[Bioperl-l] checkout_all fails on biodata

[Chris Fields]

I use TortoiseCVS via WinXP and I'm getting the same issue that Sendu has:
---------------------------
In C:\Perl\src: "C:\Program Files\TortoiseCVS\cvs.exe" "-q" "--lf"
"checkout" "-P" "bioperl_all"
CVSROOT=:ext:cjfields at dev.open-bio.org:/home/repository/bioperl

... <checking out bioperl core works fine; snipped it out>

cvs checkout: failed to create lock directory for
`/home/repository/bioperl/biodata'
(/home/repository/bioperl/biodata/#cvs.lock): Permission denied
cvs checkout: failed to obtain dir lock in repository
`/home/repository/bioperl/biodata'
cvs [checkout aborted]: read lock failed - giving up
cvs.exe checkout: in directory bioperl:
cvs.exe checkout: cannot open CVS/Entries for reading: No such file or
directory
---------------------------

I had the same problem with schema (BioSQL) a while back.  I tried again,
and...

---------------------------
cvs checkout: failed to create lock directory for
`/home/repository/bioperl/biosql-schema'
(/home/repository/bioperl/biosql-schema/#cvs.lock): Permission denied
cvs checkout: failed to obtain dir lock in repository
`/home/repository/bioperl/biosql-schema'
cvs [checkout aborted]: read lock failed - giving up
cvs.exe checkout: in directory .:
cvs.exe checkout: cannot open CVS/Entries for reading: No such file or
directory
---------------------------

I believe it had something to do with CVS commit privileges (i.e. I had none
for schema, which was fine).  So maybe this is a permissions issue via the
lock file?  Looking at the alias:

bioperl_all  -d bioperl &core &db &run &pipeline &pedigree &biodata &schema
             &network &microarray

This may mean if anyone w/o commit privs for any of the above (specifically
schema and biodata) tries checkout/update using bioperl-all, they may run
into this problem.

Since it's not integrated I don't see the problem with removing it from the
alias, but if we follow the same line of logic (and privileges are the
issue) then schema must be removed as well.  To me it doesn't make much
sense to not include schema though since we can checkout/update bioperl-db.


BTW, I like the idea of biodata as you've outlined it.  Would be nice to
gear the test suite towards a more general set of data for all the Bio*
projects versus having each one come with their own, and the data could be
updated a bit more frequently that t/data is.  Seems like it would
definitely save a large chunk of real estate for the distributions.  If one
wanted to run the full test suite then they would have to download biodata
separately, though, but not a bad compromise.   Though, if this is/was its
intent, why would it need a lock file?

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: Wednesday, July 05, 2006 8:41 AM
> To: Sendu Bala
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] checkout_all fails on biodata
> 
> The idea was once that Bioperl, Biojava, etc had all those unit tests
> that use specific sample data which take up quite a bit of space.
> Unifying the largely redundant test data into a single shared
> repository would save quite a bit of space and therefore download/
> update time for people who work on/use more than one Bio* project.
> 
> However, this was never fully implemented AFAIK. I.e., you don't need
> biodata. I guess it could be removed from the alias since it's not
> integrated anyway.
> 
> Any other opinions?
> 
> I also forwarded your report to root-l as I couldn't find the
> offending (stale) lock file.
> 
> 	-hilmar
> 
> On Jul 5, 2006, at 9:03 AM, Sendu Bala wrote:
> 
> > Hilmar Lapp wrote:
> >> Should have been fixed - I can cvs update. did you try again?
> >
> > Still doesn't work, no change. I can manually check out the other
> > packages, I just can't do it with bioperl_all alias.
> >
> > co bioperl-biodata fails because:
> > cvs server: cannot find module `bioperl-biodata' - ignored
> > cvs [checkout aborted]: cannot expand modules
> >
> > (not that I want it - if its no longer a bioperl package can it be
> > removed from the alias?)
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
> 
> 
> 
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