[Bioc-devel] R CMD build error for 3.10 (but not 3.11)

[Shepherd, Lori]

Thank you for reaching out.   Have you tried checking your keys and changing your name on the git.credentials app?

https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: L Rutter <lindsayannerutter using gmail.com>
Sent: Tuesday, February 25, 2020 1:55 AM
To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

Dear Lori:

Thanks for the suggestions. I tried to follow the linked instructions on February 4 and February 9, but was unsuccessful both times (i.e. did not see the changes pushed to the release branch). I tried following the instructions again today. I notice that when I issue the command:

git merge upstream/master

I receive the message:

merge: upstream/master - not something we can merge

So, I clicked on the "Sync existing repositories" tab and checked that the instructions there were working. After adding the upstream branch as follows:

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

When I then try to fetch all (git fetch --all), I receive the following error:

Fetching origin
Fetching upstream
FATAL: R any packages/bigpint lrutter DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream

I changed my GitHub userName about one year ago from "lrutter" to "lindsayrutter". By doing "git remote -v", I can see that my origin branches are correctly at "lindsayrutter", but I am unable to see about my upstream branches on git.bioconductor. This is my output from "git remote -v":

origin https://github.com/lindsayrutter/bigPint (fetch)
origin https://github.com/lindsayrutter/bigPint (push)
upstream git using git.bioconductor.org:packages/bigpint.git (fetch)
upstream git using git.bioconductor.org:packages/bigpint.git (push)

Do you have any advice on how I can fix this issue with fetch upstream possibly expecting my older userName? Thank you for sharing advice.

Sincerely,
Lindsay


2020$BG/(B2$B7n(B3$BF|(B($B7n(B) 21:54 Shepherd, Lori <Lori.Shepherd using roswellpark.org<mailto:Lori.Shepherd using roswellpark.org>>:
It looks like you only pushed changes to the master branch which is our devel branch (3.11).

Please see the instructions for
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

where RELEASE_X_Y   would be RELEASE_3_10  for pushing changes to the release 3.10 branch.




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<mailto:bioc-devel-bounces using r-project.org>> on behalf of L Rutter <lindsayannerutter using gmail.com<mailto:lindsayannerutter using gmail.com>>
Sent: Saturday, February 1, 2020 4:18 AM
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: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)

Dear all:

I have been receiving messages that my Bionconductor package bigPint is
producing errors on 'R CMD build' on malbec1. I believe I discovered the
source of the error, fixed it, and pushed changes to my GitHub account (
github.com/lindsayrutter<http://github.com/lindsayrutter>) on December 10, 2019. I continued to receive this
error notification and was advised to ensure I had pushed the changes to
Bioconductor. I pushed changes following these instructions (
http://bioconductor.org/developers/how-to/git/) on January 4, 2020. I am
still receiving notifications that my package produces errors on 'R CMD
build' on malbec1 (
https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/bigPint/malbec1-buildsrc.html).
However, it seems my package is no longer failing daily build reports for
version 3.11 as of January 4, 2020 (
http://bioconductor.org/checkResults/3.11/bioc-LATEST/).

I am seeking advice on what a maintainer should try in this situation? Is
it possible my changes were only recognized in version 3.11 but not version
3.10? Thank you for any advice you may have!

Sincerely,
L. Rutter

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