________________________________
From: Turaga, Nitesh <Nitesh.Turaga at RoswellPark.org>
Sent: Sunday, March 15, 2020 3:31 PM
To: L Rutter <lindsayannerutter at gmail.com>; 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)
You cannot merge your master branch into the RELEASE_3_10 branch.
The version number will not match, and all the devel changes will go into
the release.
Instead,
1) git checkout RELEASE_3_10
2) Make the changes again in the RELEASE_3_10 branch.
3) git add <files>
4) git commit -m "<message>"
5) git push upstream RELEASE_3_10
Best,
Nitesh
?On 3/15/20, 12:01 PM, "Bioc-devel on behalf of L Rutter" <
bioc-devel-bounces at r-project.org on behalf of lindsayannerutter at gmail.com>
wrote:
Dear Lori:
Thank you for all your help. I am happy to say that the landing
development
page is now building without errors
<http://bioconductor.org/packages/3.11/bioc/html/bigPint.html>. I
believe
my GitHub master branch (1.3.3) and Bioconductor development branch
are now
the same.
I am hoping to now likewise push what is on my GitHub master branch
(1.3.3)
to the release branch of Bioconductor, which is still currently failing
(1.2.0) <
http://bioconductor.org/packages/release/bioc/html/bigPint.html>.
Below are the commands I tentatively plan to use:
1) git checkout RELEASE_3_10
2) git merge master
3) Change the version number in DESCRIPTION to 1.2.1
4) git fetch --all
5) git pull upstream master
6) git push upstream master
To avoid possibly regressing on recent progress, I wanted to check
with you
first if you think those steps may be suitable. I believe you
recommended
the first three steps (in that order) in a previous e-mail. However, I
am
not sure if the last three steps may be needed.
Thank you again for your patience and help. I believe I am slowly
getting
the hang of this thanks to your support.
Sincerely,
Lindsay
2020?3?12?(?) 20:51 Shepherd, Lori <Lori.Shepherd at roswellpark.org>:
> We do see the changes now in git.bioconductor.org so yes just keep
an eye
> on the build report.
>
> 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:* Wednesday, March 11, 2020 4:05 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 your helpful e-mail. This is just a note that I
> completed the recommended steps:
>
> 1) Checked that my DESCRIPTION file contains version 1.3.2
> 2) Issued the following three commands:
> git fetch --all
> git pull upstream master
> git push upstream master
>
> There were no error messages, merge conflicts, etc. I will check the
> landing page after 24 hours and, if there remains an issue, will try
the
> same steps as above but with version 1.3.6. If that remains an
issue, I
> will update this thread.
>
> In case this could cause future problems, I notice at the top of your
> e-mail where you stated information about my latest (February 29)
commit,
> it states the author as "lrutter". My GitHub userName had originally
been
> "lrutter" but I updated it to "lindsayrutter" about one year ago.
> Similarly, I updated my name on the git.credentials app (
>
https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/
)
> from "lrutter" to "lindsayrutter" on February 25. I just checked the
app
> and my name is still listed as the updated "lindsayrutter". However,
I am
> not sure if the commit message at the top of your e-mail may signify
that
> my name still has not been comprehensively updated.
>
> I will update this thread should the problem remain and I am unsure
how to
> proceed. In any case, I want to thank you very much again for your
patience!
>
> Sincerely,
> Lindsay
>
>
> 2020?3?10?(?) 21:21 Shepherd, Lori <Lori.Shepherd at roswellpark.org>:
>
> 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]]
>
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This email message may contain legally privileged and/or confidential
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This email message may contain legally privileged and/or confidential
information. If you are not the intended recipient(s), or the employee or
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distribution, or use of this email message is prohibited. If you have
received this message in error, please notify the sender immediately by
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