[Bioc-devel] R CMD build error for 3.10 (but not 3.11)
L Rutter
||nd@@y@nnerutter @end|ng |rom gm@||@com
Tue Mar 10 09:11:02 CET 2020
Dear Lori:
Thank you very much for your very helpful response. I am sorry to say that
I still am having difficulty seeing errors I think I resolved locally get
successfully pushed to my devel branch. I would really appreciate your
feedback to help me possibly identify the problem.
First, I checked that my git remotes are set up correctly. Below is my
output:
origin https://github.com/lindsayrutter/bigPint.git (fetch)
origin https://github.com/lindsayrutter/bigPint.git (push)
upstream git using git.bioconductor.org:packages/bigPint.git (fetch)
upstream git using git.bioconductor.org:packages/bigPint.git (push)
In an attempt to push changes to my devel branch, I updated my DESCRIPTION
file to contain version 1.3.2. My last commit can be seen here
<https://github.com/lindsayrutter/bigPint/commit/1f61951168d5ba35be6464c3f082e006ff2dd220>.
I waited a few days and see that my builder
<http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/malbec2-checksrc.html>
is still failing. The ERROR seems to be coming from my R/convertSEPair.R
script in the line:
vapply(colnames(oldData), function(x) strsplit(x, "[.]")[[1]][1])
I had updated this command, changing “vapply” to “lapply”. It now reads:
lapply(colnames(oldData), function(x) strsplit(x, "[.]")[[1]][1])
I double-checked the R/convertSEPair.R file on my latest GitHub commit
<https://github.com/lindsayrutter/bigPint/blob/1f61951168d5ba35be6464c3f082e006ff2dd220/R/convertSEPair.R>
and indeed the “vapply” command is no longer present.
I also note that my “Last commit” field on the builder website
<http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/malbec2-checksrc.html>
is b810b6a from February 29, whereas my latest intended GitHub commit for
the devel branch was 1f61951 from March 8.
I should also state that I had tried a few times and kept bumping up my
version number. So, on March 7 (Commit c75da1e), I had version 1.3.5. In my
latest commit, I reduced my version number to 1.3.2 just to check that the
reason my devel branch was still failing was not simply because my z
(x.y.z) number was increased by more than a value of 1. However, it seems
my pushed changes on GitHub are not updating to the devel builder website.
I really thank you for sharing your advice with me. I wanted to ask if you
may have any ideas on what I may be missing at this stage. Thank you again
for your support.
Sincerely,
Lindsay
2020年3月3日(火) 21:30 Shepherd, Lori <Lori.Shepherd using roswellpark.org>:
> It can take up to 24 from a push to be reflected on the build report.
>
> For release 3.10 (RELEASE_3_10 branch) we see a version number of 1.2.0
> http://bioconductor.org/checkResults/release/bioc-LATEST/bigPint/
> and
> For devel 3.11 (master branch) we see a version number of 1.3.1 as well
> http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/
>
> The landing page
> http://bioconductor.org/packages/3.11/bioc/html/bigPint.html will only
> be updated on a successful build/check of the package so we don't propagate
> broken packages to users. If the fixes did not allow for a clean build and
> check it would not be reflected.
>
> Also remember that in order for a change to propagate you need a valid
> version bump. So your release version 1.2.0 in order to take effect would
> have needed to be 1.2.1. And for devel master branch you would need a
> version of 1.3.2.
>
> Never apologize for asking questions. We are here to help. And we
> appreciate that you are taking the time to fix the package and learn how to
> push the changes up correct.
>
>
> I'll answer your specific questions below:
>
> Firstly make sure your git remotes are set up correctly where origin is
> your github repository and upstream is pointing to the bioconductor
> repositories
> http://bioconductor.org/developers/how-to/git/sync-existing-repositories/
>
> origin (your github)
> origin (your github)
> upstream git using git.bioconductor.org:packages/bigPint.git (fetch)
> upstream git using git.bioconductor.org:packages/bigPint.git (push)
>
> 1) Is it acceptable for me to push what is on my GitHub master branch
> (1.3.1) to the development branch of Bioconductor?
> Yes. however you will want to bump the version number in the DESCRIPTION
> to 1.3.2 because we have version 1.3.1 on our builders as indicated
> http://bioconductor.org/checkResults/devel/bioc-LATEST/bigPint/. This
> page reflects 1.3.0 because 1.3.1 has not built without ERROR and we would
> not propagate broken packages to users
> http://bioconductor.org/packages/3.11/bioc/html/bigPint.html.
>
> 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.
> Yes although not recommended but we would rather have a working package
> than one ERRORing so if you don't think you can cherry-pick than yes. The
> best option for that would be to checkout the RELEASE_3_10 branch and do a
> git merge master. You will have to change the version number in the
> DESCRIPTION to be consistent with release version numbers. (1.2.1) AFTER
> the merge.
>
> 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 think you were on the right track so no further comments.
> Some helpful hints :
>
> 1. git fetch --all will fetch all branches from your origin github and
> the upstream bioconductor location (this will be important to do after the
> next release in april to get the next RELEASE_3_11 branch)
> 2. it is always a good idea to do a git pull upstream (branch name)
> to pull any changes we have made. occasionally if we made an infrastructure
> change bioconductor will apply patches. We also do the version bump
> changes at release time. So for your master devel branch git pull
> upstream master (git pull upstream RELEASE_3_10 for the current release)
> 3. If you do git merge read the out message carefully and make sure
> there are no conflicts. Conflicts means there is code that was changes in
> both files (locally and on the branch you want to merge) so you will have
> to check the file to make sure you don't include merge conflicts - The
> code conflicts are indicated with >>>>> and <<<<<. you delete those
> and keep the changes you want to commit. Then add and commit like normal
> and git should give you messages about resolving conflicts.
>
>
> Hope this helps. Let me know if you run into any further trouble.
>
> Cheers
>
>
> 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, March 3, 2020 5:55 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:
>
> 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
>
> [[alternative HTML version deleted]]
>
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