[Bioperl-l] looks like a Bio::SeqIO error

[fungazid]

Thanks all for your rapid replies,

1) I tried cleaned my swap space (/tmp), and this indeed delays the eruption
of the error but does not prevent it tottaly.

2) I used bioperl 1.5.2.02 lubuntu1 (this is installed automatically by
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 + 146.54
cusr  7.12 csys = 159.10 CPU)
Result: FAIL
Failed 1/318 test programs. 0/15584 subtests failed.
make: *** [test] Error 255
  CJFIELDS/BioPerl-1.6.0.tar.gz
  /usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports CJFIELDS/BioPerl-1.6.0.tar.gz
Warning (usually harmless): 'YAML' not installed, will not store persistent
state
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:
> 
> fungazid,
> 
> 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:
> 
>>
>> Hello,
>>
>> I hope this is the right address for bioperl programming issues.  
>> Bioperl
>> saves me a lot of time (not to re-invent the wheel), but there are  
>> some
>> extremely irritating problems (I would change the code myself if I  
>> knew
>> how).
>>
>> I am trying to read a file (~20MB) containing multiple fasta  
>> sequences:
>>> a
>> AGTAGTGAGTGCGCTGA.........
>>> b
>> GCGCTGAAGTAGTGAGT.......
>>> c
>> AGTAGTGAGTGCGCTGA.........
>>> d...........
>>
>> with the following lines:
>>
>> my $seqin = Bio::SeqIO->new('-format'=>'largefasta','-file'=>$file1);
>>
>> 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:
>> http://www.nabble.com/looks-like-a-Bio%3A%3ASeqIO-error-tp23559474p23559474.html
>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
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> 
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> 

-- 
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