[Bioc-devel] Help: git push complains non-existing files being too big

[Zhu, Lihua (Julie)]

Martin,

A while ago, Jim suggested to replace two big data files with two smaller ones, which I did.

Oddly, when I tried to import the package GUIDEseq to github today, it still mentions these two files being too big, although I do not see these two files in my local repository, checked out from the Bioconductor repository.

JulieZhuMac2017:GUIDEseq ZHUJ$ git rm -r inst/extdata/HEK293_site4All.bed
fatal: pathspec 'inst/extdata/HEK293_site4All.bed' did not match any files

Could you please help? Thanks!

Best regards,

Julie


FYI, I am following the steps outlined at https://bioconductor.org/developers/how-to/git/maintain-github-bioc/

JulieZhuMac2017:GUIDEseq ZHUJ$  git push origin master
Counting objects: 515, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (180/180), done.
Writing objects: 100% (515/515), 107.80 MiB | 18.38 MiB/s, done.
Total 515 (delta 344), reused 483 (delta 320)
remote: Resolving deltas: 100% (344/344), done.
remote: warning: File inst/extdata/HEK293_site4All.bam is 87.88 MB; this is larger than GitHub's recommended maximum file size of 50.00 MB
remote: error: GH001: Large files detected. You may want to try Git Large File Storage - https://git-lfs.github.com.
remote: error: Trace: faafca1a45d562b62039862ac0dfbf85
remote: error: See http://git.io/iEPt8g for more information.
remote: error: File inst/extdata/HEK293_site4All.bed is 124.11 MB; this exceeds GitHub's file size limit of 100.00 MB
To https://github.com/LihuaJulieZhu/GUIDEseq.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'https://github.com/LihuaJulieZhu/GUIDEseq.git'

From: "Zhu, Lihua (Julie)" <Julie.Zhu at umassmed.edu>
Date: Monday, October 19, 2015 at 1:32 PM
To: Michael Lawrence <lawrence.michael at gene.com>, Jim Hester <james.hester at bioconductor.org>
Subject: Re: Data files in GUIDEseq

Jim, FYI, I have removed the two large datasets with much smaller replacements. Thanks for your feedback!

Michael, please feel free to check out the new dataset in the following commit. Thanks!

Best regards,

Julie



Julie-Zhus-MacBook-Pro-Intel-Core-i7:GUIDEseq zhuj$ svn ci -m "changed to smaller test datasets"
Sending        DESCRIPTION
Deleting       inst/extdata/HEK293_site4All.bam
Deleting       inst/extdata/HEK293_site4All.bed
Adding  (bin)  inst/extdata/bowtie2.HEK293_site4_chr13.sort.bam
Adding         inst/extdata/bowtie2.HEK293_site4_chr13.sort.bed
Transmitting file data ...
Committed revision 109732.

From: Lihua Julie Zhu <julie.zhu at umassmed.edu<mailto:julie.zhu at umassmed.edu>>
Date: Thursday, October 15, 2015 2:16 PM
To: Michael Lawrence <lawrence.michael at gene.com<mailto:lawrence.michael at gene.com>>, Jim Hester <james.hester at bioconductor.org<mailto:james.hester at bioconductor.org>>
Subject: Re: Data files in GUIDEseq

Yes, we need to fetch a few enriched regions.


From: Michael Lawrence <lawrence.michael at gene.com<mailto:lawrence.michael at gene.com>>
Date: Thursday, October 15, 2015 2:13 PM
To: Jim Hester <james.hester at bioconductor.org<mailto:james.hester at bioconductor.org>>
Cc: Michael Lawrence <lawrence.michael at gene.com<mailto:lawrence.michael at gene.com>>, Lihua Julie Zhu <julie.zhu at umassmed.edu<mailto:julie.zhu at umassmed.edu>>
Subject: Re: Data files in GUIDEseq

Since this is peak calling, we probably want to keep all the reads within a smaller region.

On Thu, Oct 15, 2015 at 11:12 AM, Jim Hester <james.hester at bioconductor.org<mailto:james.hester at bioconductor.org>> wrote:
FWIW the hard limit that was causing the error with the git mirrors is 100
Mb, but I would try and shoot for a file around 20 Mb or so at max.

An easy way if you just want uniform sampling is using samtools (where -s
is the fraction of reads you want to keep).

samtools view  HEK293_site4All.bam -s .1 -b -o HEK293_site4All2.bam

Thanks,

Jim
​

On Thu, Oct 15, 2015 at 2:07 PM, Michael Lawrence <lawrence.michael at gene.com<mailto:lawrence.michael at gene.com>
> wrote:

> Probably best to come up with smaller files, because we want them in the
> package for demonstration purposes, right? Just need to filter them,
> somehow. Actually, all we need is the BAM file...
>
> On Thu, Oct 15, 2015 at 10:43 AM, Zhu, Lihua (Julie) <
> Julie.Zhu at umassmed.edu<mailto:Julie.Zhu at umassmed.edu>> wrote:
>
>> Thanks, Jim!
>>
>> These files were included for Michael to test functions he is developing


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