[Bioperl-l] BioPerl CVS EOL Inconsistency

[Nathan Haigh]

Ok, here's what I think I've found! If anyone knows more about this that I do, please feel free to interject!

I have found that the files stored in BioPerl CVS have different end-of-line chars, and when CVSnt does conversions on these chars,
it results in odd end-of-line chars, that I assume were affecting my previous "nmake test" using the files downloaded by CVSnt.

As an example, if you look at Bio::SeqIO::Interpro, this file contains the EOL char "0D 0A" (Hex) which is the DOS EOL char (CR LF).
When CVSnt downloads this file; it convert it to "0D 0D 0A" (Hex) which is not a standard EOL char (it is actually CR CR LF).
Whereas Bio::SeqIO::GenBank contains the EOL char "0A" (Hex) which is the standard UNIX EOL char (LF). CVSnt converts this correctly
into "0D 0A" (Hex) which is the DOS EOL char (CR LF).

I'm not sure how these different EOL chars occur, because as far as I understand CVS, a CVS client should convert the EOL chars to
those used by their OS when the files are downloaded, and then converts them back to those used on the CVS server during a commit. I
think the only way this mixing of EOL chars can happen is if someone uses a different CVS client or OS to commit the files.

On second thoughts, it is probably due to the fact that people will submit patched files from several OS's to BioPerl for CVS
commits, but these files do not get converted from DOS/Mac to Unix before commits.

Is there anything that can be done to bring all the EOL chars back into line as I'd really like to be able to use CVS on windows!?

Thanks
Nathan


> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Nathan Haigh
> Sent: 01 November 2004 08:37
> To: bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] nmake test
> 
> Hmm, this seems to be a problem associated with CVSnt which I used to obtain the latest BioPerl from CVS - I got fed up with
having
> to download the entire BioPerl package in tarball for small updates.
> 
> The latest tarball tested without errors, I'm now trying CVSnt again to see if I can reproduce the problem! On the first attempt I
> noticed that several of the BioPerl files contained '?' at the end of every line, so I suspected some mix up in the end of line
> characters; but replacing these files with the relevant ones from the website did not rectify the problem (unless I missed some).
> 
> I'll post again if I can replicate the problem, in case it is any help to someone else. But as far as I can see the tarball seems
to
> test without errors!
> 
> Nathan
> 
> 
> > -----Original Message-----
> > From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Nathan Haigh
> > Sent: 31 October 2004 11:36
> > To: bioperl-l at bioperl.org
> > Subject: [Bioperl-l] nmake test
> >
> > Hi, just to let you know the latest BioPerl from CVS is now giving the following errors on WinXP, and I am trying to debug them:
> >
> > Failed Test   Stat Wstat Total Fail  Failed  List of Failed
> > -----------------------------------------------------------
> > t\Index.t      255 65280    41    0   0.00%  ??
> > t\Pictogram.t  255 65280     3    3 100.00%  1-3
> > t\ProtPsm.t    255 65280     5    5 100.00%  1-5
> > t\flat.t       255 65280    16    3  18.75%  14-16
> > t\psm.t        255 65280    48   48 100.00%  1-48
> > 2 subtests skipped.
> >
> > Nathan
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
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