[Bioc-devel] paxtoolsr Bioconductor Push Issues
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 at 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 at 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 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'
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