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

Fri May 15 16:47:33 UTC 2009

Chris,  I attach to the end of this massage the specific cpan test reporting
the ClusterIO error. A

About using other module (Bio::DB Fasta): I will change the code if
necessary (in fact the same code works fine in windows, but not in linux
ubuntu). The fasta sequences are of 50-1500bp long (not a huge sequences I
admit).

t/ClusterIO/ClusterIO.t ...................... 1/12 Bio::ClusterIO: could
not load dbsnp - for more details on supported formats please see the
ClusterIO docs
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::ClusterIO::dbsnp. Can't locate XML/SAX.pm in
@INC (@INC contains: t/lib .
/home/home/Desktop/bioperl1.6/BioPerl-1.6.0/blib/lib
/home/home/Desktop/bioperl1.6/BioPerl-1.6.0/blib/arch
/home/home/Desktop/bioperl1.6/BioPerl-1.6.0 /etc/perl
/usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8
/usr/local/lib/site_perl) at Bio/ClusterIO/dbsnp.pm line 59.
BEGIN failed--compilation aborted at Bio/ClusterIO/dbsnp.pm line 59.
Compilation failed in require at Bio/Root/Root.pm line 420.

Chris Fields-5 wrote:
> 
> 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)
>>>>
>>>>
>>>>
>>>>
>>>> -- 
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>>>>
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>>
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