[Bioc-devel] paxtoolsr Bioconductor Push Issues

[Augustin Luna]

I'll keep that in mind and do it soon.

A bigger concern for me. Currently, I think that the development
version is passing checks while the the release version is not. I
committed a lot of changes, many interconnected and big, I'm unlikely
to be able tease out a narrow subset to fix the current release
version. What is the guidance? Commit this large batch of changes to
fix release or leave it in a broken state? I assume the next BioC
release is soon.

Augustin Luna
On Mon, Sep 24, 2018 at 2:14 PM Turaga, Nitesh
<Nitesh.Turaga using roswellpark.org> wrote:
>
> Hi Augustin,
>
> Please remove the .Rproj file in your repository from git version control. You can add a .gitignore file,
>
> http://bioconductor.org/developers/package-guidelines/#gitignore
>
> Please check that link.
>
> Best,
>
> Nitesh
>
>
> > On Sep 24, 2018, at 12:15 PM, Turaga, Nitesh <Nitesh.Turaga using RoswellPark.org> wrote:
> >
> > Augustin,
> >
> > I will reenable the hook for you now.
> >
> > You will not be able to push large files after this.
> >
> > Best,
> >
> > Nitesh
> >
> >> On Sep 24, 2018, at 12:00 PM, Augustin Luna <augustin_luna using 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 using 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 using 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 using 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 using 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 using git.bioconductor.org:packages/paxtoolsr.git'
> >>>>>>
> >>>>>> _______________________________________________
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> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>>
> >>>>>
> >>>>>
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