[Bioperl-l] First cut svn repository

Chris Fields cjfields at uiuc.edu
Sat Jun 30 20:40:53 EDT 2007


Checkout worked for me (Mac OS X) using both:

svn co svn+ssh://dev.open-bio.org/home/hartzell/bioperl/bioperl-live/ 
tags/release-0-9-2/t/data
svn co svn+ssh://dev.open-bio.org/home/hartzell/bioperl/bioperl-live/ 
tags/release-0-9-2/

so removing the offending file worked (good catch!).  Haven't run a  
full co but probably isn't necessary.

chris

On Jun 30, 2007, at 6:36 PM, Hilmar Lapp wrote:

>
> On Jun 28, 2007, at 3:43 PM, George Hartzell wrote:
>
>> I just did the experiment, and filename-insensitivity seems to be
>> breaking something.
>>
>> I'm using an svn I picked up from http://www.codingmonkeys.de/mbo/.
>>
>> I reformatted a memory stick to be case sensitive and co of
>>
>>   bioperl/bioperl-live/tags/release-0-9-2/t
>>
>> worked, then I made a directory in my home dir (normal mac thing) and
>> got the same error as above.
>
> You picked up a rename of a file from lower case extension to upper  
> case extension. Unfortunately, there are several months between  
> adding the upper-case and removing the lower-case version.
>
> We can reconstruct what happened with this using svn log on the  
> directory (this does not require a checkout):
>
> $ svn log --verbose svn+ssh://dev.open-bio.org/home/hartzell/ 
> bioperl/bioperl-live/trunk/t/data
>
> Searching for HUMBETGLOA yields the following two commits that  
> added one and removed the other:
>
> ---------------------------------------------------------------------- 
> --
> r2245 | jason | 2001-12-08 11:59:05 -0500 (Sat, 08 Dec 2001) | 2 lines
> Changed paths:
>    M /bioperl-live/trunk/t/SearchIO.t
>    A /bioperl-live/trunk/t/data/HUMBETGLOA.FASTA
>    A /bioperl-live/trunk/t/data/cysprot1.FASTA
>
> added tests for FASTA
>
> ---------------------------------------------------------------------- 
> --
> r2877 | jason | 2002-03-11 22:39:40 -0500 (Mon, 11 Mar 2002) | 2 lines
> Changed paths:
>    A /bioperl-live/trunk/t/data/HUMBETGLOA.fa
>    D /bioperl-live/trunk/t/data/HUMBETGLOA.fasta
>
> renaming file to avoid clobbering on windows
>
> Unfortunately, both files are in the tag (again, no checkout  
> required):
>
> $ svn list svn+ssh://dev.open-bio.org/home/hartzell/bioperl/bioperl- 
> live/tags/release-0-9-2/t/data | grep HUMBETGLOA | grep -i fasta
> HUMBETGLOA.FASTA
> HUMBETGLOA.fasta
>
> We can remove the offending version from the repository (again,  
> without needing a checkout):
>
> $ svn rm svn+ssh://dev.open-bio.org/home/hartzell/bioperl/bioperl- 
> live/tags/release-0-9-2/t/data/HUMBETGLOA.fasta
>
> I did this, and now the tag checks out fine on OSX. Can anyone  
> confirm?
>
> (BTW the ability to operate on the repository w/o needing a  
> checkout is another advantage of svn)
>
> 	-hilmar
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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