[Bioperl-l] looks like a Bio::SeqIO error
cjfields at illinois.edu
Fri May 15 12:20:10 EDT 2009
You can still install core with 'force install', but it would be nice
to see what was causing ClusterIO tests to bork. That's the first
time I recall seeing that one fail.
On May 15, 2009, at 10:45 AM, fungazid wrote:
> Thanks all for your rapid replies,
> 1) I tried cleaned my swap space (/tmp), and this indeed delays the
> of the error but does not prevent it tottaly.
> 2) I used bioperl 1.5.2.02 lubuntu1 (this is installed automatically
> linux ubuntu package manager). I unsuccessfully tried to install
> bioperl 1.6
> with 'sudo cpan' command, and I get the following report (is it
> possible to
> force install with this repeort ??).
> Test Summary Report
> t/ClusterIO/ClusterIO.t (Wstat: 65280 Tests: 2
> Failed: 0)
> Non-zero exit status: 255
> Parse errors: Bad plan. You planned 12 tests but ran 2.
> Files=318, Tests=15584, 160 wallclock secs ( 4.88 usr 0.56 sys +
> cusr 7.12 csys = 159.10 CPU)
> Result: FAIL
> Failed 1/318 test programs. 0/15584 subtests failed.
> make: *** [test] Error 255
> /usr/bin/make test -- NOT OK
> //hint// to see the cpan-testers results for installing this module,
> reports CJFIELDS/BioPerl-1.6.0.tar.gz
> Warning (usually harmless): 'YAML' not installed, will not store
> Running make install
> make test had returned bad status, won't install without force
> Failed during this command:
> CJFIELDS/BioPerl-1.6.0.tar.gz : make_test NO
> 3) I used Bio::Seq::LargeSeq (and not other modules) simply because it
> worked fine in the past, and did what I wanted with no problems.
> Brian Osborne-2 wrote:
>> What version of BioPerl are you using?
>> If I'm not mistaken this problem has been seen before, and is now
>> fixed in Bioperl 1.6.
>> Brian O.
>> On May 15, 2009, at 9:17 AM, fungazid wrote:
>>> I hope this is the right address for bioperl programming issues.
>>> saves me a lot of time (not to re-invent the wheel), but there are
>>> extremely irritating problems (I would change the code myself if I
>>> I am trying to read a file (~20MB) containing multiple fasta
>>> with the following lines:
>>> my $seqin = Bio::SeqIO->new('-format'=>'largefasta','-file'=>
>>> LOOP1: while ( my $seqobj1 = $seqin->next_seq())
>>> my $seq=$seqobj1->subseq(1,$seqobj1->length);
>>> This works right for the first ~30000 contig sequences but then the
>>> following message appears:
>>> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory
>>> /tmp/6eS92VzVjm: Too many links at /usr/share/perl5/Bio/Root/IO.pm
>>> line 744
>>> What to do ??? (this is only one of some different Bioperl related
>>> bugs that
>>> I'm experiencing)
>>> View this message in context:
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>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
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>> Bioperl-l at lists.open-bio.org
> View this message in context: http://www.nabble.com/looks-like-a-Bio%3A%3ASeqIO-error-tp23559474p23562461.html
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