problem with vendored blosc

[mdsumner]

I can't get this to install either with BiocManager or locally (I've tried devel branch and RELEASE_3_17)

I see

gcc: error: compression_tools/blosc/libblosc.a: No such file or directory

but that is built and all seems to be in the right place. I'm on R 4.3 Ubuntu 20.04, any ideas?

Thank you

[grimbough]

Can you provide the whole output from the installation. I'll try to see if there's anymore details on the problem.

Alternatively, if you install the system library of blosc via apt-get install libblosc-dev and use the devel version of Rarr, it should link against that instead, and ignore the bundled version.

I'd still appreciate the output if possible, even if the second option works, just to try and hunt down the problem.

[mdsumner]

here's the full output, with RELEASE_317

R CMD INSTALL Rarr_1.0.1.tar.gz
* installing to library ‘/perm_storage/home/mdsumner/R/x86_64-pc-linux-gnu-library/4.3’
* installing *source* package ‘Rarr’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/Makevars
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... no
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
** libs
using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
make -C compression_tools/blosc
gcc -I"/usr/share/R/include" -DNDEBUG      -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Rarr.c -o Rarr.o
gcc -I"/usr/share/R/include" -DNDEBUG      -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c bit64_conversion.c -o bit64_conversion.o
gcc -I"/usr/share/R/include" -DNDEBUG      -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c compress.c -o compress.o
gcc -I"/usr/share/R/include" -DNDEBUG      -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c decompress.c -o decompress.o
gcc -I"/usr/share/R/include" -DNDEBUG      -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c float16_conversion.c -o float16_conversion.o
gcc -I"/usr/share/R/include" -DNDEBUG      -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c type_conversion.c -o type_conversion.o
make[1]: Entering directory '/perm_storage/home/data/r_tmp/Rtmp6OLkrw/R.INSTALL35eef473132a09/Rarr/src/compression_tools/blosc'
make -C lib/snappy-1.1.1
make -C lib/lz4-1.9.2
make -C lib/zstd-1.4.5
make[2]: Entering directory '/perm_storage/home/data/r_tmp/Rtmp6OLkrw/R.INSTALL35eef473132a09/Rarr/src/compression_tools/blosc/lib/snappy-1.1.1'
g++ -std=gnu++17 -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -I/usr/share/R/include -DUSING_R -c snappy.cc
make[2]: Entering directory '/perm_storage/home/data/r_tmp/Rtmp6OLkrw/R.INSTALL35eef473132a09/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2'
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -DNLZ4_DEBUG -c lz4.c
g++ -std=gnu++17 -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -I/usr/share/R/include -DUSING_R -c snappy-c.cc
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -DNLZ4_DEBUG -c lz4hc.c
g++ -std=gnu++17 -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -I/usr/share/R/include -DUSING_R -c snappy-sinksource.cc
make[2]: Entering directory '/perm_storage/home/data/r_tmp/Rtmp6OLkrw/R.INSTALL35eef473132a09/Rarr/src/compression_tools/blosc/lib/zstd-1.4.5'
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/debug.c -o common/debug.o
g++ -std=gnu++17 -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -I/usr/share/R/include -DUSING_R -c snappy-stubs-internal.cc
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/entropy_common.c -o common/entropy_common.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/error_private.c -o common/error_private.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/fse_decompress.c -o common/fse_decompress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -I. -c common/pool.c -o common/pool.o -o common/pool.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/threading.c -o common/threading.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/xxhash.c -o common/xxhash.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c common/zstd_common.c -o common/zstd_common.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/fse_compress.c -o compress/fse_compress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/hist.c -o compress/hist.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/huf_compress.c -o compress/huf_compress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_compress.c -o compress/zstd_compress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_fast.c -o compress/zstd_fast.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_lazy.c -o compress/zstd_lazy.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_ldm.c -o compress/zstd_ldm.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstd_opt.c -o compress/zstd_opt.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rarr.so Rarr.o bit64_conversion.o compress.o decompress.o float16_conversion.o type_conversion.o compression_tools/blosc/libblosc.a -L/usr/lib/R/lib -lR
gcc: error: compression_tools/blosc/libblosc.a: No such file or directory
make: *** [/usr/share/R/share/make/shlib.mk:10: Rarr.so] Error 1
make: *** Waiting for unfinished jobs....
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c decompress/huf_decompress.c -o decompress/huf_decompress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -DNDEBUG -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make[2]: Leaving directory '/perm_storage/home/data/r_tmp/Rtmp6OLkrw/R.INSTALL35eef473132a09/Rarr/src/compression_tools/blosc/lib/snappy-1.1.1'
make[2]: Leaving directory '/perm_storage/home/data/r_tmp/Rtmp6OLkrw/R.INSTALL35eef473132a09/Rarr/src/compression_tools/blosc/lib/lz4-1.9.2'
make[2]: Leaving directory '/perm_storage/home/data/r_tmp/Rtmp6OLkrw/R.INSTALL35eef473132a09/Rarr/src/compression_tools/blosc/lib/zstd-1.4.5'
make -C lib/blosc-1.20.1 all
make[2]: Entering directory '/perm_storage/home/data/r_tmp/Rtmp6OLkrw/R.INSTALL35eef473132a09/Rarr/src/compression_tools/blosc/lib/blosc-1.20.1'
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -I/usr/share/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2  -DUSING_R -c bitshuffle-sse2.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -I/usr/share/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2  -DUSING_R -c shuffle-sse2.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -I/usr/share/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2  -DUSING_R -c bitshuffle-generic.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -I/usr/share/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2  -DUSING_R -c shuffle-generic.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -I/usr/share/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2  -DUSING_R -DSHUFFLE_SSE2_ENABLED  -c shuffle.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -I/usr/share/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2  -DUSING_R -c blosclz.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -I/usr/share/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2  -DUSING_R -c blosc.c
gcc -g -O2 -fdebug-prefix-map=/build/r-base-dIDxrQ/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic  -I/usr/share/R/include -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5 -msse2  -DUSING_R -c fastcopy.c
make[2]: Leaving directory '/perm_storage/home/data/r_tmp/Rtmp6OLkrw/R.INSTALL35eef473132a09/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/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/lz4-1.9.2/lz4.o lib/lz4-1.9.2/lz4hc.o lib/zstd-1.4.5/common/debug.o lib/zstd-1.4.5/common/entropy_common.o lib/zstd-1.4.5/common/error_private.o lib/zstd-1.4.5/common/fse_decompress.o lib/zstd-1.4.5/common/pool.o lib/zstd-1.4.5/common/threading.o lib/zstd-1.4.5/common/xxhash.o lib/zstd-1.4.5/common/zstd_common.o lib/zstd-1.4.5/compress/fse_compress.o lib/zstd-1.4.5/compress/hist.o lib/zstd-1.4.5/compress/huf_compress.o lib/zstd-1.4.5/compress/zstd_compress.o lib/zstd-1.4.5/compress/zstd_compress_literals.o lib/zstd-1.4.5/compress/zstd_compress_sequences.o lib/zstd-1.4.5/compress/zstd_compress_superblock.o lib/zstd-1.4.5/compress/zstd_double_fast.o lib/zstd-1.4.5/compress/zstd_fast.o lib/zstd-1.4.5/compress/zstd_lazy.o lib/zstd-1.4.5/compress/zstd_ldm.o lib/zstd-1.4.5/compress/zstd_opt.o lib/zstd-1.4.5/compress/zstdmt_compress.o lib/zstd-1.4.5/decompress/huf_decompress.o lib/zstd-1.4.5/decompress/zstd_ddict.o lib/zstd-1.4.5/decompress/zstd_decompress.o lib/zstd-1.4.5/decompress/zstd_decompress_block.o
ranlib libblosc.a
make[1]: Leaving directory '/perm_storage/home/data/r_tmp/Rtmp6OLkrw/R.INSTALL35eef473132a09/Rarr/src/compression_tools/blosc'
ERROR: compilation failed for package ‘Rarr’
* removing ‘/perm_storage/home/mdsumner/R/x86_64-pc-linux-gnu-library/4.3/Rarr’

I do already have apt-get install libblosc-dev, so I guess I can try on a system without that?

[grimbough]

I do already have apt-get install libblosc-dev, so I guess I can try on a system without that?

Sorry, I'm getting confused between this package and rhdf5filters, which also uses blosc. I've only applied the local version detection to that package, so Rarr won't use a system library at the moment. It's on the imminent road map.

Thanks for the log. I'll take a look and see if there's anything that jumps out.

[grimbough]

Do you have make defaulting to working in parallel? I notice the the compilation messages for the three sub-libraries snappy-1.1.1, lz4-1.9.2, zstd-1.4.5 are all interleaved. It also looks like it tries to compiled Rarr.so before those processes have completed, which is probably why libblosc.a doesn't exist.

Presumably my Makevars should be modified so that it definitely completes the other parts first, but perhaps turning off parallel building might be a temporary work around. This is the first time I've seen this issue, so it might take a some trial and error until I solve the issue in the Makevars.

[mdsumner]

ah, indeed I do! I have it set in ~/.Renviron

thank you, working fine now, much appreciated

[grimbough]

Great, glad that got you up and running. I think I've also address the underlying issue in de1149e so hopefully you can go back to using parallel make if you like. That should roll out in both release and devel in the next few days.

[mdsumner]

awesome, working fine now with parallel make