[Bioc-devel] ENCODExplorer: file size error

Charles Joly ch@r|e@@jo|y-be@up@r|@nt @end|ng |rom crchu|@u|@v@|@c@
Thu Apr 4 21:02:00 CEST 2019


Thank you for the quick reply! Is the deadline for submitting an ExperimentHub package the same as the one to submit a new package?


On Thu, Apr 4, 2019 at 2:32 PM Shepherd, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>> wrote:

Bioconductor over the years has put in some new policies regarding file sizes.  Considering this is a data file  (from the looks of it a  .rda file),  we would highly recommended updating the package to utilized ExperimentHub and move the data to be stored in S3 bucket.

Please read over the following documentation and email me  (lori.shepherd using roswellpark.org<mailto:lori.shepherd using roswellpark.org>) with any further questions regarding the conversion and upload of data.


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Charles Joly <charles.joly-beauparlant using crchul.ulaval.ca<mailto:charles.joly-beauparlant using crchul.ulaval.ca>>
Sent: Thursday, April 4, 2019 12:15:59 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
Subject: [Bioc-devel] ENCODExplorer: file size error


I'm getting the following error when I try to push the latest changes of ENCODExplorer on the Bioconductor's git:

git push upstream master
Counting objects: 318, done.
Delta compression using up to 48 threads.
Compressing objects: 100% (106/106), done.
Writing objects: 100% (265/265), 356.41 MiB | 14.55 MiB/s, done.
Total 265 (delta 181), reused 230 (delta 155)
remote: Resolving deltas: 100% (181/181), completed with 40 local objects.
remote: Error: file larger than 5 Mb.
remote:     File name: 'data/encode_df.rda'
remote:     File size: 25.4 Mb
remote: Please see Biocondcutor guidelines
remote: https://bioconductor.org/developers/package-guidelines/
To git using git.bioconductor.org:packages/ENCODExplorer.git
 ! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to 'git using git.bioconductor.org:packages/ENCODExplorer.git'

We tried to reduce the size of the files, but it will be difficult to go lower than this.

Since the data is an important part of the ENCODExplorer package, would there be a way to tolerate larger file sizes?

Thank you for your input,

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