gmapR source package contains x86_64 binaries
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Tom Lin • 0
@f2732dfd
Last seen 6 weeks ago
United Kingdom

Hi, I'm trying to build https://bioconductor.org/packages/release/bioc/html/gmapR.html on an AArch64 Linux machine and something a bit strange show up during compilation:

# some R CMD INSTALL lines...
gcc -shared -L"/root/r/dist/lib" -L/usr/local/lib -o gmapR.so bamreader.o bamtally.o iit.o variantsummary.o genome.o R_init_gmapR.o /root/tmp/build/gmapR/src/../inst/usr/lib/libgstruct-1.0.a samtools/libbam.a -lz   -L"/root/r/dist/lib" -lR
/usr/bin/ld: i386:x86-64 architecture of input file `samtools/libbam.a(bgzf.o)' is incompatible with aarch64 output
/usr/bin/ld: i386:x86-64 architecture of input file `samtools/libbam.a(bam_aux.o)' is incompatible with aarch64 output
/usr/bin/ld: i386:x86-64 architecture of input file `samtools/libbam.a(bam.o)' is incompatible with aarch64 output
/usr/bin/ld: i386:x86-64 architecture of input file `samtools/libbam.a(bam_import.o)' is incompatible with aarch64 output
/usr/bin/ld: i386:x86-64 architecture of input file `samtools/libbam.a(bam_index.o)' is incompatible with aarch64 output
/usr/bin/ld: i386:x86-64 architecture of input file `samtools/libbam.a(knetfile.o)' is incompatible with aarch64 output
/usr/bin/ld: i386:x86-64 architecture of input file `samtools/libbam.a(sam_header.o)' is incompatible with aarch64 output
/usr/bin/ld: i386:x86-64 architecture of input file `samtools/libbam.a(samtools_patch.o)' is incompatible with aarch64 output
/usr/bin/ld: i386:x86-64 architecture of input file `samtools/libbam.a(kstring.o)' is incompatible with aarch64 output
/usr/bin/ld: samtools/libbam.a(sam_header.o): unrecognized relocation type 0x2a in section `.text'

After inspecting the source package from https://bioconductor.org/packages/release/bioc/src/contrib/gmapR_1.46.0.tar.gz, I can see the tarball actually contains build artefacts, including libbam.a which apparently was compiled on a x86_64 machine.

This appears to be limited to the src/samtools directory, the rest seems OK and the artefacts does not show up in https://code.bioconductor.org/browse/gmapR/tree/RELEASE_3_19/src/samtools/ or https://github.com/lawremi/gmapR/tree/master/src/samtools.

I'm not sure who to report this to: I feel like this isn't an upstream issue but more on BioC packaging.

Tom

gmapR • 149 views
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