[Bioc-devel] Warning about the size of git pack file

[Turaga, Nitesh]

Hi Vinh,

See in line replies,


On Feb 22, 2019, at 2:30 PM, Vinh Tran <tran using bio.uni-frankfurt.de<mailto:tran using bio.uni-frankfurt.de>> wrote:

Dear all,

I am planning to submit a package into Bioconductor. But BiocCheck() gave a warning about the size of the git pack file:

$warning
[1] "The following files are over 5MB in size: '.git/objects/pack/pack-29a3f2d2d1ed7d701d59dd2ce921229f2b9dab68.pack'"

I tried to use git filter-branch to delete the big files in git history, but the pack file is still almost 25MB. I also tried BFG-Tool to do the same task, but I couldn’t push the changes from BFG to github due the some hidden branches (or deleted/merged git pulls) that denied the commit.

I would like to ask, if it is a serious warning that must be resolved? If yes, could you please suggest me another way to reduce the size of the git pack file?


Yes, we consider it a warning that needs to be resolved. Please see if any of the following links help you first,

http://bioconductor.org/developers/how-to/git/remove-large-data/

There is an older post https://stat.ethz.ch/pipermail/bioc-devel/2018-November/014274.html which deals with the same issue. Cleaning up large .git files with BFG cleaner. Please take a look at that as well and see if it helps you.

Another thing to keep in mind is, unless you go through with “git —prune”, your package size doesn’t actually get smaller because the previous data is still stored in the .git/pack files


Secondly, I also got a note from BiocCheck() that I am not listed in the bioc-devel mailing list. But it is unclear to me, because I've already subscribed to both bioc-devel and also the support.bioonductor.org<http://support.bioonductor.org> <http://support.bioonductor.org/> using this email (tran using bio.uni-frankfurt.de<mailto:tran using bio.uni-frankfurt.de> <mailto:tran using bio.uni-frankfurt.de>). Could anyone check this for me, please?

$note
[1] "Cannot determine whether maintainer is subscribed to the bioc-devel\nmailing list (requires admin credentials).  Subscribe here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel”


You should be able to submit the package and if the issue persists on the build machine, we can take a look at it. One of the admin’s on the mailing list can see if you are subscribed successfully or not.

I wouldn’t worry about this till your package gets submitted without the large files issue.

Best,

Nitesh


Thanks so much for your help!
Best regards,
Vinh

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