Jfortin1 commented 2 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/Jfortin1/Rbwa

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bioc-issue-bot commented 2 years ago

Hi @Jfortin1

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: Rbwa
Version: 0.99.0
Date: 2022-01-21
Title: R wrapper for BWA-backtrack and BWA-MEM aligners
Authors@R: c(
    person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre")))
Depends:
    R (>= 4.1)
Suggests:
    testthat,
    BiocStyle,
    knitr,
    rmarkdown
SystemRequirements: GNU make
Description: Provides an R wrapper for BWA alignment algorithms.
    Both BWA-backtrack and BWA-MEM are available.
    Convenience function to build a BWA index from a reference genome
    is also provided. Currently not supported for Windows machines.
License: GPL-3
URL: https://github.com/Jfortin1/Rbwa
BugReports: https://github.com/Jfortin1/Rbwa/issues
biocViews: Sequencing, Alignment
VignetteBuilder: knitr
RoxygenNote: 7.1.2
OS_type: unix

bioc-issue-bot commented 2 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.

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bioc-issue-bot commented 2 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, 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/Rbwa to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Jfortin1 commented 2 years ago

Hi Nitesh @nturaga,

Thank you for reviewing my package. The error above comes form the fact that the Windows machine is trying to build the package while I did specify in the DESCRIPTION file that it's UNIX only.

lshep commented 2 years ago

By eliminating Windows you will lose nearly half of Bioconductor users; is there no way to implement a solution on windows? If you would like to proceed with excluding windows, Please create a .BBSoptions file in the top level of your package repository (dot and caps matter) and include a single line in the file UnsupportedPlatforms: win .

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8bde9dc513091c0b0b81e8482ceb50329802b78d

bioc-issue-bot commented 2 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, UNSUPPORTED, 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/Rbwa to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Jfortin1 commented 2 years ago

Hi @lshep, I would also like to make the package accessible to all users, but BWA itself was not built with Windows machines in mind. I did attempt to modify the source code to make it windows-friendly, but I was unsuccessful as some of the core libraries used are unix only.

Jfortin1 commented 2 years ago

Good morning, is there something I can do to move this forward? I would like to submit crisprBwa soon so that we can also submit our major package for CRISPR gRNA design called crisprDesign.

nturaga commented 2 years ago

Hi @Jfortin1 I'll send you the package review today. Can you issue a new build please?

nturaga commented 2 years ago

Review

DESCRIPTION

ok

NAMESPACE

ok

man

ok

tests

good

src

I'm guessing this is just the BWA source code copied into the src folder?

R

Use system2 instead here: https://github.com/Jfortin1/Rbwa/blob/master/R/xa2multi.R#L65, it's more robust than system. The same change should be made in other places where system is used.
Overall, good code.

Vignette

This line seems incomplete - https://github.com/Jfortin1/Rbwa/blob/master/vignettes/Rbwa.Rmd#L35

bioc-issue-bot commented 2 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: fae455605f915cbb2abfef67f5a471ce84b17a8c

bioc-issue-bot commented 2 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: "UNSUPPORTED, skipped, 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/Rbwa to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Jfortin1 commented 2 years ago

Thank you @nturaga. I've now addressed your reviews (see below) and pushed the latest version:

src

I'm guessing this is just the BWA source code copied into the src folder?

JP: yes.

R

Use system2 instead here: https://github.com/Jfortin1/Rbwa/blob/master/R/xa2multi.R#L65, it's more robust than system. The same change should be made in other places where system is used.

JP: thank you for the suggestion; I've now changed system to system2 everywhere in the package

Vignette

This line seems incomplete - https://github.com/Jfortin1/Rbwa/blob/master/vignettes/Rbwa.Rmd#L35

JP: indeed, removed now. thanks!

nturaga commented 2 years ago

Thanks, @Jfortin1 ! Package accepted.

Hope things are well otherwise.

bioc-issue-bot commented 2 years ago

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

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

Jfortin1 commented 2 years ago

Thanks @nturaga !

Jfortin1 commented 2 years ago

Hi @nturaga, I still cannot see Rbwa in https://www.bioconductor.org/checkResults/3.15/bioc-LATEST/#C -- do I need to do anything else?

nturaga commented 2 years ago

@lshep will better answer this question.

Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute

On Mar 24, 2022, at 12:22 PM, Jean-Philippe Fortin @.***> wrote:

Hi @nturaga, I still cannot see Rbwa in https://www.bioconductor.org/checkResults/3.15/bioc-LATEST/#C -- do I need to do anything else?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

lshep commented 2 years ago

I have not run the ingest for accepting packages yet. I will do so shortly. Once that occurs the package will appear in the build report within 48 hours.

lshep commented 2 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/Jfortin1.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("Rbwa"). The package 'landing page' will be created at

https://bioconductor.org/packages/Rbwa

If you have any questions, please contact the bioc-devel mailing list (https://stat.ethz.ch/mailman/listinfo/bioc-devel); this issue will not be monitored further.

Jfortin1 commented 2 years ago

ah thanks @lshep !

Bioconductor / Contributions

Rbwa #2511

Review

DESCRIPTION

NAMESPACE

man

tests

src

R

Vignette

src

R

Vignette