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This queue is for tickets about the Bio-Trace-ABIF CPAN distribution.

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The Basics
Id: 55908
Status: stalled
Worked: 15 min
Priority: 0/
Queue: Bio-Trace-ABIF
People
Owner: vita [...] cpan.org
Requestors: fink [...] ch.pkts.ca
Cc:
AdminCc:
Bug Information
Severity: (no value)
Broken in: (no value)
Fixed in: (no value)
Attachments
test_bug.zip

History Show all quoted text
  Wed Mar 24 13:57:16 2010 fink [...] ch.pkts.ca - Ticket created
Subject: Windows incompatibility
Date: Wed, 24 Mar 2010 10:56:42 -0700
To: bug-Bio-Trace-ABIF [...] rt.cpan.org
From: "P Fudd" <fink [...] ch.pkts.ca>
Hi! I'm attempting to rewrite the DATA1 track of an FSA file, and I've found a weird error. My program works when I run it in linux, but it fails completely when I run in windows 7 using ActiveState perl 5.10.1 Build 1006. This is the smallest example I could produce: my $OUTFILE="existing-file.fsa"; my $abif = Bio::Trace::ABIF->new(); my @raw=(0)x10000; $abif->open_abif($OUTFILE,1); my $r=$abif->write_tag("DATA","1",\@raw); if ($r==0) {die("DATA1 not written");} $abif->close_abif(); The problem is in _scan_tags; for some unknown reason, seek() works (if tell() is telling the truth), but the read() returns unexpected data, not the tag name or number. I've tried using sys_seek() and sys_read(), and I've tried various binmode() settings, to no avail. I've run out of time to tinker with it, but thought you might be interested. Thanks for writing this module!
  Wed Mar 24 15:24:21 2010 vita [...] cpan.org - Correspondence added 15 min
Not easy for me to debug that, as I don't have access to a machine running Windows, and your example runs fine in my *nix system. Can you please run the test script in the attached archive and report its output? Also, are you sure the data file is your Windows machine is not corrupted? Can you open it with some other program?
Subject: test_bug.zip
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  Wed Mar 24 15:24:22 2010 The RT System itself - Status changed from 'new' to 'open'
  Wed Mar 24 15:24:23 2010 vita [...] cpan.org - Given to VITA
  Fri Mar 26 13:38:28 2010 fink [...] ch.pkts.ca - Correspondence added
Subject: [rt.cpan.org #55908] Windows incompatibility
Date: Fri, 26 Mar 2010 10:38:01 -0700
To: bug-Bio-Trace-ABIF [...] rt.cpan.org
From: "P Fudd" <fink [...] ch.pkts.ca>
The output was 'little-endian', 14, 14. The same file worked in linux, but not windows. -- PFudd - fink@ch.pkts.ca
  Sat Mar 27 05:06:31 2010 vita [...] cpan.org - Correspondence added
Show quoted text
> The output was 'little-endian', 14, 14.
That's fine (I assume this was run in Windows). If it is a problem with read()/seek() (but I don't think so), some tests should have failed when installing the module. Are you passing command line options (e.g., perl -CioD ...)? If you put print ${^OPEN}; in your script, does it print anything? I have no other idea. I'll try to get my hands on a Windows machine.
  Wed Apr 07 20:07:41 2010 kernel [...] pkts.ca - Correspondence added
Subject: [rt.cpan.org #55908] Windows incompatibility
Date: Wed, 7 Apr 2010 17:07:05 -0700
To: bug-Bio-Trace-ABIF [...] rt.cpan.org
From: "P Fudd" <kernel [...] pkts.ca>
Hi.. We're not passing command line options. The ${^OPEN} value reports "Use of uninitialized value $^OPEN in print at ....". Sorry this isn't giving many clues!
  Wed Mar 16 11:56:48 2011 vita [...] cpan.org - Status changed from 'open' to 'stalled'