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

Thu Mar 29 20:12:41 CEST 2018

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.
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>>>      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,
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>> 
>> 
>> 
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