I don't think you were pushing to the devel builders correctly. The last
commit we have on the builder is Sat Feb 29th.
commit b810b6a81198438d6ad26b7d86b14eece00dfa59
Author: lrutter <lindsayannerutter at gmail.com>
Date: Sat Feb 29 23:44:08 2020 +0900
Fix version issue
So you never actually pushed the changes to the git.biocnductor upstream
server.
Based on what you have below please do the following and if you have any
ERRORs please paste the command with the output so we can better assist
you.
git fetch --all
git pull upstream master
# make sure your version number is 1.3.2
# I'm not sure if the version number higher in the history will cause
problems. If you get an error about version number I suggest then doing
1.3.6
# which is one higher than it looks like
git push upstream master
The upstream in these commands says to pull/push to the upstream remote
which is pointed at the bioconductor git servers.
The master says to pull/push from the master branch of the given
repository.
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 at gmail.com>
*Sent:* Tuesday, March 10, 2020 4:11 AM
*To:* Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
*Cc:* bioc-devel at r-project.org <bioc-devel at r-project.org>
*Subject:* Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
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 at git.bioconductor.org:packages/bigPint.git (fetch)
upstream git at 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?3?3?(?) 21:30 Shepherd, Lori <Lori.Shepherd at 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 at git.bioconductor.org:packages/bigPint.git (fetch)
upstream git at 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 at gmail.com>
*Sent:* Tuesday, March 3, 2020 5:55 AM
*To:* Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
*Cc:* bioc-devel at r-project.org <bioc-devel at 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?2?25?(?) 21:14 Shepherd, Lori <Lori.Shepherd at 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 at gmail.com>
*Sent:* Tuesday, February 25, 2020 1:55 AM
*To:* Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
*Cc:* bioc-devel at r-project.org <bioc-devel at 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 at 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 at git.bioconductor.org:packages/bigpint.git (fetch)
upstream git at 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?2?3?(?) 21:54 Shepherd, Lori <Lori.Shepherd at 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 at r-project.org> on behalf of L
Rutter <lindsayannerutter at gmail.com>
*Sent:* Saturday, February 1, 2020 4:18 AM
*To:* bioc-devel at r-project.org <bioc-devel at 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]]