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

Tue Mar 3 11:55:05 CET 2020

Dear Lori:

Thank you for this helpful advice. I did successfully now manage to change
my keys and name on the git.credentials app you suggested on February 25.

At that time, my development version was building but my release version
was failing. So, I followed the instructions in the link you provided on
February 3 (
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/)
to update my release version. I was able to also follow the "Sync existing
repositories" tab at the beginning of the guideline.

After waiting for the updates, when I checked into my package (bigPint), I
noticed now both the development (
https://bioconductor.org/packages/devel/bioc/html/bigPint.html) and release
(https://bioconductor.org/packages/release/bioc/html/bigPint.html) version
are not building. I was surprised because I did not think I was making any
changes to the development version through these instructions. I also
notice my development version is 1.3.0, my release version is 1.2.0, and my
GitHub master branch (
https://github.com/lindsayrutter/bigPint/blob/master/DESCRIPTION) is
version 1.3.1. It also seems that the version on my local computer reversed
to 1.2.0.

I tentatively plan to:

1) Clone my GitHub master branch (version 1.3.1) back to my local computer
(to make sure I do not lose many recent changes I have made to my package).
2) Try to push my most current version (1.3.1) to the development branch of
Bioconductor.
3) Try to push changes to the release branch of Bioconductor.

I am pretty stuck even to the point where it is hard for me to formulate
questions but below are a few questions that might help me identify the
point of confusion:
1) Is it acceptable for me to push what is on my GitHub master branch
(1.3.1) to the development branch of Bioconductor?
2) Is it acceptable for me to likewise push what is on my GitHub master
branch (1.3.1) to the release branch of Bioconductor? I am assuming I am
only supposed to push the "cherry-pick" commits that resolve what had been
causing an error originally? This may be difficult for me as I have since
added many more changes to the master branch on GitHub after resolving that
release error.
3) Is it possible to ask if there is anything else identifiably "out of
line" with my setup (on my GitHub master, development branch, or release
branch)? I am sure that once I complete this process successfully I will
have be better positioned to critically think of what is happening - but
right now I worry that due to my earlier mistakes, something may be "off"
with my setup that will make it difficult for me to successfully follow any
set of instructions.

I apologize for reaching out about this headache of an issue now. I am just
concerned I may not be able to resolve this in a timely manner with my
current scope of knowledge.

Sincerely,
Lindsay

2020年2月25日(火) 21:14 Shepherd, Lori <Lori.Shepherd using roswellpark.org>:

> 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年2月3日(月) 21:54 Shepherd, Lori <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> on behalf of L
> Rutter <lindsayannerutter using gmail.com>
> *Sent:* Saturday, February 1, 2020 4:18 AM
> *To:* bioc-devel using r-project.org <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) 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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>
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