[Bioperl-l] First cut svn repository

Hilmar Lapp hlapp at gmx.net
Sat Jun 30 22:56:04 EDT 2007


It turns out that both files are also present on the release-0-9-3,  
bioperl-1-0-0, bioperl-1-0-alpha, and bioperl-1-0-alpha2-rc tags, so add

$ svn rm -m "Removing offending duplicate" svn+ssh://dev.open-bio.org/ 
home/hartzell/bioperl/bioperl-live/tags/release-0-9-3/t/data/ 
HUMBETGLOA.fasta
$ svn rm -m "Removing offending duplicate" svn+ssh://dev.open-bio.org/ 
home/hartzell/bioperl/bioperl-live/tags/bioperl-1-0-0/t/data/ 
HUMBETGLOA.fasta
$ svn rm -m "Removing offending duplicate" svn+ssh://dev.open-bio.org/ 
home/hartzell/bioperl/bioperl-live/tags/bioperl-1-0-alpha/t/data/ 
HUMBETGLOA.fasta
$ svn rm -m "Removing offending duplicate" svn+ssh://dev.open-bio.org/ 
home/hartzell/bioperl/bioperl-live/tags/bioperl-1-0-alpha2-rc/t/data/ 
HUMBETGLOA.fasta

to the post-processing commands.

	-hilmar

On Jun 30, 2007, at 8:40 PM, Chris Fields wrote:

> 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
>
>

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







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