[Bioc-devel] GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

Thu, Mar 29, 2018 11:12 AM

Hi Julie,

It doesn?t matter if it is the RELEASE_3_6 branch. If the problem is duplicate commits, just force your Github RELEASE_3_6 to Bioconductor?s RELEASE_3_6. 

Best,

Nitesh

On Mar 29, 2018, at 2:10 PM, Zhu, Lihua (Julie) <Julie.Zhu at umassmed.edu> wrote:

Nitesh,

I will try it. Since it is a released version, I thought I will first get your input .

Thanks!

Best regards,

Julie

On Mar 29, 2018, at 1:59 PM, Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org> wrote:

Hi Julie,

Did you try #8 from the documentation pointed out by the error message?

Take a look at the documentation to fix this,
https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_git_sync-2Dexisting-2Drepositories_&d=DwIGaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=OG7WMDBqoQVKJFHZTsUdWZqvKVtXFuNzXCJTP2tT3Ew&s=ulmFiIgA6VkaJJI8iAtWRnQRGa9F_KC7J_dGgxhi-3I&e=,
particularly, point #8 (force Bioconductor master to Github master).

The idea is to force sync your Github repo, with what exists on Bioconductor. 

Let me know if this works. 

Best,

Nitesh

On Mar 28, 2018, at 4:23 PM, Zhu, Lihua (Julie) <Julie.Zhu at umassmed.edu> wrote:

Nitesh,

I am trying to fix the following error in the released version by adding the correct encoding in the DESCRIPTION file. However, I encountered the following message. Could you please help? Thanks!

Best regards,

Julie

git push upstream RELEASE_3_6

Counting objects: 401, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (135/135), done.
Writing objects: 100% (401/401), 103.37 MiB | 15.55 MiB/s, done.
Total 401 (delta 294), reused 355 (delta 257)
remote: Resolving deltas: 100% (294/294), completed with 23 local objects.
remote: Error: duplicate commits.
remote: 
remote: There are duplicate commits in your commit history, These cannot be
remote: pushed to the Bioconductor git server. Please make sure that this is
remote: resolved.
remote: 
remote: Take a look at the documentation to fix this,
remote: https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_developers_how-2Dto_git_sync-2Dexisting-2Drepositories_&d=DwIGaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=OG7WMDBqoQVKJFHZTsUdWZqvKVtXFuNzXCJTP2tT3Ew&s=ulmFiIgA6VkaJJI8iAtWRnQRGa9F_KC7J_dGgxhi-3I&e=,
remote: particularly, point #8 (force Bioconductor master to Github master).
remote: 
remote: For more information, or help resolving this issue, contact
remote: <bioc-devel at r-project.org>. Provide the error, the package name and
remote: any other details we might need.
remote: 
remote: Use
remote: 
remote:     git show c2479629841859aaa49b97f391bfe593555e0f01
remote:     git show 1d6bbf4039de44f8692dcecb6f160d32332375a7
remote: 
remote: to see body of commits.
remote: 
To https://urldefense.proofpoint.com/v2/url?u=http-3A__git.bioconductor.org&d=DwIGaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=OG7WMDBqoQVKJFHZTsUdWZqvKVtXFuNzXCJTP2tT3Ew&s=fKHTvRcM_qA273rntN5pKeY64ugxsWi18nY7fujtkVg&e=:packages/GUIDEseq.git
! [remote rejected] RELEASE_3_6 -> RELEASE_3_6 (pre-receive hook declined)
error: failed to push some refs to 'git at git.bioconductor.org:packages/GUIDEseq.git'


?On 3/28/18, 3:10 PM, "BBS-noreply at bioconductor.org" <BBS-noreply at bioconductor.org> wrote:

 [This is an automatically generated email. Please don't reply.]

 Hi GUIDEseq maintainer,

 According to the Multiple platform build/check report for BioC 3.6,
 the GUIDEseq package has the following problem(s):

   o ERROR for 'R CMD INSTALL' on malbec1. See the details here:
       https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.6_bioc-2DLATEST_GUIDEseq_malbec1-2Dinstall.html&d=DwIBAg&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=y48XkJjUXE37oYzjnEKE0XU2TEuoXk6-6dGUJl4KtxE&s=zLAhZJZFZQDA3vBaCZj9-XewRgQ4usUa-1nqq76LpbA&e=

   o ERROR for 'R CMD build' on malbec1. See the details here:
       https://urldefense.proofpoint.com/v2/url?u=https-3A__master.bioconductor.org_checkResults_3.6_bioc-2DLATEST_GUIDEseq_malbec1-2Dbuildsrc.html&d=DwIBAg&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=y48XkJjUXE37oYzjnEKE0XU2TEuoXk6-6dGUJl4KtxE&s=x7RWQGG-QihmXuNRTVPm_zTTf6LNdEyaAMFhO3SCsxk&e=

 Please take the time to address this by committing and pushing
 changes to your package at https://urldefense.proofpoint.com/v2/url?u=http-3A__git.bioconductor.org&d=DwIBAg&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=y48XkJjUXE37oYzjnEKE0XU2TEuoXk6-6dGUJl4KtxE&s=FzPy60AJ_IqYrWU_CO1n-OssQeuoyFUlKnoiJusbaRM&e=

 Notes:

   * This was the status of your package at the time this email was sent to you.
     Given that the online report is updated daily (in normal conditions) you
     could see something different when you visit the URL(s) above, especially if
     you do so several days after you received this email.

   * It is possible that the problems reported in this report are false positives,
     either because another package (from CRAN or Bioconductor) breaks your
     package (if yours depends on it) or because of a Build System problem.
     If this is the case, then you can ignore this email.

   * Please check the report again 24h after you've committed your changes to the
     package and make sure that all the problems have gone.

   * If you have questions about this report or need help with the
     maintenance of your package, please use the Bioc-devel mailing list:

       https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_help_mailing-2Dlist_&d=DwIBAg&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=y48XkJjUXE37oYzjnEKE0XU2TEuoXk6-6dGUJl4KtxE&s=DiX130a6NZREvmXdgX9TptApnY4PYi1yL-R3wKc4seg&e=

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[Bioc-devel] GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

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