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

[Chris Fields]

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.

chris

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  
> 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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>>
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>>
>
> -- 
> View this message in context: http://www.nabble.com/looks-like-a-Bio%3A%3ASeqIO-error-tp23559474p23562461.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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