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grimbough / rhdf5filters

Distributing additional HDF5 compression filters as an R package. Intended to be used with rhdf5, however the compiled filters can also be used with external applications.

Home Page:https://bioconductor.org/packages/rhdf5filters/

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assembler error with gcc 4.8.5

vjcitn opened this issue · comments

commented

for the record, this occurred with an installation attempt of rhdf5filters in R 4.1

gcc -std=gnu99 -m64 -I/app/intelMKL-2017.0.098_i86-rhel6.0/intelMKL/compilers_and_libraries_2017.0.098/linux/mkl/include -I/app/zlib-1.2.8@i86-rhel6.0/include -I/app/curl-7.49.1@i86-rhel6.0/include/curl -I/app/bzip2-1.0.6@i86-rhel6.0/include -I/app/xz-5.2.2@i86-rhel6.0/include -I/app/pcre-8.39@i86-rhel6.0/include -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
/udd/stvjc/tmpdir/cc30qL41.s: Assembler messages:
/udd/stvjc/tmpdir/cc30qL41.s:2768: Error: no such instruction: `shrx %eax,%ecx,%eax'

if more info is needed let me know

commented

assume it is just obsolete compiler

commented

I got the same error in R 4.0.3 :

> BiocManager::install("rhdf5filters")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'rhdf5filters'
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/rhdf5filters_1.2.1.tar.gz'
Content type 'application/x-gzip' length 803330 bytes (784 KB)
==================================================
downloaded 784 KB

* installing *source* package ‘rhdf5filters’ ...
** using staged installation
configuring the BLOSC filter...
checking for gcc... /usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99
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 we are using the GNU C compiler... yes
checking whether /usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 accepts -g... yes
checking for /usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 option to accept ISO C89... none needed
checking whether C compiler accepts -msse2... yes
checking for gcc __builtin_cpu_init function... yes
checking for x86 sse2 instruction support... yes
checking whether C compiler accepts -mavx2... yes
checking for x86 avx2 instruction support... no
configure: creating ./config.status
config.status: creating src/blosc/lib/blosc-1.16.3/Makefile
config.status: creating src/blosc/Makefile
configure:    HDF5_INCLUDE=/src
configure:    BZIP2_LIB=bzip2/libH5Zbz2.so
configure:    BLOSC_LIB=blosc/libH5Zblosc.so
configure: creating ./config.status
config.status: creating src/blosc/lib/blosc-1.16.3/Makefile
config.status: creating src/blosc/Makefile
config.status: creating src/Makevars
** libs
make -C blosc
make[1]: Entering directory `/tmp/RtmpBWH8Cb/R.INSTALL3c224b8462a6/rhdf5filters/src/blosc'
make -C lib/snappy-1.1.1
make[2]: Entering directory `/tmp/RtmpBWH8Cb/R.INSTALL3c224b8462a6/rhdf5filters/src/blosc/lib/snappy-1.1.1'
/usr/local/software/gcc-4.8.5/bin/c++ -std=gnu++11 -g -O2 -fpic -I"/usr/local/software/R/R-4.0.3/lib64/R/library/Rhdf5lib/include" -c snappy.cc
/usr/local/software/gcc-4.8.5/bin/c++ -std=gnu++11 -g -O2 -fpic -I"/usr/local/software/R/R-4.0.3/lib64/R/library/Rhdf5lib/include" -c snappy-c.cc
/usr/local/software/gcc-4.8.5/bin/c++ -std=gnu++11 -g -O2 -fpic -I"/usr/local/software/R/R-4.0.3/lib64/R/library/Rhdf5lib/include" -c snappy-sinksource.cc
/usr/local/software/gcc-4.8.5/bin/c++ -std=gnu++11 -g -O2 -fpic -I"/usr/local/software/R/R-4.0.3/lib64/R/library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make[2]: Leaving directory `/tmp/RtmpBWH8Cb/R.INSTALL3c224b8462a6/rhdf5filters/src/blosc/lib/snappy-1.1.1'
make -C lib/lz4-1.8.3
make[2]: Entering directory `/tmp/RtmpBWH8Cb/R.INSTALL3c224b8462a6/rhdf5filters/src/blosc/lib/lz4-1.8.3'
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -c lz4.c
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -c lz4hc.c
make[2]: Leaving directory `/tmp/RtmpBWH8Cb/R.INSTALL3c224b8462a6/rhdf5filters/src/blosc/lib/lz4-1.8.3'
make -C lib/zstd-1.3.8
make[2]: Entering directory `/tmp/RtmpBWH8Cb/R.INSTALL3c224b8462a6/rhdf5filters/src/blosc/lib/zstd-1.3.8'
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o
/usr/local/software/gcc-4.8.5/bin/gcc -std=gnu99 -g -O2 -fpic -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o
/tmp/cc3gWnyK.s: Assembler messages:
/tmp/cc3gWnyK.s:804: Error: no such instruction: `shlx %r10,%r9,%r10'
/tmp/cc3gWnyK.s:829: Error: no such instruction: `shlx %r9,%rax,%rax'
/tmp/cc3gWnyK.s:890: Error: no such instruction: `shrx %r9,%rax,%r9'
/tmp/cc3gWnyK.s:1002: Error: no such instruction: `shlx %rcx,%r14,%rcx'
/tmp/cc3gWnyK.s:1012: Error: no such instruction: `shlx %rax,%r15,%rax'
/tmp/cc3gWnyK.s:1037: Error: no such instruction: `shlx %rbx,%rcx,%rbx'
/tmp/cc3gWnyK.s:1063: Error: no such instruction: `shlx %r10,%rcx,%rcx'
/tmp/cc3gWnyK.s:1146: Error: no such instruction: `shrx %r9,%rax,%r9'
/tmp/cc3gWnyK.s:1165: Error: no such instruction: `shlx %rax,%rdx,%rax'
make[2]: *** [compress/huf_compress.o] Error 1
make[2]: Leaving directory `/tmp/RtmpBWH8Cb/R.INSTALL3c224b8462a6/rhdf5filters/src/blosc/lib/zstd-1.3.8'
make[1]: *** [lib/zstd-1.3.8] Error 2
make[1]: Leaving directory `/tmp/RtmpBWH8Cb/R.INSTALL3c224b8462a6/rhdf5filters/src/blosc'
make: *** [blosc/libH5Zblosc.so] Error 2
ERROR: compilation failed for package ‘rhdf5filters’
* removing ‘/usr/local/software/R/R-4.0.3/lib64/R/library/rhdf5filters’

Warning message:
In install.packages(...) :
  installation of package ‘rhdf5filters’ had non-zero exit status

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.5 (Santiago)

Matrix products: default
BLAS:   /usr/local/software/R/R-4.0.3/lib64/R/lib/libRblas.so
LAPACK: /usr/local/software/R/R-4.0.3/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_4.0.3      tools_4.0.3

$ gcc --version
gcc (GCC) 4.8.5
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
commented

Please provide the result of sessionInfo() after the error. Also provide the result of gcc -v if you are using gcc, or, if it succeeds,

`R CMD CONFIG CC` --version