[Bioc-devel] DMCHMM problems reported in the Multiple platform build/check report for BioC 3.14

Wed Feb 16 20:34:21 CET 2022

As mentioned in the previous response.  You fixed the ERROR on the devel branch.

You need to make the same changes on a RELEASE_3_14 branch.   It does not appear as if you did commit changes to an origin/RELEASE_3_14 to be able to merge.  And there are no updates on our git.bioconductor.org that should correspond to upstream/RELEASE_3_14

You can check your remotes with
git remote -v

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Farhad Shokoohi <shokoohi using icloud.com>
Sent: Wednesday, February 16, 2022 2:27 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] DMCHMM problems reported in the Multiple platform build/check report for BioC 3.14

I have already fixed the problem; when I try to push the changes it says everything is uptodate.

On Feb 16, 2022, at 11:14 AM, Kern, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>> wrote:

There are no changes on the RELEASE_3_14 branch.
You need to checkout the RELEASE_3_14 branch.  Commit the necessary changes to fix the ERROR. Commit a version bump to 1.16.1.  And then push back to RELEASE_3_14

Lori Shepherd - Kern
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Farhad Shokoohi <shokoohi using icloud.com<mailto:shokoohi using icloud.com>>
Sent: Wednesday, February 16, 2022 1:58 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>>
Cc: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] DMCHMM problems reported in the Multiple platform build/check report for BioC 3.14

Hello

I think I have fixed the problem; see the log; However, I do not know how to make sure everything is up-to-date.
Best,

farhad using Farhads-iMac DMCHMM %  git push upstream master
Everything up-to-date
farhad using Farhads-iMac DMCHMM %  git push origin master
Everything up-to-date
farhad using Farhads-iMac DMCHMM % git checkout RELEASE_3_14
Already on 'RELEASE_3_14'
Your branch is up to date with 'origin/RELEASE_3_14'.
farhad using Farhads-iMac DMCHMM % git merge upstream/RELEASE_3_14
Already up to date.
farhad using Farhads-iMac DMCHMM % git merge origin/RELEASE_3_14
Already up to date.
farhad using Farhads-iMac DMCHMM % git push upstream RELEASE_3_14
Everything up-to-date
farhad using Farhads-iMac DMCHMM % git push origin RELEASE_3_14
Everything up-to-date
farhad using Farhads-iMac DMCHMM % git push upstream RELEASE_3_14
Everything up-to-date
farhad using Farhads-iMac DMCHMM % git push origin RELEASE_3_14
Everything up-to-date
farhad using Farhads-iMac DMCHMM % git checkout RELEASE_3_14
Already on 'RELEASE_3_14'
Your branch is up to date with 'origin/RELEASE_3_14'.

On Feb 7, 2022, at 10:41 AM, Kern, Lori <Lori.Shepherd using RoswellPark.org<mailto:Lori.Shepherd using RoswellPark.org>> wrote:

As often stated Bioconductor has two different branches a RELEASE_3_14 and a devel branch.  You have pushed changes only to the master branch that corresponds to devel.

You must also push changes to the RELEASE_3_14 branch to fix the Bioc 3.14 version of the package.

See:
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/<http://secure-web.cisco.com/1-QI2WWddDLwW1h9mtghZtNCZxpol-AqkiYkRg3CIz0Ot18YYS9tzWRTD5WRo_D4JbbSzldhyf5iw65sRUukPZYNYhhPVMnyoZkFk4SJSOQ5J1QoZ37mM3tfj4ShtODqlVvSZZzElSi4gLlIOObXNOgt0uYxmm1kS1mendUdmluYc3PFdqL_iIk0hsH6MroWBHQJs0oiK184k25oIzOFwr1oiOAUSdD4AC0sgeZDKVVGjZD0ohK4lkANmVkJyKP_mI3Yn1AHiXSTNV7Rg6nDYEHXxwGK4TE9dQwBzg3lOvYNRsHxml6FMmqJa-X-Vy5pE/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F>

Cheers,

Lori Shepherd - Kern
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> on behalf of Farhad Shokoohi via Bioc-devel <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Sent: Monday, February 7, 2022 1:35 PM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org> <bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
Subject: Re: [Bioc-devel] DMCHMM problems reported in the Multiple platform build/check report for BioC 3.14

Hello,
I have fixed the problem and uploaded the new version of my package.
I don�t understand why I get the following message :

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

Hi DMCHMM maintainer,

According to the Multiple platform build/check report for BioC 3.14,
the DMCHMM package has the following problem(s):

 o ERROR for 'R CMD build' on nebbiolo2. See the details here:
     https://secure-web.cisco.com/1orvjT1F0A8Kb2qBMadMQzdTu5DcniWrLBCeXh-uOCUt8YYDSo6oCzNxe0Xn0tf-okh7lRqBuQ842Cz347vLeopiMrcBGggpW9t5HeiDD-Bc2p2yzYfJdlCM7u-ZxOh7IDTmHtgp5EVx1ly05kIh5W5P3LVykoZd9r5n29mlh1TLEBHZ1CYcIUz5IiFLILUQMcRImRCf0p2Ltnun__v6T1U70OGKXbAuaRXiRBw5fNf1gIbySrkyPrvatg3o1HgXaRNsH1apdsVjoUmyznlRD3lkxxaK48rkq8QHmccIT5NOoaX41MAd61JEfA2DxPOhD/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.14%2Fbioc-LATEST%2FDMCHMM%2Fnebbiolo2-buildsrc.html <https://secure-web.cisco.com/1orvjT1F0A8Kb2qBMadMQzdTu5DcniWrLBCeXh-uOCUt8YYDSo6oCzNxe0Xn0tf-okh7lRqBuQ842Cz347vLeopiMrcBGggpW9t5HeiDD-Bc2p2yzYfJdlCM7u-ZxOh7IDTmHtgp5EVx1ly05kIh5W5P3LVykoZd9r5n29mlh1TLEBHZ1CYcIUz5IiFLILUQMcRImRCf0p2Ltnun__v6T1U70OGKXbAuaRXiRBw5fNf1gIbySrkyPrvatg3o1HgXaRNsH1apdsVjoUmyznlRD3lkxxaK48rkq8QHmccIT5NOoaX41MAd61JEfA2DxPOhD/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.14%2Fbioc-LATEST%2FDMCHMM%2Fnebbiolo2-buildsrc.html>

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org<http://secure-web.cisco.com/1nD0C1B5bcxbSndtf3SiNfSxx-oc7FOfAN3NpXj159XQDk0Bk4cwFuVxBs8hWmGVynw0wlMg_DOJaAU0AKv5fWfpNes5W-PQSmc-n907aYTsXW3TRz2d1_68yHWjIYD3gb4tUQMdNzG13FlcePSoflFG_a6-Fzqo0TJ5-n8PaBpwdfr6oAuMqIhBT7FG52yK_cyQJmtfRY0OwHGL1RHxiKCFbGtq4nP1i20tAvGFLLlUfAbi2dDlgS3op2zr3etIfjnWFhbTTqqfaWsiovdEv2-03VEwKxiNktb1XIW0xY-Cu2fCMYvn6J5-BkMem3pfx/http%3A%2F%2Fgit.bioconductor.org%2F> <http://secure-web.cisco.com/1aDeESrR98AvHxh4i43VmaShO71JlXCoL1b7ZM1bUOyQNKhYqk_Wem616ytR_7ERi1gVXM-ZJPrCDpHn8YK2g8tqHRhoai-JmDB6bwtFiICTCMhFt-fTzRIprGb553TUV1DUJh_1QGBVir4KBLb6Q2TH-r7Bc59RUkGeFwJ47rHXuw0yEpEldKbnGNMc3ZWpGBAlk91-g5nUB0vIunDXvBXSyVYP_Y7kBW4IX4oeuNA10BGWI0ysZ2jb34vW_whutuwHMHitG7TvDqvu6dcjZWvsykInEjGiDHsaKj41NImxiBfQCWEE033AfOGl1A7vF/http%3A%2F%2Fgit.bioconductor.org%2F>

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.
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 * Please check the report again 24h after you've committed your changes to the
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