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(inactive) PeCorA #1836

Closed demar01 closed 3 years ago

demar01 commented 3 years ago

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

Confirm the following by editing each check box to '[x]'

I am familiar with the essential aspects of Bioconductor software management, including:

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

bioc-issue-bot commented 3 years ago

Hi @demar01

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: PeCorA
Title: Peptide correlation analysis
Version: 0.99.0
Authors@R: c(
    person("Maria", "Dermit",
    email = "maria.dermit@qmul.ac.uk",
    comment = c(ORCID = "0000-0002-6287-8367"),
    role = c("aut", "cre")),
    person("Jesse", "Meyer",
        email = "jesmeyer@mcw.edu",
        comment = c(ORCID = "0000-0003-2753-3926"),
        role = "aut"))
Description: The PeCorA package detects quantitative disagreements between 
    peptides mapped to the same protein. It initially format the output of 
    proteomics processing tools such as MaxQuant into an adecuate format for
    the PeCorA algorithm. This algorithm fits linear models to assess whether
    the slope of a peptide’s change across treatment groups differs from the 
    slope of all other peptides assigned to the same protein. Finally, 
    visualization tools are provided to explore resulting discordant peptides,
    including boxplots.
License: GPL-2
Encoding: UTF-8
LazyData: true
Packaged: 2020-10-14 13:01:20 BST; Maria Dermit
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Depends: 
    R (>= 4.1), reshape, ggplot2
Imports: 
    utils,
    stats,
    dplyr,
    magrittr,
    rmarkdown,
    assertthat
Suggests: 
    testthat,
    BiocStyle,
    knitr,
biocViews: DataImport,Proteomics, MassSpectrometry   
VignetteBuilder: knitr
URL: https://github.com/demar01/PeCorA
BugReports: https://github.com/demar01/PeCorA/issues
bioc-issue-bot commented 3 years ago

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/PeCorA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

demar01 commented 3 years ago

Hello BiocCheck FAILED because

I have subscribed to bioc-devel mailing list.

Do you know why this is failing?

Thanks

mtmorgan commented 3 years ago

When you subscribe, the mailing list sends a confirmation email that you need to reply to. This often ends in a spam mail folder. The address you subscribe with has to match the address of the cre in the DESCRIPTION file. Increment your package version (to 0.99.1) and push a change to the 'master' branch of your git.bioconductor.org repository.

demar01 commented 3 years ago
mtmorgan commented 3 years ago

...looks like 0.99.1 wasn't pushed to git.bioconductor.org?

demar01 commented 3 years ago

It should be pushed now. Can you confirm?

vjcitn commented 3 years ago

It looks like it was pushed to your github repo. But you need to push the corrected version to git.bioconductor.org. If the documentation is not clear on how to do this please respond to this issue. Probably you need to do a clone of git@git.bioconductor.org:packages/PeCorA (which will have 0.99.0 at this moment), make corrections, git add/commit/push

vjcitn commented 3 years ago

and be sure to change the DESCRIPTION In the git.bioconductor.org:packages/PeCorA repo to have 0.99.x with x > 0 and increasing every time you make a new change.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 08cd51ed383c35179a2d2a3061121417f71d3628

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/PeCorA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

demar01 commented 3 years ago

I fixed the gitignore but it is still giving an error because of it apparently. I cannot see what is wrong

vjcitn commented 3 years ago

Here's what I see at the current pull of 

stvjc@stvjc-XPS-13-9300:~/SUBMISSIONS/PeCorA/vignettes$ git remote -v
origin  git@git.bioconductor.org:packages/PeCorA (fetch)
origin  git@git.bioconductor.org:packages/PeCorA (push)

total 72
drwxrwxr-x  9 stvjc stvjc  4096 Jan  7 08:24 .
-rw-rw-r--  1 stvjc stvjc  1406 Jan  7 08:24 DESCRIPTION
drwxrwxr-x  8 stvjc stvjc  4096 Jan  7 08:24 .git
-rw-rw-r--  1 stvjc stvjc   169 Jan  7 08:24 .gitignore
drwxrwxr-x  3 stvjc stvjc  4096 Jan  6 07:23 man
drwxrwxr-x  3 stvjc stvjc  4096 Jan  6 06:53 inst
drwxrwxr-x  3 stvjc stvjc  4096 Jan  6 06:53 tests
drwxrwxr-x  2 stvjc stvjc  4096 Jan  6 06:53 vignettes
drwxrwxr-x  2 stvjc stvjc  4096 Jan  6 06:53 data
-rw-rw-r--  1 stvjc stvjc 10244 Jan  6 06:53 .DS_Store
-rw-rw-r--  1 stvjc stvjc   571 Jan  6 06:53 NAMESPACE
-rw-rw-r--  1 stvjc stvjc   356 Jan  6 06:53 PeCorA.Rproj
drwxrwxr-x  2 stvjc stvjc  4096 Jan  6 06:53 R
-rw-rw-r--  1 stvjc stvjc    48 Jan  6 06:53 .Rbuildignore
-rw-rw-r--  1 stvjc stvjc  2663 Jan  6 06:53 README.md
drwxrwxr-x 10 stvjc stvjc  4096 Jan  6 06:53 ..
stvjc@stvjc-XPS-13-9300:~/SUBMISSIONS/PeCorA$ cd vig*
stvjc@stvjc-XPS-13-9300:~/SUBMISSIONS/PeCorA/vignettes$ ls -tla
total 1100
drwxrwxr-x 9 stvjc stvjc    4096 Jan  7 08:24 ..
-rw-rw-r-- 1 stvjc stvjc 1094644 Jan  6 06:53 PeCorA.html
drwxrwxr-x 2 stvjc stvjc    4096 Jan  6 06:53 .
-rw-rw-r-- 1 stvjc stvjc    6148 Jan  6 06:53 .DS_Store
-rw-rw-r-- 1 stvjc stvjc    1225 Jan  6 06:53 PeCorA.bib
-rw-rw-r-- 1 stvjc stvjc    4633 Jan  6 06:53 PeCorA.Rmd

Note the .DS_Store files ... you'll have to remove them from your .git repo, along with any other files noted in messages like the following, seen at http://bioconductor.org/spb_reports/PeCorA_buildreport_20210106071755.html

The error message:

    * ERROR: System Files found that should not be git tracked:
        PeCorA.Rproj
        man/.Rapp.history
        .DS_Store
        inst/.DS_Store
        R/.DS_Store
        tests/.DS_Store
        tests/testthat/.DS_Store
        vignettes/.DS_Store
demar01 commented 3 years ago

DS are removed and +1 version is added and pushed to git.bioconductor.org.

I cannot see changes in the build report?

Thanks

mtmorgan commented 3 years ago

I'm not exactly sure what the problem is; perhaps @lshep can help / trigger a new build. It might be that the version bump is only recognized if it is in the 'last' commit. You could test this hypothesis by bumping to 0.99.2...

lshep commented 3 years ago

From the looks of it, you committed the DESCRIPTION version bump only to github and not to bioconductor git.bioconductor.org. You will need to push to upstream remote as well.

vjcitn commented 3 years ago

I confirm this. On my checkout pf PeCorA from git.bioconductor.org

stvjc@stvjc-XPS-13-9300:~/SUBMISSIONS/PeCorA$ git remote -v
origin  git@git.bioconductor.org:packages/PeCorA (fetch)
origin  git@git.bioconductor.org:packages/PeCorA (push)
stvjc@stvjc-XPS-13-9300:~/SUBMISSIONS/PeCorA$ git pull
Already up to date.
stvjc@stvjc-XPS-13-9300:~/SUBMISSIONS/PeCorA$ ls -tla
total 72
drwxrwxr-x  8 stvjc stvjc  4096 Jan 11 18:56 .git
drwxrwxr-x  9 stvjc stvjc  4096 Jan 11 18:56 .
-rw-rw-r--  1 stvjc stvjc  1406 Jan  7 08:24 DESCRIPTION
-rw-rw-r--  1 stvjc stvjc   169 Jan  7 08:24 .gitignore
drwxrwxr-x  3 stvjc stvjc  4096 Jan  6 07:23 man
drwxrwxr-x  3 stvjc stvjc  4096 Jan  6 06:53 inst
drwxrwxr-x  3 stvjc stvjc  4096 Jan  6 06:53 tests
drwxrwxr-x  2 stvjc stvjc  4096 Jan  6 06:53 vignettes
drwxrwxr-x  2 stvjc stvjc  4096 Jan  6 06:53 data
-rw-rw-r--  1 stvjc stvjc 10244 Jan  6 06:53 .DS_Store

Note the .DS_Store is still present. An explicit git push 

git push git@git.bioconductor.org:packages/PeCorA

might work for you and illustrate the task very clearly.

demar01 commented 3 years ago

git push git@git.bioconductor.org:packages/PeCorA

I get

git@git.bioconductor.org: Permission denied (publickey). fatal: Could not read from remote repository

lshep commented 3 years ago

Are you using a different computer because you were able to push earlier last week? @nturaga

demar01 commented 3 years ago

Yes, I am. Would easiest be to create a new issue?

vjcitn commented 3 years ago

No, you do not have to create a new issue. Look at part 8 of https://www.bioconductor.org/developers/how-to/git/faq/

You would use BiocCredentials to provide the key generated on your new computer.

mtmorgan commented 3 years ago

Also if you add you new public key to github, so that it appears at https://github.com/demar01.keys, it will be copied to the credentials app; I'm not sure about the frequency of the copy, but it would likely be hourly??

demar01 commented 3 years ago

Ok, I added a key and updated the Description file now

vjcitn commented 3 years ago

Let us know when it looks as if your push to the bioconductor git repo has succeeded. I see no change in my checkout.

lshep commented 3 years ago

I can confirm this too. There are no changes pushed to the bioconductor git repo. You need to push your change with a valid version bump to git.bioconductor.org every time you want changes to propagate. If you are on a new computer you may want to set up remotes as originally documented when submitted.

demar01 commented 3 years ago

Thanks. It should now be pushed

lshep commented 3 years ago

It is still not pushed to upstream for git.bioconductor.org. The last pushed changes were from January 6th 

commit e7a2bd084b36c62e29299a9a6173e3f5bbe2ae9a (HEAD -> master, origin/master, origin/HEAD)
Author: Maria <maria.dermit@qmul.ac.uk>
Date:   Wed Jan 6 12:52:34 2021 +0000

    Modifying gitignore

commit 08cd51ed383c35179a2d2a3061121417f71d3628
Author: Maria <maria.dermit@qmul.ac.uk>
Date:   Wed Jan 6 12:04:01 2021 +0000

    Adding version

Again please check your remotes and make sure you are pushing to git push upstream master as documented and outlined here or doing as @vjcitn suggested with git push git@git.bioconductor.org:packages/PeCorA

demar01 commented 3 years ago

I cannot see what I am missing. Following this: https://bioconductor.org/developers/how-to/git/new-package-workflow/

However, on git push git@git.bioconductor.org:packages/PeCorA fatal: Could not read from remote repository.

git push origin master Everything up-to-date

mtmorgan commented 3 years ago

The BiocCredentials app knows about the first two keys at https://github.com/demar01.keys. From http://bioconductor.org/developers/how-to/git/faq/ what does

ssh -T git@git.bioconductor.org

report? If it doesn't include PeCorA, try

ssh -Tv git@git.bioconductor.org

It should report debugging information, including keys that it is trying to use. Also the key and public key on your system need to have particular permissions; mine is

$ ls -al ~/.ssh/*
drwx------  11 ma38727  735121457    352 Dec 21 10:55 .
-rw-------@ 1 ma38727  735121457  951 Dec  1  2019 /Users/ma38727/.ssh/id_rsa
-rw-------@ 1 ma38727  735121457  226 Dec  1  2019 /Users/ma38727/.ssh/id_rsa.pub

Note also that your github is using https; you likely run into the problems you are seeing with bioconductor.org if you were to replace the remote with the ssh remote

git remote remove origin
git remote add origin git@github.com:demar01/PeCorA.git
demar01 commented 3 years ago

Hi Martin

I added the 3rd key to my Bioconductor Git Credentials more than one hour ago, but ssh -T git@git.bioconductor.org

still reports Permission denied (publickey).

I replaced the remote to ssh remote with git remote remove origin git remote add origin git@github.com:demar01/PeCorA.git

Permission denied (publickey).

mtmorgan commented 3 years ago

So I guess you now have

$ git remote -v
origin git@github.com:demar01/PeCorA.git (fetch)
origin git@github.com:demar01/PeCorA.git (push)
upstream git@git.bioconductor.org:packages/PeCorA.git (fetch)
upstream git@git.bioconductor.org:packages/PeCorA.git (push)

You say that you see Permission denied, but do you see it when now pushing to GitHub (git push origin)? This would indicate that the problem is with your ssh keys.

The third key was picked up by our system at Mon Jan 25 08:27:53 2021 -0500.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0547beccab5b528fc5049f83f06b93ee0684b2f9

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, skipped". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/PeCorA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

mtmorgan commented 3 years ago

Looks like there was a successful push! Glad that we worked through this.

demar01 commented 3 years ago

Yes, indeed. There is a problem with the build, but at least I can make and push changes back.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: c35714209954f32a366cf5e51a87cbcf255032de

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/PeCorA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5f58c3fadf212427fb38a01131b45aa0b924d99f

bioc-issue-bot commented 3 years ago

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/PeCorA to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

mtmorgan commented 3 years ago

11 February, 2021

Thanks for your patience

Warnings on the build report

DESCRIPTION, NAMESPACE

vignettes

R (comments on specific lines usually apply throughtout code)

tests

demar01 commented 3 years ago

Hi Martin

Thanks so much for your feedback. I will address these changes accordingly.

mtmorgan commented 3 years ago

please update your submission

vjcitn commented 3 years ago

@demar01 per your email to me of 22 March, this package will be labeled inactive. Open this issue when you wish to resume development of the Bioconductor contribution.

bioc-issue-bot commented 3 years ago

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for your interest in Bioconductor.