[Bioc-devel] paxtoolsr Bioconductor Push Issues

On Sep 24, 2018, at 12:00 PM, Augustin Luna <augustin_luna at hms.harvard.edu> wrote:

I just pushed. I guess we'll soon see if my updates fix some problems
have been happening with the package.

Augustin Luna

On Mon, Sep 24, 2018 at 11:24 AM, Turaga, Nitesh
<Nitesh.Turaga at roswellpark.org> wrote:

Hi Augustin,

You should be able to push to your repository now.

Please notify me once you have been able to push with the new .jar file, and also make sure your version bump (1.15.1 ?> 1.15.2) is correct.

Best,

Nitesh

On Sep 21, 2018, at 10:10 AM, Augustin Luna <augustin_luna at hms.harvard.edu> wrote:

As far as Git is concerned yes a change was made, but it was probably
a move or a rename. So how do we move forward? paxtoolsr has been
greater than 5MB for all of its history (4-5 years) on Bioconductor;
the package cannot exist without that jar.

Thanks,
Augustin Luna

On Thu, Sep 20, 2018 at 4:50 PM, Turaga, Nitesh
<Nitesh.Turaga at roswellpark.org> wrote:

Hi Augustin,

There is a software package size limit to Bioconductor packages which is 5 MB. You cannot push because the pre-receive hook on the Bioconductor git repo is catching that it?s a bad commit.

I guess you are making a change to the jar file for the first time after the git-hooks have been put in place(about 9-10 months ago) to make sure that packages are obeying the 5MB limit. Is this accurate?

Best,

Nitesh

On Sep 20, 2018, at 5:09 PM, Augustin Luna <augustin_luna at hms.harvard.edu> wrote:

I've made needed changes to paxtoolsr for the next release. I cannot
push to Bioconductor; see below. paxtoolsr is essentially a wrapper
around the jar with helper functions; the jar has been there since the
beginning. Please advise.

Augustin Luna

Writing objects: 100% (1252/1252), 22.33 MiB | 1.65 MiB/s, done.
Total 1252 (delta 988), reused 741 (delta 596)
remote: Resolving deltas: 100% (988/988), completed with 80 local objects.
remote: Error: file larger than 5 Mb.
remote:
remote:     File name: 'inst/java/paxtools-4.3.1.jar'
remote:     File size: 24.5 Mb
remote:
remote: Please see Biocondcutor guidelines
remote: https://bioconductor.org/developers/package-guidelines/
remote:
To git.bioconductor.org:packages/paxtoolsr.git
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to
'git at git.bioconductor.org:packages/paxtoolsr.git'

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.