[Bioperl-l] First cut svn repository

Hilmar Lapp hlapp at gmx.net
Sat Jun 30 19:36:45 EDT 2007

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/ 

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

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- 

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 Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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