[Bioc-devel] Request to reverse package deprecation (and support pushing changes)

[L Rutter]

Good afternoon:

I'm the maintainer for the Bioconductor package "bigPint", located here
.

I've recently tried to push changes I made to resolve ERRORS in my package
by the command " git push upstream devel". However, this has led to an
ERROR, which I am pasting beneath my signature below.

I see in Bioc-devel mail archives (here
) that
this error can be something on the Bioconductor developer side. I also see
that my package has been deprecated, and, when seeking support for this
error on the bioc_git Slack channel, it was suggested to me to send a
message here asking for my package to be undeprecated.

I apologize for the inconvenience, and thank you for any assistance you can
provide.

Kind regards,
Lindsay

Enumerating objects: 114, done.
Counting objects: 100% (96/96), done.
Delta compression using up to 4 threads
Compressing objects: 100% (50/50), done.
Writing objects: 100% (72/72), 12.06 KiB | 3.01 MiB/s, done.
Total 72 (delta 53), reused 27 (delta 21), pack-reused 0
remote: fatal: Not a valid object name
f7c29bb3d981eb1080813b334bdc3731e6cd9b4d:"\033\033"
remote: Traceback (most recent call last):
remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line
93, in 
remote: apply_hooks(hooks_dict)
remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line
76, in apply_hooks
remote: prevent_large_files(oldrev, newrev, refname)
remote:   File 
"/home/git/.gitolite/local/hooks/repo-specific/prevent_large_files.py",
line 42, in prevent_large_files
remote: newrev + ":" + fl.decode()])
remote:   File "/usr/lib/python3.5/subprocess.py", line 626, in check_output
remote: **kwargs).stdout
remote:   File "/usr/lib/python3.5/subprocess.py", line 708, in run
remote: output=stdout, stderr=stderr)
remote: subprocess.CalledProcessError: Command '['git', 'cat-file',
'-s', 'f7c29bb3d981eb1080813b334bdc3731e6cd9b4d:"\\033\\033"']'
returned non-zero exit status 128
To git.bioconductor.org:packages/bigPint.git
 ! [remote rejected] devel -> devel (pre-receive hook declined)
error: failed to push some refs to 'git.bioconductor.org:packages/bigPint.git'

[[alternative HTML version deleted]]

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

[L Rutter]

Dear Lori and Nitesh:

Thank you so much for your help. I was able to make the changes and fix the
error. It seems my release version is also now building without error
<https://bioconductor.org/packages/release/bioc/html/bigPint.html>. Your
feedback has helped me a lot and allowed me to get this right finally. I
think I have a better understanding of how to maintain these branches in
the future now. Thank you very much again for all your patience and support!

Sincerely,
Lindsay


2020年3月16日(月) 20:07 Shepherd, Lori :

> If you can make the changes just to fix the error in release than nitesh
> is right and it would be better to do that and follow his commands he sent
> earlier.
>
> Get Outlook for Android <https://aka.ms/ghei36>
>
> ------
> *From:* L Rutter 
> *Sent:* Sunday, March 15, 2020 11:03:42 PM
> *To:* Shepherd, Lori 
> *Cc:* Turaga, Nitesh ;
> bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
>
> Dear Lori and Nitesh:
>
> Thank you both for your support. I should clarify that the changes in the
> devel branch (unfortunately) do include new features in addition to
> correcting the original source of failure. This happened inadvertently due
> to me still building my git skills and also me adding features requested
> while an associated paper was under peer review.
>
> I am hesitant to attempt commands without consulting first as I am still
> improving these skillsets. Thank you again for sharing your expertise.
>
> Sincerely,
> Lindsay
>
>
> 2020年3月16日(月) 6:50 Shepherd, Lori :
>
> Lindsay, please wait for niteshs response as there could be intracacies
> with the versioning git hook that I'm not aware of.
>
> Get Outlook for Android <https://aka.ms/ghei36>
>
> --
> *From:* Bioc-devel  on behalf of
> Shepherd, Lori 
> *Sent:* Sunday, March 15, 2020 4:59:14 PM
> *To:* Turaga, Nitesh ; L Rutter <
> lindsayannerut...@gmail.com>
> *Cc:* bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
>
> Hello,
>
> Nitesh I disagree.  Given this is a bug correction and the release version
> is failing it is perfectly reasonable for them to merge the master branch
> in the RELEASE_3_10 branch as long as they change the version number before
> committing to the git.biconductor.org  branch; The changes in the devel
> branch as far as I am aware were to correct the failure occurring and not
> introducing any new features.  Ideally it would have been better to do the
> correction on the RELEASE_3_10 and then have merged into master but as far
> as I am aware as long as the version number is corrected before the push
> they should be okay.
>
> Lindsay  then the last two steps are not correct . You should not pull and
> push to master as you are working on the RELEASE_3_10 branch
>
> 1) git fetch --all (get any updated branches)
> 2) git checkout RELEASE_3_10  upstream/RELEASE_3_10   (checkout branch)
> 3) git pull upstream RELEASE_3_10(pull before any changes are made)
> 4) git merge master
> 5) Change the version number in DESCRIPTION to 1.2.1   (DO NOT FORGET
> THIS STEP)
> 6) git add DESCRIPTION
> 7) git commit -m 
> 8) git push upstream RELEASE_3_10
>
>
> Nitesh can you verify these steps?
> And Nitesh is right in the sense that in the future bug corrections should
> be done on the release branch and merged into the master branch as it is
> cleaner.
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Turaga, Nitesh 
> Sent: Sunday, March 15, 2020 3:31 PM
> To: L Rutter ; Shepherd, Lori
> 
> Cc: bioc-devel@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 
> 4) git commit -m ""
> 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-boun...@r-project.org on behalf of lindsayannerut...@gmail.com>
> wrote:
>
> Dear Lori:
>
> Thank you for all your help. I am happy to say that the landing
> development
> 

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

[L Rutter]

Dear Lori and Nitesh:

Thank you both for your support. I should clarify that the changes in the
devel branch (unfortunately) do include new features in addition to
correcting the original source of failure. This happened inadvertently due
to me still building my git skills and also me adding features requested
while an associated paper was under peer review.

I am hesitant to attempt commands without consulting first as I am still
improving these skillsets. Thank you again for sharing your expertise.

Sincerely,
Lindsay


2020年3月16日(月) 6:50 Shepherd, Lori :

> Lindsay, please wait for niteshs response as there could be intracacies
> with the versioning git hook that I'm not aware of.
>
> Get Outlook for Android <https://aka.ms/ghei36>
>
> --
> *From:* Bioc-devel  on behalf of
> Shepherd, Lori 
> *Sent:* Sunday, March 15, 2020 4:59:14 PM
> *To:* Turaga, Nitesh ; L Rutter <
> lindsayannerut...@gmail.com>
> *Cc:* bioc-devel@r-project.org 
> *Subject:* Re: [Bioc-devel] R CMD build error for 3.10 (but not 3.11)
>
> Hello,
>
> Nitesh I disagree.  Given this is a bug correction and the release version
> is failing it is perfectly reasonable for them to merge the master branch
> in the RELEASE_3_10 branch as long as they change the version number before
> committing to the git.biconductor.org  branch; The changes in the devel
> branch as far as I am aware were to correct the failure occurring and not
> introducing any new features.  Ideally it would have been better to do the
> correction on the RELEASE_3_10 and then have merged into master but as far
> as I am aware as long as the version number is corrected before the push
> they should be okay.
>
> Lindsay  then the last two steps are not correct . You should not pull and
> push to master as you are working on the RELEASE_3_10 branch
>
> 1) git fetch --all (get any updated branches)
> 2) git checkout RELEASE_3_10  upstream/RELEASE_3_10   (checkout branch)
> 3) git pull upstream RELEASE_3_10(pull before any changes are made)
> 4) git merge master
> 5) Change the version number in DESCRIPTION to 1.2.1   (DO NOT FORGET
> THIS STEP)
> 6) git add DESCRIPTION
> 7) git commit -m 
> 8) git push upstream RELEASE_3_10
>
>
> Nitesh can you verify these steps?
> And Nitesh is right in the sense that in the future bug corrections should
> be done on the release branch and merged into the master branch as it is
> cleaner.
>
>
>
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> 
> From: Turaga, Nitesh 
> Sent: Sunday, March 15, 2020 3:31 PM
> To: L Rutter ; Shepherd, Lori
> 
> Cc: bioc-devel@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 
> 4) git commit -m ""
> 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-boun...@r-project.org on behalf of lindsayannerut...@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 

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

[L Rutter]

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年3月12日(木) 20:51 Shepherd, Lori :

> 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 
> *Sent:* Wednesday, March 11, 2020 4:05 AM
> *To:* Shepherd, Lori 
> *Cc:* bioc-devel@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年3月10日(火) 21:21 Shepherd, Lori :
>
> 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 
> 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 
> *Sent:* Tuesday, March 10, 2020 4:11 AM
> *To:* Shepherd, Lori

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

[L Rutter]

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年3月10日(火) 21:21 Shepherd, Lori :

> 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 
> 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 
> *Sent:* Tuesday, March 10, 2020 4:11 AM
> *To:* Shepherd, Lori 
> *Cc:* bioc-devel@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 g...@git.bioconductor.org:packages/bigPint.git (fetch)
> upstream g...@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-che

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

[L Rutter]

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 
> *Sent:* Tuesday, March 3, 2020 5:55 AM
> *To:* Shepherd, Lori 
> *Cc:* bioc-devel@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

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

[L Rutter]

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 :

> 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 
> *Sent:* Tuesday, February 25, 2020 1:55 AM
> *To:* Shepherd, Lori 
> *Cc:* bioc-devel@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 g...@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 &q

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

[L Rutter]

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 g...@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 g...@git.bioconductor.org:packages/bigpint.git (fetch)
upstream g...@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 :

> 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  on behalf of L
> Rutter 
> *Sent:* Saturday, February 1, 2020 4:18 AM
> *To:* bioc-devel@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]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
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> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.

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

[L Rutter]

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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Re: [Bioc-devel] 80% of man pages must have runnable examples (package with numerous Shiny apps)

[L Rutter]

Hi Lori and Kevin:

Thank you for your helpful responses! I was able to use "if
(interactive()) { ... }" format and return the appDir object for the
user. Thanks again!

Lindsay
On Mon, Nov 19, 2018 at 3:02 PM Kevin RUE  wrote:
>
> Hi Lindsay,
>
> Check out https://github.com/csoneson/iSEE/blob/master/R/iSEE-main.R function 
> "iSEE" for an example of both the function return value, and the man page.
>
> First, I would suggest that your function _returns_ the "appDir" object to 
> the user, and that you leave it to the user to call "shiny::runApp" with 
> options appropriate to their system or preferences (e.g launch.browser=FALSE, 
> port=1234, etc).
>
> Second, for the man page, you don't have to put the _entire_ @example block 
> inside \dontrun{}. You can put everything that doesn't launch the Shiny app 
> outside the \dontrun{} block and only put the one "shiny" line inside the 
> \dontrun{}. The one line will represent less than 80% of the man page.
>
> However, even better, you can avoid the \dontrun{} option altogether and put 
> the "shiny" statement within a "if (interactive()) { ... }" block.
>
> So adapting you existing code, I would have
> #' @examples
> #' # Example 1: Create an interactive litre plot for the logged data using
> #' # default background of hexagons.
> #'
> #' data(soybean_ir_sub)
> #' data(soybean_ir_sub_metrics)
> #' soybean_ir_sub_log <- soybean_ir_sub
> #' soybean_ir_sub_log[,-1] <- log(soybean_ir_sub[,-1]+1)
> #' if (interactive()){
> #' plotLitreApp(data = soybean_ir_sub_log, dataMetrics = 
> soybean_ir_sub_metrics)
> #' }
> #'
> #' # Example 2: Repeat the same process, only now plot background data as
> #' # individual points. Note this may be too slow now that all points are 
> drawn
> #' # in the background.
> #' if (interactive()){
> #' plotLitreApp(data = soybean_ir_sub_log, dataMetrics = 
> soybean_ir_sub_metrics,
> #' option = "allPoints", pointColor = "red")
> #' }
>
> However, once more, I suggest that you return "appDir", and you would then 
> have something like:
> #' app <- plotLitreApp(data = soybean_ir_sub_log, dataMetrics = 
> soybean_ir_sub_metrics)
> #' if (interactive()){
> #'shiny::runApp(app, [options defined by your user])
> #' }
>
> I hope this helps. Otherwise, let me know and I can chime in the review of 
> your package
>
> Best wishes
> Kevin
>
> On Mon, Nov 19, 2018 at 7:00 PM Shepherd, Lori 
>  wrote:
>>
>> Submit with the dontrun{} and temporarily ignore the ERROR -  when 
>> submitting please reference the explanation below.  Your reviewer could 
>> provide more information and will decide how to proceed -  generally 
>> examples will be run manually to check for accuracy and an exception can be 
>> made.
>>
>>
>> Lori Shepherd
>>
>> Bioconductor Core Team
>>
>> Roswell Park Cancer Institute
>>
>> Department of Biostatistics & Bioinformatics
>>
>> Elm & Carlton Streets
>>
>> Buffalo, New York 14263
>>
>> 
>> From: Bioc-devel  on behalf of L Rutter 
>> 
>> Sent: Monday, November 19, 2018 1:49:50 PM
>> To: bioc-devel@r-project.org
>> Subject: [Bioc-devel] 80% of man pages must have runnable examples (package 
>> with numerous Shiny apps)
>>
>> Hello all:
>>
>> I am planning to submit a package to Bioconductor and have one last
>> item from BiocCheck (error, warning, note) I have been unable to
>> resolve:
>>
>> ERROR: At least 80% of man pages documenting exported objects must
>> have runnable examples. The following pages do not: plotLitreApp.Rd,
>> plotPCPApp.Rd, plotSMApp.Rd, plotVolcanoApp.Rd
>>
>> I have 18 man pages (9 function-related, 8 data-related, and 1
>> package-related). Of these, 4 of the function-related man pages (the
>> ones listed in the ERROR) are Shiny applications of the following
>> format:
>>
>> appDir <- system.file("shiny-examples", "plotLitreApp", package = "bigPint")
>> shiny::runApp(appDir, display.mode = "normal")
>>
>> If I do not have \dontrun{} around these shiny app examples, then R
>> CMD check permanently halts on the "checking examples..." step. If I
>> do have \dontrun{} around these shiny app examples, then R CMD
>> BiocCheck gives me the error above. My question is: What is the
>> recommended procedure in such a situation where the package is being
>> prepared for Bioconductor submission?
>>
>> An example of on

[Bioc-devel] 80% of man pages must have runnable examples (package with numerous Shiny apps)

[L Rutter]

Hello all:

I am planning to submit a package to Bioconductor and have one last
item from BiocCheck (error, warning, note) I have been unable to
resolve:

ERROR: At least 80% of man pages documenting exported objects must
have runnable examples. The following pages do not: plotLitreApp.Rd,
plotPCPApp.Rd, plotSMApp.Rd, plotVolcanoApp.Rd

I have 18 man pages (9 function-related, 8 data-related, and 1
package-related). Of these, 4 of the function-related man pages (the
ones listed in the ERROR) are Shiny applications of the following
format:

appDir <- system.file("shiny-examples", "plotLitreApp", package = "bigPint")
shiny::runApp(appDir, display.mode = "normal")

If I do not have \dontrun{} around these shiny app examples, then R
CMD check permanently halts on the "checking examples..." step. If I
do have \dontrun{} around these shiny app examples, then R CMD
BiocCheck gives me the error above. My question is: What is the
recommended procedure in such a situation where the package is being
prepared for Bioconductor submission?

An example of one script causing the error can be found at:
https://github.com/lrutter/bigPint/blob/master/R/plotLitreApp.R

Thank you for any advice!
Lindsay

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Re: [Bioc-devel] Manually editing man/.Rd files to pass BiocCheck

[L Rutter]

Thanks for the confirmation. I will post if I do find ways to resolve
this issue without manually editing the .Rd file.
On Mon, Nov 19, 2018 at 12:31 AM Michael Lawrence
 wrote:
>
> On Sun, Nov 18, 2018 at 9:16 PM L Rutter  wrote:
> >
> > Hello all:
> >
> > I am preparing to submit a package to Bioconductor and have one note
> > from R CMD BiocCheck that I have been unable to resolve. The note I
> > receive is:
> >
> > NOTE: Consider multiples of 4 spaces for line indents, 40 lines(1%) are not.
> > First 6 lines:
> >   man/plotClusters.Rd:8   threshVal = 0.05, outDir = getwd(), colList = 
> > r...
> >   man/plotClusters.Rd:9   aggMethod = "ward.D", yAxisLabel = "Count", 
> > xAx...
> >   man/plotClusters.Rd:10   lineSize = 0.1, lineAlpha = 0.5, 
> > clusterAllDat...
> >   man/plotClusters.Rd:11   verbose = FALSE, saveFile = TRUE, vxAxis = 
> > FALSE,
> >   man/plotClusters.Rd:12   geneList = NULL)
> >   man/plotLitre.Rd:8   pointSize = 2, pointColor = "orange", xbins = 10,
> >
> > Lines 6-13 of man/plotClusters.Rd appear as follows:
> >
> > \usage{
> > plotClusters(data, dataMetrics = NULL, nC = 4, threshVar = "FDR",
> >   threshVal = 0.05, outDir = getwd(), colList = rainbow(nC),
> >   aggMethod = "ward.D", yAxisLabel = "Count", xAxisLabel = "Sample",
> >   lineSize = 0.1, lineAlpha = 0.5, clusterAllData = TRUE,
> >   verbose = FALSE, saveFile = TRUE, vxAxis = FALSE,
> >   geneList = NULL)
> > }
> >
> > In case the formatting of my post causes misconceptions, I will state
> > that Lines 8-12 above are indented two spaces (instead of the four
> > spaces they evidently should be, which the note catches). At the top
> > of man/plotClusters.Rd, I have the statement:
> >
> > % Generated by roxygen2: do not edit by hand
> > % Please edit documentation in R/plotClusters.R
> >
> > So, I tried to edit what I believe are the corresponding lines in
> > R/plotClusters.R, which appear as follows:
> >
> > plotClusters <- function(data, dataMetrics = NULL, nC = 4, threshVar="FDR",
> > threshVal=0.05, outDir=getwd(), colList = rainbow(nC),
> > aggMethod = "ward.D", yAxisLabel = "Count", xAxisLabel = "Sample",
> > lineSize = 0.1, lineAlpha = 0.5, clusterAllData = TRUE, verbose=FALSE,
> > saveFile = TRUE, vxAxis = FALSE, geneList = NULL){
> >
> > In case the formatting of my post causes misconceptions, I will state
> > that the last four lines above are indented FOUR spaces. I tried
> > deleting the man folder and rerunning devtools::document() on my
> > package to recreate the man folder, but this note persists and the
> > FOUR spaces in the .R file continue to be reduced to TWO spaces in the
> > .Rd file.
> >
> > I did manually edit the man/plotClusters.Rd file and added two more
> > spaces to the lines in question. After that, the note in BiocCheck was
> > resolved. My question is: Is it acceptable for me to manually edit the
> > man/.Rd file by manually adding two more spaces?
>
> Of course it's acceptable. Some developers write all of their Rd manually.
>
> > If not, is there a
> > way to solve this note?
> >
>
> There's probably a way to adjust how Roxygen formats its usage.
>
> > The R/plotClusters.R file causing the issues is accessible at:
> > https://raw.githubusercontent.com/lrutter/bigPint/master/R/plotClusters.R.
> >
> > Thank you for any input!...
> > Lindsay
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel

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[Bioc-devel] Manually editing man/.Rd files to pass BiocCheck

[L Rutter]

Hello all:

I am preparing to submit a package to Bioconductor and have one note
from R CMD BiocCheck that I have been unable to resolve. The note I
receive is:

NOTE: Consider multiples of 4 spaces for line indents, 40 lines(1%) are not.
First 6 lines:
  man/plotClusters.Rd:8   threshVal = 0.05, outDir = getwd(), colList = r...
  man/plotClusters.Rd:9   aggMethod = "ward.D", yAxisLabel = "Count", xAx...
  man/plotClusters.Rd:10   lineSize = 0.1, lineAlpha = 0.5, clusterAllDat...
  man/plotClusters.Rd:11   verbose = FALSE, saveFile = TRUE, vxAxis = FALSE,
  man/plotClusters.Rd:12   geneList = NULL)
  man/plotLitre.Rd:8   pointSize = 2, pointColor = "orange", xbins = 10,

Lines 6-13 of man/plotClusters.Rd appear as follows:

\usage{
plotClusters(data, dataMetrics = NULL, nC = 4, threshVar = "FDR",
  threshVal = 0.05, outDir = getwd(), colList = rainbow(nC),
  aggMethod = "ward.D", yAxisLabel = "Count", xAxisLabel = "Sample",
  lineSize = 0.1, lineAlpha = 0.5, clusterAllData = TRUE,
  verbose = FALSE, saveFile = TRUE, vxAxis = FALSE,
  geneList = NULL)
}

In case the formatting of my post causes misconceptions, I will state
that Lines 8-12 above are indented two spaces (instead of the four
spaces they evidently should be, which the note catches). At the top
of man/plotClusters.Rd, I have the statement:

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plotClusters.R

So, I tried to edit what I believe are the corresponding lines in
R/plotClusters.R, which appear as follows:

plotClusters <- function(data, dataMetrics = NULL, nC = 4, threshVar="FDR",
threshVal=0.05, outDir=getwd(), colList = rainbow(nC),
aggMethod = "ward.D", yAxisLabel = "Count", xAxisLabel = "Sample",
lineSize = 0.1, lineAlpha = 0.5, clusterAllData = TRUE, verbose=FALSE,
saveFile = TRUE, vxAxis = FALSE, geneList = NULL){

In case the formatting of my post causes misconceptions, I will state
that the last four lines above are indented FOUR spaces. I tried
deleting the man folder and rerunning devtools::document() on my
package to recreate the man folder, but this note persists and the
FOUR spaces in the .R file continue to be reduced to TWO spaces in the
.Rd file.

I did manually edit the man/plotClusters.Rd file and added two more
spaces to the lines in question. After that, the note in BiocCheck was
resolved. My question is: Is it acceptable for me to manually edit the
man/.Rd file by manually adding two more spaces? If not, is there a
way to solve this note?

The R/plotClusters.R file causing the issues is accessible at:
https://raw.githubusercontent.com/lrutter/bigPint/master/R/plotClusters.R.

Thank you for any input!...
Lindsay

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