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

Martin Morgan martin.morgan at roswellpark.org
Tue Nov 15 13:30:29 CET 2016 

On 11/14/2016 10:52 PM, Hervé Pagès wrote:
> 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.

The mirror did get stuck, which typically occurs when svn commits come 
faster than the mirror processes them. Usually this is when a git branch 
with several commits is merged in a way that triggers one svn commit per 
git commit.

I think LOBSTAHS is back on track; it's hard to know where the tar files 
re-emerged from; if they showed up during git svn rebase it implies they 
were (still?) in svn, but svn says they were deleted here

r121293 | j.collins | 2016-09-23 10:13:36 -0400 (Fri, 23 Sep 2016) | 1 line

then added here

r123979 | j.collins | 2016-11-14 17:37:17 -0500 (Mon, 14 Nov 2016) | 26 
lines
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

Merge branch 'master' into devel
...

which looks like they came from a commit from your git repository.

Sorry for the trouble and let us know if these zombies come back to 
haunt you.

Martin

>
> 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
>>
>


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