(inactive) cytofkit2

[raman91]

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

• Repository: https://github.com/JinmiaoChenLab/cytofkit2

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

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• [x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

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

[bioc-issue-bot]

Dear @raman91,

The package version number, '1.99.0', does not start with 0. Expecting format: '0.99.z' for new packages. Starting with non-zero x of 'x.y.z' format is generally only allowed if the package has been pre-released.

We recommend fixing the version number. See Bioconductor version numbers

[bioc-issue-bot]

Hi @raman91

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: cytofkit2
Type: Package
Title: cytofkit: an integrated mass cytometry data analysis pipeline
Version: 1.99.0
Date: 2018-01-19
Author: Jinmiao Chen, Hao Chen, Matthew Myint
Description: An integrated mass cytometry data analysis pipeline that enables
    simultaneous illustration of cellular diversity and progression.
License: Artistic-2.0
Maintainer: Jinmiao Chen <Chen_Jinmiao@immunol.a-star.edu.sg>, Matthew Myint <a0124008@u.nus.edu>
URL: https://github.com/JinmiaoChenLab/cytofkit
BugReports: https://github.com/JinmiaoChenLab/cytofkit/issues
biocViews: FlowCytometry, GUI, CellBiology, Clustering,
    DimensionReduction, BiomedicalInformatics
Depends:
    R (>= 3.4.0), ggplot2, plyr
VignetteBuilder: knitr
Suggests:
    knitr,
    RUnit,
    testthat,
    BiocGenerics
Imports:
    grDevices,
    plotly,
    shinyjs,
    DT,
    shinydashboard,
    shinyalert,
    shinyWidgets,
    data.table,
    graphics,
    utils,
    stats,
    Rtsne,
    e1071,
    flowCore,
    gplots,
    colourpicker,
    VGAM,
    reshape2,
    ggrepel,
    shiny,
    shinyFiles,
    vegan,
    Biobase,
    doParallel,
    parallel,
    pdist,
    methods,
    destiny,
    FlowSOM(>= 1.4.0),
    igraph(>= 1.1.2),
    RANN(>= 2.5),
    Rcpp (>= 0.12.0)
Remotes:
    bioc::BiocGenerics,
    bioc::flowCore,
    bioc::Biobase,
    bioc::destiny,
    bioc::FlowSOM   
LinkingTo: Rcpp
RoxygenNote: 6.1.1

[mtmorgan]

Can you remind me why this package was removed from an earlier version of Bioconductor?

[mtmorgan]

But I mean your package was previously in Bioconductor http://bioconductor.org/about/removed-packages/ but was removed at version 3.9. Why was it removed?

[raman91]

This is a totally different package from the one removed earlier

[mtmorgan]

I'm asking why the previous version was removed? Were you not responsive as a maintainer?

[raman91]

Due to limited manpower in the past, we were not responsive as a maintainer. But now we will be responsive.

[raman91]

Is it possible to submit cytofkit (previous version) again along with the new one? Thank you

[mtmorgan]

cytofkit2 is presumably a 'new, improved' version of cytofkit, and it would not be appropriate to also add the old version -- users of the old version can obtain it from other sources, e.g., a github repository you maintain, or an old release of Bioconductor.

[raman91]

Ok, noted. Thank you Is it possible to add cytofkit2 only to Bioconductor?

[mtmorgan]

cytofkit2 will go through the review process. This can take several weeks.

[raman91]

Ok noted. Thank you for the information

[raman91]

Awaiting the review process. We hope that cytofkit2 can be useful to the research community. Thanks

[bioc-issue-bot]

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]

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: "skipped, ERROR". 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/cytofkit2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

Bioconductor package cytofkit was removed in Bioconductor 3.9. Your package can only rely on dependencies that are actively in CRAN or Bioconductor. Please update the package to not use cytofkit

[raman91]

Hi Ishep, can we add cytofkit first which was removed from bioconductor? cytofkit2 relies on cytofkit. Thanks

[raman91]

cytofkit2 is presumably a 'new, improved' version of cytofkit, and it would not be appropriate to also add the old version -- users of the old version can obtain it from other sources, e.g., a github repository you maintain, or an old release of Bioconductor.

Hi @mtmorgan, cytofkit2 relies on cytofkit. So, cytofkit should be added to Bioconductor for cytofkit2 to work. Thanks

[mtmorgan]

I see you opened an issue for a new version of cytofkit https://github.com/Bioconductor/Contributions/issues/1821#issuecomment-747276066 but I indicated that is not appropriate https://github.com/Bioconductor/Contributions/issues/1792#issuecomment-734237216 . I suggest you revise cytofkit2 to be a stand-alone version of your updated package. As mentioned, users wanting access to the package that has previously been removed from Bioconductor can install it via some other means.

[raman91]

Can we submit cytofkit again to BioConductor?

[lshep]

Please don't ignore our previous comments. It is not recommended and not appropriate to add cytofkit back into Bioconductor. Again, we recommend adding any functionality from the previous package into this newly submitted package so it can work stand-alone from the original cytofkit.

[lshep]

Do you plan on updating cytofkit2?

[raman91]

Yes, we are updating cytofkit2 at the moment.

[lshep]

I'm closing this issue for inactivity for now. When you are done updating cytofkit2 and are ready for review please tag me on this issue to reopen.

[bioc-issue-bot]

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.

[raman91]

Hi @lshep , can we reopen the issue please? We are done with updating cytofkit2. Thanks

[lshep]

The issue is now reopened and the review process will continue. Please do a version bump to trigger a new build report with the updated changes.

[raman91]

Hi @lshep, we have done version bump for the updated package

[lshep]

Did you remember to push to git.bioconductor.org to trigger a new build report? You may need to set up your credentials and remotes. Credentials document and setting up remotes.

[raman91]

Hi @lshep, Bioconductor Git Credentials is giving me a message : Server Error (500) Please advise. Thanks

[lshep]

Please ask git credential errors on the bioc-devel@r-project.org mailing list. Please include as much information as possible.

[raman91]

Ok, thank you

[lshep]

@nturaga responded to the question on the bioc-devel mailing list. We are having trouble reproducing. Could you please respond back to his email on what url you are trying to use that is causing a 500 error. You have tried going to the account activation url: https://git.bioconductor.org/BiocCredentials/account_activation/

[raman91]

Hi @lshep, i will respond to his email and take necessary action on this. Thank you

[raman91]

We want to add the github repository: https://github.com/raman91/cytofkit2 to Bioconductor. This repository doesn't use cytofkit

[lshep]

You need to push your updated code to git.bioconductor.org to trigger a new build so a review will take place. we have said this numerous times. Nitesh responded to the bioc-devel mailing list question regarding access. A link to the response is found here

[raman91]

Hi @lshep , we have done the needful. Please let us know if more action is required by us. Thank you

[lshep]

You need to push to git.bioconductor.org with a valid version bump to trigger a new build here for review. That has not been done. The last change in git.bioconductor.org was pushed Nov 24. Please see the workflow here . Until that is complete I will not review the package.

[raman91]

Hi @lshep, we have done version bump. Is it successful? Thanks

[lshep]

@raman91 No it is not. Please show the commands you are trying to push to git.bioconductor.org. You need to be pushing to the upstream remote that is linked with git.bioconductor.org in addition to pushing to the origin location that is linked to your github.

[raman91]

Thanks @lshep. I have done version bump in DESCRIPTION file from 1.99.0 (on Nov 24) to 1.99.1 (today)

I am running the below commands:

git remote -v origin https://github.com/JinmiaoChenLab/cytofkit2 (fetch) origin https://github.com/JinmiaoChenLab/cytofkit2 (push)

git remote add upstream https://github.com/JinmiaoChenLab/cytofkit2 origin https://github.com/JinmiaoChenLab/cytofkit2 (fetch) origin https://github.com/JinmiaoChenLab/cytofkit2 (push) upstream https://github.com/JinmiaoChenLab/cytofkit2 (fetch) upstream https://github.com/JinmiaoChenLab/cytofkit2 (push)

git fetch --all

git merge upstream/master

git merge origin/master

git add DESCRIPTION

git commit

git push upstream master

git push origin master

[lshep]

when you added the upstream remote you added a second remote to your github repository.
git remote add upstream https://github.com/JinmiaoChenLab/cytofkit2 You need to add to git.bioconductor.org. It is documented as step 2 in the documentation I have sent you several times git remote add upstream git@git.bioconductor.org:packages/<YOUR-REPOSITORY-NAME>.git so in your case git remote add upstream git@git.bioconductor.org:packages/cytofkit2.git

[raman91]

Sure, thanks but when i run: git remote add upstream git@git.bioconductor.org:packages/cytofkit2.git

I get an error message:

git@git.bioconductor.org: Permission denied (publickey) 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

[lshep]

You can add additional keys in the git credentials app.

[raman91]

Yes, i have added 3 keys in the git credentials app but still getting the same error

[lshep]

When I look at your git credentials account there is only 1 ssh key listed. Please log in and make sure you add a key and save at the bottom of the page after you add.

[lshep]

I realized your github id was not active in the credentials account. It is now recognized your keys you have associated with your github id. Could you please try git push to git.bioconductor.org again?

[raman91]

Ok sure @lshep , i tried again but still getting the same message :

git@git.bioconductor.org: Permission denied (publickey) 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

[lshep]

@nturaga is there a delay for picking up keys?

[nturaga]

Hi Raman,

If you have questions about the key being wrong, just add it to your BiocCredentials account. This is the easiest way.

Nitesh

From: lshep @.> Reply-To: Bioconductor/Contributions @.> Date: Friday, April 2, 2021 at 1:53 PM To: Bioconductor/Contributions @.> Cc: Nitesh Turaga @.>, Mention @.***> Subject: Re: [Bioconductor/Contributions] cytofkit2 (#1792)

@nturagahttps://github.com/nturaga is there a delay for picking up keys?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/1792#issuecomment-812639777, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAU6QSYSKXQINIDJFKZIDPTTGYAAJANCNFSM4UAQC27A.