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

Wed Mar 2 21:57:15 CET 2022

Hello,
I tried everything. I cannot fix the problem. It is defiantly BIoC 3.14 problem. 
It does not let me commit my changes. 

All the best,

> On Feb 16, 2022, at 12:27 PM, Martin Morgan <mtmorgan.bioc using gmail.com> wrote:
> 
> I cloned your repository and made sure that the upstream remote points to Bioconductor
> 
> $ git remote -v
> ...
> upstream	git using git.bioconductor.org <mailto:git using git.bioconductor.org>:packages/DMCHMM (fetch)
> upstream	git using git.bioconductor.org <mailto:git using git.bioconductor.org>:packages/DMCHMM (push)
> 
> I then made a local branch from the upstream branch
> 
> git checkout -b RELEASE_3_14 upstream/RELEASE_3_14
> 
> I then looked for differences between the RELEASE_3_14 and master branches
> 
> git diff --stat RELEASE_3_14 master
> DESCRIPTION         | 2 +-
> R/findDMCs-method.R | 7 ++++---
> 2 files changed, 5 insertions(+), 4 deletions(-)
> 
> and I see that there are changes in two files. In more detail, from the output of
> 
> git diff RELEASE_3_14 master
> 
> I see that the DESCRIPTION difference is version bump, and the change in R/findDMCs-method.R is I guess the change that you'd like to make.
> 
> Is that what you see? If so it means that you need to make (or copy) the same changes on the release branch as on the master branch, but using the correct version bump. I did this manually, by checking out the RELEASE_3_14 branch and updating according to the diff; there are much more clever ways of doing this... After making and committing the changes, I see
> 
> $ git diff --stat master
> DESCRIPTION | 2 +-
> 1 file changed, 1 insertion(+), 1 deletion(-)
> 
> so only the DESCRIPTION file differs between branches, with the reason being that I have made a slightly different 'version bump'
> 
> $ git diff master
> diff --git a/DESCRIPTION b/DESCRIPTION
> index 1412398..a1531d0 100644
> --- a/DESCRIPTION
> +++ b/DESCRIPTION
> @@ -1,7 +1,7 @@
> Package: DMCHMM
> Type: Package
> Title: Differentially Methylated CpG using Hidden Markov Model
> -Version: 1.17.1
> +Version: 1.16.1
> Authors using R: c(person("Farhad", "Shokoohi", role = c("aut", "cre"),
>                      email = "shokoohi using icloud.com <mailto:shokoohi using icloud.com>", comment = c(ORCID = "0000-0002-6224-2609"))
>               )
> 
> When I ask about the status of my local branch I now see
> 
> $ git status
> On branch RELEASE_3_14
> Your branch is ahead of 'upstream/RELEASE_3_14' by 1 commit.
>  (use "git push" to publish your local commits)
> 
> nothing to commit, working tree clean
> 
> and I am ready to git push upstream
> 
> 
> On 2/16/22, 2:27 PM, "Bioc-devel on behalf of Farhad Shokoohi via Bioc-devel" <bioc-devel-bounces using r-project.org <mailto:bioc-devel-bounces using r-project.org> on behalf of bioc-devel using r-project.org <mailto:bioc-devel using r-project.org>> wrote:
> 
>    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> 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>
>> Sent: Wednesday, February 16, 2022 1:58 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
>> 
>> 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> <mailto: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://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 <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> <mailto: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> <mailto: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> <mailto: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> <mailto: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> <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>> <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> <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://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/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 <http://secure-web.cisco.com/1aDeESrR98AvHxh4i43VmaShO71JlXCoL1b7ZM1bUOyQNKhYqk_Wem616ytR_7ERi1gVXM-ZJPrCDpHn8YK2g8tqHRhoai-JmDB6bwtFiICTCMhFt-fTzRIprGb553TUV1DUJh_1QGBVir4KBLb6Q2TH-r7Bc59RUkGeFwJ47rHXuw0yEpEldKbnGNMc3ZWpGBAlk91-g5nUB0vIunDXvBXSyVYP_Y7kBW4IX4oeuNA10BGWI0ysZ2jb34vW_whutuwHMHitG7TvDqvu6dcjZWvsykInEjGiDHsaKj41NImxiBfQCWEE033AfOGl1A7vF/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 <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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