[Bioperl-l] checkout_all fails on biodata

Wed Jul 5 15:38:14 UTC 2006

Same problem here. I've never used the bioperl_all alias before (I 
always check-out dirs individually), but to me it seems like a 
privileges issue as Chris suggests.

Also browsed through all the repository in dev.open-bio.org and didn't 
found such lock file. I guess Chris D. or Jason will know better what's 
happening here.

Mauricio.

Chris Fields wrote:
> 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 :
>> ===========================================================
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM