Can't install prodigal - Githubissues

mortonjt commented 8 years ago

Got this error when trying to install prodigal

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/mortonjt/Documents/micronota/micronota/bfillings/tests/test_prodigal.py", line 75, in test_predict_genes_wrong_input
    predict_genes(fp, self.temp_dir, 'foo')
AssertionError: "Sequence read failed \(file must be Fasta, Genbank, or EMBL format\)." does not match "Unacceptable application exit status: 1
Command:
cd "/home/mortonjt/Documents/micronota/micronota/bfillings/"; prodigal -d "/tmp/tmpei3o_9q3/foo.fna" -i "/home/mortonjt/Documents/micronota/micronota/bfillings/tests/data/empty" -o "/tmp/tmpei3o_9q3/foo.gbk" -a "/tmp/tmpei3o_9q3/foo.faa" > "/tmp/tmpFQMWrZcnRv8owY5dGdxd.txt" 2> "/tmp/tmpIUmEUFyqgxMcDOnPgbrt.txt"
StdOut:

StdErr:
prodigal: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by prodigal)

RNAer commented 8 years ago

@Jorge-C, is there a way to specify the library to compile against in recipe?

Jorge-C commented 8 years ago

@mortonjt what OS, installation process?

mortonjt commented 8 years ago

Sorry about the late response. I was installing against Redhat linux.

Jorge-C commented 8 years ago

Ah, this is actually not surprising.

If we take advantage of travis (i.e., ubuntu 12.04, which is already old-ish) to build packages, we get glibc 2.14, which works on any {d|r}ecent desktop linux. However, it doesn't work in older/more stable server OS (think Red Hat, CentOS...).

IMO, travis is too nice to pass it up (do we really want to maintain a build farm?). If we want to build binaries that work in servers and keep using travis, I think we can explicitly make the packages depend on an old glibc (see this recipe).

biocore / conda-recipes

Can't install prodigal #8