############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Rarr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * 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/bbs-3.20-bioc/meat/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/bbs-3.20-bioc/meat/Rarr/src/compression_tools/zstd' make -C compression_tools/blosc make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rarr/src/compression_tools/blosc' make -C lib/snappy-1.1.1 make[2]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/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/bbs-3.20-bioc/meat/Rarr/src/compression_tools/blosc/lib/snappy-1.1.1' make -C lib/lz4-1.9.2 make[2]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/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/bbs-3.20-bioc/meat/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2' make -C lib/blosc-1.20.1 all make[2]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/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/bbs-3.20-bioc/meat/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/bbs-3.20-bioc/meat/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/R/R-4.4.1/site-library/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/R/R-4.4.1/site-library/00LOCK-Rarr/00new/Rarr/libs/Rarr.so': /home/biocbuild/R/R-4.4.1/site-library/00LOCK-Rarr/00new/Rarr/libs/Rarr.so: undefined symbol: pthread_atfork Error: loading failed Execution halted ERROR: loading failed * removing ‘/home/biocbuild/R/R-4.4.1/site-library/Rarr’ * restoring previous ‘/home/biocbuild/R/R-4.4.1/site-library/Rarr’