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(inactive) protlocassign #2541

Closed mooredf22 closed 9 months ago

mooredf22 commented 2 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]'

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Comments: The "protlocassign" package presents R functions that take use mass spectrometry data from serial fractionation experiments to proportionally assign proteins to possibly multiple residences in subcellular organelles. The package includes seven vignettes that describe the methods in detail. There is also an accompanying manuscript describing the methods; a revision is under review.

Here are my comments on BiocCheck notes:

1 "Consider adding these automatically suggested biocViews: RNASeq"
This is not relevant to this proteomics-related package

2 "Recommended function length <= 50 lines."
Many of the functions that are longer than 50 lines create complex plots. There is no natural way to break them up into smaller components.

3 "Consider adding runnable examples to the following man pages which document exported objects:"
Most of the functions that are not service functions include runnable examples. The small number that are not are explained and illustrated in detail in the accompanying vignettes; setting up runnable examples for these functions withing the help files would be cumbersome.

4 "Consider shorter lines; 235 lines (3%) are > 80 characters long."
All lines in the functions are shorter than 80 characters. Much of the explanatory text in the vignettes are longer than 80 characters, and we believe that that text is readable and clear in its current form.

5 "Consider multiples of 4 spaces for line indents, 1133 lines(15%) are not."
We have chosen to use descriptive variable names in our code in order to clearly link them to the to the concepts explained in the vignettes and in the accompanying manuscript. As a consequence, some of these variable names are rather long, which makes it difficult to adhere strictly to the "multiples of 4 spaces" suggestion. We have chosen indentation amounts to be as readable as possible and also conform to the limit of 80 characters per line.

6 "Cannot determine whether maintainer is subscribed to the bioc-devel mailing list (requires admin credentials).\nSubscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel" I am listed as the maintainer and I have subscribed to this mailing list.

bioc-issue-bot commented 1 year ago

Additional Package has been approved for building.

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.

bioc-issue-bot commented 1 year 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". 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/protlocassigndoc to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

mooredf22 commented 1 year ago

Just so you know, I am still working through the issues.

lgatto commented 1 year ago

Thanks @mooredf22.

I would suggest to focus on protlocassign and then, once it's ready to be accepted, provide comment for protlocassigndoc.

mooredf22 commented 1 year ago

Yes, thanks, that plan will help.

On Mon, Dec 5, 2022 at 11:48 AM Laurent Gatto @.***> wrote:

Thanks @mooredf22 https://github.com/mooredf22.

I would suggest to focus on protlocassign and then, once it's ready to be accepted, provide comment for protlocassigndoc.

— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/2541#issuecomment-1337713853, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALOEZWIADQ7YP7YOTFN74HLWLYME5ANCNFSM5POB2K3Q . You are receiving this because you were mentioned.Message ID: @.***>

lgatto commented 1 year ago

And in the meantime, if you have any questions, feel free to ask here or on the bioc-devel mailing list.

bioc-issue-bot commented 1 year ago

Received a valid push on git.bioconductor.org; starting a build for commit id: cbae12b4f1f2b2ba2ebeb52dc91e83d2f918f9cb

bioc-issue-bot commented 1 year 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/protlocassigndoc to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 1 year ago

Additional Package has been approved for building.

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.

bioc-issue-bot commented 1 year 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/protlocassigndoc to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

lgatto commented 1 year ago

Hi @mooredf22 - do you plan to submit an update, or can the issue be closed?

mooredf22 commented 1 year ago

Thank you so much for asking, I have set aside time now to continue the "protlocassign" project. The main remaining task is integration of the "pRoloc" protein data structure procedures with those in "protlocassign", and this is going well. Another change I will make regards the documentation. Previously we were trying to integrate "protlocassign" with "protlocassigndoc", the latter of which is only documentation. I plan to leave "protlocassigndoc" completely out of bioconductor, and simply refer to the users to the github package. The more compact vignette in "protlocassign" is sufficient for the bioconductor package. This will make everything much simpler.

Currently, I am working on the version of the package on my local computer, but I will upload it to github soon. From there I will send it over to Bioconductor for automatic validation, although someone at Bioconductor may have to alter a setting to allow me to do this. (A while back I tried to push it to Bioconductor using the usual procedure, and it didn't work.)

Dirk

On Fri, Jul 14, 2023 at 11:02 AM Laurent Gatto @.***> wrote:

Hi @mooredf22 https://github.com/mooredf22 - do you plan to submit an update, or can the issue be closed?

— Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/2541#issuecomment-1635992544, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALOEZWK5ARC4EMTVGGVZFA3XQFNQTANCNFSM5POB2K3Q . You are receiving this because you were mentioned.Message ID: @.***>

lgatto commented 1 year ago

OK, thanks for letting me know.

mooredf22 commented 1 year ago

I have put an updated version of the "protocassign" package on GitHub: https://github.com/mooredf22/protlocassign

and followed the instructions in Chapter 21 of the Bioconductor package development webpage, specifically,

push to Bioc (upstream remote at git@git.bioconductor.org)

git push upstream main:devel

but received a message that it failed and that I must ensure that I have correct access rights.

This procedure used to work fine for me, but much time has passed since I last submitted an update. Perhaps a Bioconductor administrator has to restore permission for me to update my package?

lshep commented 1 year ago

No restore from us should be necessary. Are you using the same computer and have the same ssh keys as before? You might need to update keys on the BiocCredentials account. Please show the full command and output if issue persists.

lshep commented 9 months ago

We haven't heard anything else and there have been no more changes. We will close this for inactivity. When you are ready to push changes, leave a message here to reopen.

bioc-issue-bot commented 9 months 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.