dpelegri commented 3 years ago

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

Repository: https://github.com/isglobal-brge/methylclockData

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bioc-issue-bot commented 3 years ago

Hi @dpelegri

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: methylclockData
Title: Data for methylclock package
Description: Collection of 9 datasets, andrews and bakulski cord blood,
    blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood,
    cord blood gse68456, gervin and lyle cord blood, guintivano dlpfc and
    saliva gse48472" downloaded from [meffil](https://github.com/perishky/meffil/) 
    used to estimate cell counts using EEAA method
Version: 0.99.0
Author: Juan R Gonzalez
Maintainer: Juan R Gonzalez <juanr.gonzalez@isglobal.org>
biocViews: 
  GEO,
  ExperimentHub,
  Tissue
URL: https://github.com/isglobal-brge/methylclockData
Depends: 
  Biobase, 
  ExperimentHubData,
  ExperimentHub
License: MIT + file LICENSE
NeedsCompilation: no

bioc-issue-bot commented 3 years ago

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LiNk-NY commented 3 years ago

Hi @dpelegri ,

Do you intend to also submit methylclock to Bioconductor? It seems like you advertise it as such without going through the review process first. https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btaa825/5909987

dpelegri commented 3 years ago

Hi Marcel,

Yes, we want to send the methylclock package to Bioconductor.

Sorry, it's true that we advertise it as such without going through the review process, the package initially depended on meffil library (https://github.com/perishky/meffil) that is neither in r-cran nor in bioconductor and we had problems to meet the bioconductor requirements, we needed to publish the paper and we did not solve it in time.

Dolors

LiNk-NY commented 3 years ago

Hi Dolors, @dpelegri

Having a publication like that is quite misleading. It's unfortunate that the reviewers did not catch that. Any Bioconductor user wanting to use your package would do BiocManager::install("methylclock") and of course it would not work.

Please see the methylclockData review below.

We are looking forward to the submission of methylclock.

Best, Marcel

methylclockData #1780

DESCRIPTION

Include a BugReports field.
Update the biocViews field so that it matches the tree in https://www.bioconductor.org/packages/release/BiocViews.html
Spell out the acronym before using it in the Description field
Because you don't have any code in the package, avoid using the Depends field for your dependencies. Use the Imports field.
Add utils and ExperimentHub to your Imports

NAMESPACE

Looks good

vignette

Show how the user is supposed to download the data from ExperimentHub

(Enhancement)

Ideally, you'd have a function where the user can see a table of the data resources available along with the text data that you provide in the "Cell counts" section.
This table would show the user what kind of cells are available in each dataset.
Your main function could then provide users with the data they've selected.

R/zzz.R

Avoid library calls in package code and use utils::read.csv etc.

LiNk-NY commented 3 years ago

Issue closed due to inactivity

dpelegri commented 3 years ago

Hello,

I apologise for not solve the different points before It is possible to reopen the thread or I have to start the process again?

Sorry,

Dolors Pelegrí

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: df5b9643f73692ff3b8fb498a8351f2e4805a635

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: a508339ea7056b9398356719eaa6ed9132e0f356

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/methylclockData 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: db0b50640171a1fe3c8c412ea48b7aa6fe3329c9

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/methylclockData 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: 7c998f3d23554f4d7d4e30c44a4ce9a0541b2b19

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/methylclockData 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: 19bef18b2363f1aca76f9f3802a843d6a3d1ad0b

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/methylclockData 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: dc97e2dd610045acf0a55b060aca380d5cab1a33

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.

Congratulations! The package built without errors or warnings on all platforms.

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dpelegri commented 3 years ago

It is possible to continue with the review process?.
I have applied the proposed changes.

Thanks

Dolors

LiNk-NY commented 3 years ago

Hi Dolors, @dpelegri Sorry for the late response. I will re-open the issue and have a look at the changes. Thank you!

LiNk-NY commented 3 years ago

Hi Dolors, @dpelegri In order for the review to continue, you should respond to the review line by line. Thank you! -Marcel

dpelegri commented 3 years ago

Hi Marcel @LiNk-NY,

Thanks for your time and review on the methylclockData package! Following are my point-to-point reply:

DESCRIPTION

Include a BugReports field. --> Added

Update the biocViews field so that it matches the tree in https://www.bioconductor.org/packages/release/BiocViews.html --> Modified with : ExperimentData, SpecimenSource, Tissue, OrganismData, Homo_sapiens_Data

Spell out the acronym before using it in the Description field --> Added the spell out : Extrinsic epigenetic age acceleration (EEAA)

Because you don't have any code in the package, avoid using the Depends field for your dependencies. Use the Imports field. Add utils and ExperimentHub to your Imports --> Added and removed Depends field from Description

NAMESPACE

Looks good

vignette

Show how the user is supposed to download the data from ExperimentHub --> Added in vignette

(Enhancement)

Ideally, you'd have a function where the user can see a table of the data resources available along with the text data that you provide in the "Cell counts" section. This table would show the user what kind of cells are available in each dataset. Your main function could then provide users with the data they've selected.

R/zzz.R

Avoid library calls in package code and use utils::read.csv etc. --> Removed

LiNk-NY commented 3 years ago

Hi Dolors, @dpelegri Thanks for making those changes. I will accept the package. Please address these two minor NOTES either before inclusion to Bioconductor or right after.

* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
### This can be resolved by adding a period at the end of the `Description` field text.
* checking Rd files ... NOTE
prepare_Rd: references.Rd:40-42: Dropping empty section \details
prepare_Rd: references.Rd:43-45: Dropping empty section \source
prepare_Rd: references.Rd:46-48: Dropping empty section \references
### These should be removed if empty

I would also encourage you to check out the results of BiocCheck::BiocCheck() to address Bioconductor-specific concerns such as including a NEWS file and expanding the Description field in the DESCRIPTION file.

Thank you for your contribution. Best regards, Marcel

bioc-issue-bot commented 3 years ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

dpelegri commented 3 years ago

Hi @LiNk-NY,

Thanks a lot for your help.

Dolors

mtmorgan commented 3 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/dpelegri.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ https://bioconductor.org/developers/how-to/git/sync-existing-repositories/

to keep your GitHub and Bioconductor repositories in sync.

Your package will be included in the next nigthly 'devel' build (check-out from git at about 6 pm Eastern; build completion around 2pm Eastern the next day) at

https://bioconductor.org/checkResults/

(Builds sometimes fail, so ensure that the date stamps on the main landing page are consistent with the addition of your package). Once the package builds successfully, you package will be available for download in the 'Devel' version of Bioconductor using BiocManager::install("methylclockData"). The package 'landing page' will be created at

https://bioconductor.org/packages/methylclockData

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