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:microscope: BEDOPS: high-performance genomic feature operations
https://bedops.readthedocs.io/
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problem with compile finding standard c libraries #221

Closed mforde84 closed 5 years ago

mforde84 commented 5 years ago

Hi I've tried compiling with gcc 4.8.5 and 7.4.0, however I'm getting peculiar linking errors for stuff which should be already supplied with the compiler libraries.

E.g.,


collect2: error: ld returned 1 exit status
make[3]: *** [../bin/sort-bed-typical] Error 1
make[3]: Leaving directory `/mnt/beegfs/spackroot/var/spack/stage/bedops-2.4.35-iynedkbyuqtabmo5kxpp4o37izrc6ijv/bedops-2.4.35/bedops/applications/bed/sort-bed/src'
make[2]: *** [applications/bed/sort-bed/src] Error 2
/bin/ld: cannot find -lstdc++
/bin/ld: cannot find -lm
/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
make[3]: *** [../bin/closest-features-typical] Error 1
make[3]: Leaving directory `/mnt/beegfs/spackroot/var/spack/stage/bedops-2.4.35-iynedkbyuqtabmo5kxpp4o37izrc6ijv/bedops-2.4.35/bedops/applications/bed/closestfeats/src'
make[2]: *** [applications/bed/closestfeats/src] Error 2
/bin/ld: cannot find -lstdc++
/bin/ld: cannot find -lm
/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
make[3]: *** [../bin/bedops-typical] Error 1
make[3]: Leaving directory `/mnt/beegfs/spackroot/var/spack/stage/bedops-2.4.35-iynedkbyuqtabmo5kxpp4o37izrc6ijv/bedops-2.4.35/bedops/applications/bed/bedops/src'
make[2]: *** [applications/bed/bedops/src] Error 2
/bin/ld: cannot find -lstdc++
/bin/ld: cannot find -lm
/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
make[3]: *** [../bin/bedmap-typical] Error 1
make[3]: Leaving directory `/mnt/beegfs/spackroot/var/spack/stage/bedops-2.4.35-iynedkbyuqtabmo5kxpp4o37izrc6ijv/bedops-2.4.35/bedops/applications/bed/bedmap/src'
make[2]: *** [applications/bed/bedmap/src] Error 2
make[2]: Leaving directory `/mnt/beegfs/spackroot/var/spack/stage/bedops-2.4.35-iynedkbyuqtabmo5kxpp4o37izrc6ijv/bedops-2.4.35/bedops'
make[1]: *** [default] Error 2
make[1]: Leaving directory `/mnt/beegfs/spackroot/var/spack/stage/bedops-2.4.35-iynedkbyuqtabmo5kxpp4o37izrc6ijv/bedops-2.4.35/bedops'
make: *** [default] Error 2

Distro - Cent7, kernel 3.10.0-693.21.1.el7.x86_64

alexpreynolds commented 5 years ago

Please check that you have static libraries installed. For CentOS, this may involve:

$ sudo yum install libstdc++-static
$ sudo yum install glibc-static