Closed Jfortin1 closed 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
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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
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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.
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
.
Received a valid push on git.bioconductor.org; starting a build for commit id: 8bde9dc513091c0b0b81e8482ceb50329802b78d
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.
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.
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
.
Hi @Jfortin1 I'll send you the package review today. Can you issue a new build please?
ok
ok
ok
good
src
folder?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.
This line seems incomplete - https://github.com/Jfortin1/Rbwa/blob/master/vignettes/Rbwa.Rmd#L35
Received a valid push on git.bioconductor.org; starting a build for commit id: fae455605f915cbb2abfef67f5a471ce84b17a8c
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.
Thank you @nturaga. I've now addressed your reviews (see below) and pushed the latest version:
I'm guessing this is just the BWA source code copied into the src folder?
JP: yes.
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
This line seems incomplete - https://github.com/Jfortin1/Rbwa/blob/master/vignettes/Rbwa.Rmd#L35
JP: indeed, removed now. thanks!
Thanks, @Jfortin1 ! Package accepted.
Hope things are well otherwise.
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.
Thanks @nturaga !
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?
@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.
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.
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See further instructions at
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ah thanks @lshep !
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