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

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Thu Mar 29 20:12:39 CEST 2018


Thanks, Nitesh!

Since it is a released version, I thought I will get input from you first. I will try #8 and let you know if it does not work.

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
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>> 
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>>   Thanks for contributing to the Bioconductor project!
>> 
>> 
>> 
> 
> 
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