[ensembl-dev] Can not update API...

[Andreas Kahari]

On Thu, Nov 25, 2010 at 12:44:03PM +0000, Steve Moss wrote:
> Hi Hashem,
> 
> Perhaps you need to do a sudo cvs -q update -d -P -r branch-ensembl-60??
> Looks like directory permission issues?
> 
> Cheers,
> 
> Steve

No, this is not on the client, it is on the CVS server (over here).
However, it is just a warning and will not stop you from updating the
checkout.

The real problem is the "sql/patch_59_60_d.sql" file.  Unless you have
changed anything in that directory it is perfectly safe to remove the
whole directory.  Then run the CVS update again.

The reason this is happening is that CVS seems to have forgotten that
it checked this file out at some point in the past.  It now refuses to
overwrite it with the version in the repository.  I don't know why your
checkout has become confused, but it's easily fixed by removing the
file or the whole directory (assuming you haven't actually made local
modifications to these).


Regards,
Andreas


> 
> 
> > Message: 7
> > Date: Thu, 25 Nov 2010 11:48:12 +0000
> > From: Hashem Koohy <hk3 at sanger.ac.uk>
> > Subject: [ensembl-dev] Can not update API
> > To: <dev at ensembl.org>
> > Message-ID: <C913FD7C.3F6%hk3 at sanger.ac.uk<C913FD7C.3F6%25hk3 at sanger.ac.uk>
> > >
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Hi guys,
> > I have  already had API in my local machine and now I want to update to
> > version 60 by running the command ?cvs -q update -d -P -r
> > branch-ensembl-60?
> > from the  documents. But it returns many of the followings:
> > cvs update: warning: cannot open history file
> > `/cvsroot/ensembl/CVSROOT/history' for write: Permission denied
> > cvs update: move away `sql/patch_59_60_d.sql'; it is in the way
> >
> > And my perl code works as befor, for instance it returns:
> >
> > species/group    homo_sapiens/otherfeatures
> > database    homo_sapiens_otherfeatures_59_37d
> > host:port    ensembldb.ensembl.org:5306
> >
> > I will appreciate for any help.
> > Thanks
> > Hashem
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> 
> -- 
> Kindest regards,
> 
> Steve Moss
> http://stevemoss.ath.cx

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-- 
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom