVecWriter::AppendFromSelf(size_t, size_t)':
snappy.cc:1103:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long unsigned int'} [-Wsign-compare]
 1103 |           if (curr_iov_index_ + 1 >= output_iov_count_) {
      |               ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
snappy.cc: At global scope:
snappy.cc:578:13: warning: 'void snappy::ComputeTable()' defined but not used [-Wunused-function]
  578 | static void ComputeTable() {
      |             ^~~~~~~~~~~~
g++ -std=gnu++17 -g -O2 -Wall -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.4.1/include -DUSING_R  -c snappy-c.cc
g++ -std=gnu++17 -g -O2 -Wall -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.4.1/include -DUSING_R  -c snappy-sinksource.cc
g++ -std=gnu++17 -g -O2 -Wall -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.4.1/include -DUSING_R  -c snappy-stubs-internal.cc
make[2]: Leaving directory '/home/biocbuild/tmp/RtmpJRsFkM/Rbuild2a523734ebc6b5/Rarr/src/compression_tools/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.9.2
make[2]: Entering directory '/home/biocbuild/tmp/RtmpJRsFkM/Rbuild2a523734ebc6b5/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2'
gcc -g -O2 -Wall -fPIC -DNLZ4_DEBUG -c lz4.c
gcc -g -O2 -Wall -fPIC -DNLZ4_DEBUG -c lz4hc.c
make[2]: Leaving directory '/home/biocbuild/tmp/RtmpJRsFkM/Rbuild2a523734ebc6b5/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/home/biocbuild/tmp/RtmpJRsFkM/Rbuild2a523734ebc6b5/Rarr/src/compression_tools/blosc/lib/blosc-1.20.1'
gcc -g -O2 -Wall -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.4.1/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c bitshuffle-generic.c
gcc -g -O2 -Wall -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.4.1/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c shuffle-generic.c
gcc -g -O2 -Wall -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.4.1/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R    -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:
shuffle-generic.h: 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-4.4.1/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c blosclz.c
gcc -g -O2 -Wall -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.4.1/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c blosc.c
blosc.c:303:12: warning: 'compname_to_clibcode' defined but not used [-Wunused-function]
  303 | static int compname_to_clibcode(const char *compname)
      |            ^~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Wall -fPIC -I/usr/local/include -I/home/biocbuild/R/R-4.4.1/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../../../zstd   -DUSING_R  -c fastcopy.c
make[2]: Leaving directory '/home/biocbuild/tmp/RtmpJRsFkM/Rbuild2a523734ebc6b5/Rarr/src/compression_tools/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/lz4-1.9.2/lz4.o lib/lz4-1.9.2/lz4hc.o
ranlib libblosc.a
make[1]: Leaving directory '/home/biocbuild/tmp/RtmpJRsFkM/Rbuild2a523734ebc6b5/Rarr/src/compression_tools/blosc'
gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o Rarr.so Rarr.o bit64_conversion.o compress.o decompress.o float16_conversion.o type_conversion.o ./compression_tools/blosc/libblosc.a ./compression_tools/zstd/libzstd.a -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/tmp/RtmpJRsFkM/Rinst2a5237749ca092/00LOCK-Rarr/00new/Rarr/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
Error: package or namespace load failed for ‘Rarr’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/biocbuild/tmp/RtmpJRsFkM/Rinst2a5237749ca092/00LOCK-Rarr/00new/Rarr/libs/Rarr.so':
  /home/biocbuild/tmp/RtmpJRsFkM/Rinst2a5237749ca092/00LOCK-Rarr/00new/Rarr/libs/Rarr.so: undefined symbol: pthread_atfork
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/biocbuild/tmp/RtmpJRsFkM/Rinst2a5237749ca092/Rarr’
      -----------------------------------
ERROR: package installation failed