[Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

Wed Dec 23 22:10:36 CET 2020

Did you 'git commit' the changes to the branch?

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________________________________
From: Xiaowen Chen <Xiaowen.Chen using jax.org>
Sent: Wednesday, December 23, 2020 2:56:01 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

Hi Kern,

I am sorry. I ran the following command, I also show the output of the corresponding commands.

However the release branch still is not updated.

Could you help me?

Thank you.

Best,

Xiaowen

1.go to https://github.com/TheJacksonLaboratory/epihet/blob/master/DESCRIPTION

update version 1.7.1 of DESCRIPTION FILE to 1.6.1

2.(base) [chenx using helix ~]$ git clone https://github.com/TheJacksonLaboratory/epihet.git<https://secure-web.cisco.com/10MdtT2vtU5z5f6CdVlC7mUvYXYpLKtzYPugTqMgU9x_pQJeHAMy6b5aKZ0bJko-d--Tqm5c-uyiepw4-o6NxQ8d6Opn7MWIl4QHE2iiZuyHZ1kKGNqh3uMyS0ekkQHf19hOm87R7C077XBSjlBGr05qkqKY99p4IXQyCn1Hz0D3bNr1eG97oTB1qDwVJOW-e3vQuC5lW7fHQ5krFVSeyE3PNA_tHhMJmIfY-kvBq56_2ukpEx3vYWe4O_UrAyLtrl9fakMFvyP8bqj3_10vEL-JnCaMP4GxMNfSxZWoCeFeK_IdqHfIiqtt1QbsQ-hJU/https%3A%2F%2Fgithub.com%2FTheJacksonLaboratory%2Fepihet.git>

Initialized empty Git repository in /home/c-chenx/epihet/.git/

remote: Enumerating objects: 35, done.

remote: Counting objects: 100% (35/35), done.

remote: Compressing objects: 100% (32/32), done.

remote: Total 874 (delta 16), reused 5 (delta 2), pack-reused 839

Receiving objects: 100% (874/874), 4.61 MiB, done.

Resolving deltas: 100% (465/465), done.

3. (base) [chenx using helix ~]$ cd epihet

4. (base) [chenx using helix epihet]$ git remote add upstream git using git.bioconductor.org:packages/epihet.git

(base) [chenx using helix epihet]$ git remote -v

origin     https://github.com/TheJacksonLaboratory/epihet.git (fetch)

origin     https://github.com/TheJacksonLaboratory/epihet.git (push)

upstream             git using git.bioconductor.org:packages/epihet.git (fetch)

upstream             git using git.bioconductor.org:packages/epihet.git (push)

5.(base) [chenx using helix epihet]$ git fetch --all

Fetching origin

Fetching upstream

Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':

From git.bioconductor.org:packages/epihet

* [new branch]      RELEASE_3_10 -> upstream/RELEASE_3_10

* [new branch]      RELEASE_3_11 -> upstream/RELEASE_3_11

* [new branch]      RELEASE_3_12 -> upstream/RELEASE_3_12

* [new branch]      RELEASE_3_9 -> upstream/RELEASE_3_9

* [new branch]      master     -> upstream/master

6.(base) [chenx using helix epihet]$ git checkout RELEASE_3_12

error: pathspec 'RELEASE_3_12' did not match any file(s) known to git.

7. (base) [chenx using helix epihet]$ git checkout -b RELEASE_3_12 upstream/RELEASE_3_12

Branch RELEASE_3_12 set up to track remote branch RELEASE_3_12 from upstream.

Switched to a new branch 'RELEASE_3_12'

8. (base) [chenx using helix epihet]$ git checkout RELEASE_3_12

Already on 'RELEASE_3_12'

9.(base) [chenx using helix epihet]$ git merge upstream/RELEASE_3_12

Already up-to-date.

(base) [chenx using helix epihet]$ git merge origin/RELEASE_3_12

Already up-to-date.

(base) [chenx using helix epihet]$ git push upstream RELEASE_3_12

Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':

Everything up-to-date

(base) [chenx using helix epihet]$ git push origin RELEASE_3_12

Everything up-to-date

From: "Kern, Lori" <Lori.Shepherd using RoswellPark.org>
Date: Friday, December 18, 2020 at 3:24 PM
To: Xiaowen Chen <Xiaowen.Chen using jax.org>
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

If you are on the RELEASE_3_12 branch and made changes, you will need to update the version number regardless.  The numbering schema in release and devel are different.

of version  x.y.z   the y is even in release and odd in devel...

you could try while you are on the release branch to bump the version to 1.6.1 and push that up.  but again, I do not see any code changes on the RELEASE_3_12 branch so you would need to make sure those changes are also there before pushing up.

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________

From: Xiaowen Chen <Xiaowen.Chen using jax.org>
Sent: Friday, December 18, 2020 3:19 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

I totally understand what you are talking about.

I need to push the latest code to release branch3_12. but I ran the following command line several days.

git clone https://github.com/TheJacksonLaboratory/epihet.git

cd epihet

git remote add upstream git using git.bioconductor.org:packages/epihet.git

git remote -v

git fetch �all

git checkout master

git merge origin/master

git merge upstream/master

git push upstream master

 git push origin master

git checkout RELEASE_3_12

 git merge upstream/RELEASE_3_12

 git merge origin/RELEASE_3_12

 git push upstream RELEASE_3_12

 git push origin RELEASE_3_12

And everything looked fine. No error. But RELEASE_3_12 branch still is not updated.

From: "Kern, Lori" <Lori.Shepherd using RoswellPark.org>
Date: Friday, December 18, 2020 at 3:15 PM
To: Xiaowen Chen <Xiaowen.Chen using jax.org>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

That is the code on the devel branch.

You need to make the same code changes you did on devel to fix the ERROR on the RELEASE_3_12 branch. It does not get carried over across branches.

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________

From: Xiaowen Chen <Xiaowen.Chen using jax.org>
Sent: Friday, December 18, 2020 3:13 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

Yes,

I pretty sure I changed it.

See http://bioconductor.org/checkResults/devel/bioc-LATEST/epihet/<http://secure-web.cisco.com/1ss2p3h9ANyNT9W8y-gVvJ1KbvbgAU6VoEbg03GV6jHmEl4erXbnsDaG-ROfqsyQGMzad9KFhNgmVA_ivTR1W03ngAunrGPvRx24iE6IlZUvaTJCabDEqPOjoejdyK7lYLqmU27lqVi60M4TeOZK4kTLkq_wrawtGkv35wwbEGtpqPi1PQomhuSdJ9sYfJqiZ6E-iE05qOZu7VPtMKOhzwZvPeNaABthKkMYfR_7TIwj_C9n3Of2u_3LmP_o0xWSWjcHAdq2c8tvCUzLZ3AbfpG5Vavxl7t4U3I8kcSYYZJDk_28xQLE1HOoSnU-wkMx9/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2Fepihet%2F>

Everything is ok.

No error.

Should I change version from 1.7.1 to 1.7.2 before pushing RELEASE_3_12?

From: "Kern, Lori" <Lori.Shepherd using RoswellPark.org>
Date: Friday, December 18, 2020 at 3:10 PM
To: Xiaowen Chen <Xiaowen.Chen using jax.org>
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

I don't see any changes pushed to the release 12 branch.  You did remember to make the code changes and commit before pushing?

git checkout RELEASE_3_12

git merge upstream/RELEASE_3_12

git merge origin/RELEASE_3_12

#

# Make code changes

#  Make version bump in DESCRIPTION

# git commit

#

git push upstream RELEASE_3_12

git push origin RELEASE_3_12

Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________

From: Xiaowen Chen <Xiaowen.Chen using jax.org>
Sent: Friday, December 18, 2020 3:07 PM
To: Kern, Lori <Lori.Shepherd using RoswellPark.org>
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

Yes, I changed to RELEASE_3_12.

From: "Kern, Lori" <Lori.Shepherd using RoswellPark.org>
Date: Friday, December 18, 2020 at 3:05 PM
To: Xiaowen Chen <Xiaowen.Chen using jax.org>, "bioc-devel using r-project.org" <bioc-devel using r-project.org>
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

The current Bioconductor release is 3.12  so you changed the commands below to reflect 3_12?

(i.e    git checkout RELEASE_3_12 )

Lori Shepherd

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> on behalf of Xiaowen Chen <Xiaowen.Chen using jax.org>
Sent: Friday, December 18, 2020 1:30 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] FW: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

Hi ,
I have follow the website http://secure-web.cisco.com/1ki-xUKhxTFvXD89R9PKgLZ7QzTWrJmmqO4-C2dcwSY6S49z9pnD4Uwb-IwLQbPQwqTXgzORisNeH2wSNY2LGbVsu6Axv1BGH6AFGEgbF0RjwLdoVd8_1EWbXbGSoFT8nzhz8y9QLN3NmeV8g1C37v3rXOnIn0PaxcvwSRWlw_I6lrx6I1qNqBsuxUqrEbv2wpn0P1b5zwzLFvKglQ0-Ay0F-L2Iv-pjGVy94y0VFe2YY862AIjuNwQqALODdPILpFNstWCEVWe32N2i8DbTGyzHZEUwimKkmMI18LIIZy8NKviBBdNJ7NPr5Xm9H37-Sd28eqzkh0_BNFquKNP1M9Q/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F
To push the latest epihet version to release branch.
Why I still to receive the email to complain there are error, seem I did not push successfully.
What should I do, I did not see some error when I run the following commands

git checkout RELEASE_3_6
 git merge upstream/RELEASE_3_6
 git merge origin/RELEASE_3_6
 git push upstream RELEASE_3_6
 git push origin RELEASE_3_6

Best,
Xiaowen

On 12/18/20, 1:00 PM, "BBS-noreply using bioconductor.org" <BBS-noreply using bioconductor.org> wrote:

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

    Hi epihet maintainer,

    According to the Multiple platform build/check report for BioC 3.12,
    the epihet package has the following problem(s):

      o ERROR for 'R CMD build' on malbec1. See the details here:
          https://secure-web.cisco.com/1N16ddKrue9rDFh3tuFZy4oYqtH_lPGE1wFJSNmYq9CGAPOvjzxWr2oNJaeWVDpF1cXtgBetx3wy-j7xKSfCPiZ5s7aBmpsg3HnS5ZBVNbUFEmX1N_NOw41wLgrar1BDgzhYbz3aUjR-iQfBsr3o44hHi3aFi2TqrnSD7QvBX9oU9X71vskBLNE0qLn4zb7F2m0QRZNn3FfzwrDFx2HPgmEFmCn20nhjLeNHNqVQpcDEZFWE7ksGBgwz01pay9miJogls3v_CQGMK3uxJcocmNUdAGHsGpnHk_2At5DutG5Gk4_-zdU96cwayYzY_XETE4uWmv7diTM5fPpKZds1qjQ/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.12%2Fbioc-LATEST%2Fepihet%2Fmalbec1-buildsrc.html

    Please take the time to address this by committing and pushing
    changes to your package at git.bioconductor.org

    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:

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