[Bioc-devel] Files removed from svn are not disappearing from Git mirror

[Hervé Pagès]

Hi James,

On 11/14/2016 06:38 PM, James Collins wrote:
> I have attempted to remove several .tar.gz files from the LOBSTAHS package
> directory using a series of cherry-picked commits. (I had successfully
> removed these .tar files a few months ago, but somehow they just reappeared
> in the directory after I invoked git svn rebase during a recent attempt to
> commit some other changes.) I was able to successfully remove them a second
> time from the svn directory, but they are still showing up on the
> Bioconductor GIt mirror. I even tried re-committing the files, and then
> making a new commit that deleted them, but this did not work as far as the
> Git mirror is concerned (it was successful on svn). Please advise, any help
> appreciated.

I'm not sure I understand what you are trying to achieve with these
commits e.g. the last 3 svn commits for LOBSTAHS are:

hpages at latitude:~$ svn log -v 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LOBSTAHS -r 
124003:HEAD --username readonly --password readonly

------------------------------------------------------------------------
r124003 | j.collins | 2016-11-14 17:58:22 -0800 (Mon, 14 Nov 2016) | 1 line
Changed paths:
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.1.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.2.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.3.1.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.3.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.0.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.1.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.2.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.3.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.4.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.5.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.6.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.7.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.8.tar.gz

Remove .tar.gz files
------------------------------------------------------------------------
r124004 | j.collins | 2016-11-14 18:05:14 -0800 (Mon, 14 Nov 2016) | 1 line
Changed paths:
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.1.tar.gz
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.2.tar.gz
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.3.1.tar.gz
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.3.tar.gz
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.0.tar.gz
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.1.tar.gz
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.2.tar.gz
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.3.tar.gz
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.4.tar.gz
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.5.tar.gz
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.6.tar.gz
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.7.tar.gz
    A /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.8.tar.gz

Commit .tar.gz files
------------------------------------------------------------------------
r124005 | j.collins | 2016-11-14 18:08:32 -0800 (Mon, 14 Nov 2016) | 1 line
Changed paths:
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.1.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.2.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.3.1.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.3.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.0.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.1.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.2.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.3.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.4.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.5.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.6.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.7.tar.gz
    D /trunk/madman/Rpacks/LOBSTAHS/LOBSTAHS_0.99.8.tar.gz

Remove .tar.gz files
------------------------------------------------------------------------

Why would you delete files, then add them, and then delete them again?

It's true though that the deleted files still show up on the
Bioconductor-mirror:

   https://github.com/Bioconductor-mirror/LOBSTAHS

which indicates that there might be a problem with our mirroring
script. Your last svn commit was less than 2 hours ago so maybe
it's just because of the lag between the moment you commit to svn
and the moment the commit shows up on Bioconductor-mirror.
So let's wait and see.

The truth is that the .tar.gz files are not in the svn repo anymore,
which I guess is what really matters for now:

   hpages at latitude:~$ svn ls 
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/LOBSTAHS 
--username readonly --password readonly
   .BBSoptions
   .Rbuildignore
   .gitignore
   DESCRIPTION
   LICENSE
   LOBSTAHS.Rproj
   NAMESPACE
   R/
   README.md
   data/
   inst/
   man/
   vignettes/

so no need to fight so hard against these zombie .tar.gz files ;-)

Cheers,
H.


> Jamie Collins
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319