Contributions crisprViz

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Repository: https://github.com/Jfortin1/crisprViz

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Aug 01 '22 16:08 Jfortin1

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: crisprViz
Title: Visualization Functions for CRISPR gRNAs
Version: 0.99.16
Authors@R: c(
    person("Jean-Philippe", "Fortin", email = "[email protected]", role = c("aut", "cre")),
    person("Luke", "Hoberecht", email = "[email protected]", role = c("aut"))
    )
Description: Provides functionalities to visualize and contextualize
    CRISPR guide RNAs (gRNAs) across nucleases and applications.
    Works in conjunction with the crisprBase and crisprDesign 
    Bioconductor packages. Plots are produced using the Gviz framework.
Depends: R (>= 4.2.0),
    crisprBase (>= 0.99.15),
    crisprDesign (>= 0.99.77)
Imports:
    BiocGenerics,
    Biostrings,
    BSgenome,
    GenomeInfoDb,
    GenomicFeatures,
    GenomicRanges,
    grDevices,
    Gviz,
    IRanges,
    methods,
    S4Vectors
Suggests:
    AnnotationHub,
    BiocStyle,
    BSgenome.Hsapiens.UCSC.hg38,
    knitr,
    rmarkdown,
    rtracklayer,
    testthat,
    utils
biocViews:
    CRISPR,
    FunctionalGenomics,
    GeneTarget
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.0
VignetteBuilder: knitr
BugReports: https://github.com/Jfortin1/crisprViz/issues
URL: https://github.com/Jfortin1/crisprViz

Aug 01 '22 16:08 bioc-issue-bot

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Aug 08 '22 14:08 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: "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 [email protected]:packages/crisprViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Aug 08 '22 15:08 bioc-issue-bot

@Jfortin1 - Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be (though we strongly encourage them). Comment back here with updates that have been made and when the package is ready for a re-review.

General package development

[ ] REQUIRED: README installation instructions should also include Bioconductor installation instructions. For the .Rmd file these instructions should be included in an eval = FALSE code chunk.

DESCRIPTION

[ ] SUGGESTION: I see 'testthat' listed under Suggests but you don't have any unit tests. I would suggest removing this package or adding in unit tests.

Data

[ ] REQUIRED: Could you add a bit of source information to the two Ideogram data files? Where does this data come from?
[ ] REQUIRED: I didn't see the Ideogram datasets used in the vignette or in code. Are these actually used somewhere?

Vignette

[ ] REQUIRED: The installation sections needs to show users how to download and load the package from Bioconductor, not github. This code can be included in an eval = FALSE code chunk.
[ ] REQUIRED: The figure in the figures directory is not referenced in the vignette. It should be removed if not used.

Unit tests

[ ] SUGGESTION: Consider adding unit tests.We strongly encourage them. See https://contributions.bioconductor.org/tests.html.

R code

[ ] SUGGESTION: Avoid suppressWarnings/*Messages if possible (found 4 times)
[ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 42 lines that are > 80 characters long.
[ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 263 lines that are not.

Best, Kayla

Aug 17 '22 15:08 Kayla-Morrell

Received a valid push on git.bioconductor.org; starting a build for commit id: 8d8b090a4eadae633f7c29283c42ed5c2d109838

Aug 17 '22 18:08 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: "ERROR, 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 [email protected]:packages/crisprViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Aug 17 '22 18:08 bioc-issue-bot

Thank you Kayla for your review @Kayla-Morrell. Please find below my comments.

Best, JP

General package development

[x] REQUIRED: README installation instructions should also include Bioconductor installation instructions. For the .Rmd file these instructions should be included in an eval = FALSE code chunk.

Done.

DESCRIPTION

[x] SUGGESTION: I see 'testthat' listed under Suggests but you don't have any unit tests. I would suggest removing this package or adding in unit tests.

We have now added unit tests.

Data

[x] REQUIRED: Could you add a bit of source information to the two Ideogram data files? Where does this data come from?
[x] REQUIRED: I didn't see the Ideogram datasets used in the vignette or in code. Are these actually used somewhere?

Great catch, we have now removed those files as they are irrelevant to the current version of the package.

Vignette

[x] REQUIRED: The installation sections needs to show users how to download and load the package from Bioconductor, not github. This code can be included in an eval = FALSE code chunk.

Done.

[x] REQUIRED: The figure in the figures directory is not referenced in the vignette. It should be removed if not used.

Indeed, now removed.

Unit tests

[x ] SUGGESTION: Consider adding unit tests.We strongly encourage them. See https://contributions.bioconductor.org/tests.html.

Thanks for the suggestion, we have now added unit tests.

R code

[x] SUGGESTION: Avoid suppressWarnings/*Messages if possible (found 4 times)

Necessary for not-so-useful warnings from external packages.

[x] SUGGESTION: For formatting reasons, consider shorter lines. There are 42 lines that are 80 characters long.

Done, besides a couple of lines that have long urls.

[x] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 263 lines that are not.

Our (unpopular) indentation style for function parameters across our R packages is to align with the opening bracket, causing this BiocCheck warning.

Aug 17 '22 18:08 Jfortin1

Received a valid push on git.bioconductor.org; starting a build for commit id: b6e8bc6c29512046e3515737c00c9fc492d69968

Aug 17 '22 18:08 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: "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 [email protected]:packages/crisprViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Aug 17 '22 18:08 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 169767cede9e1c193faf96032b0655957d3fa6a9

Aug 22 '22 23:08 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: "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 [email protected]:packages/crisprViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Aug 22 '22 23:08 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: cee850ec62bfce58768e92968fdcd8412a93f754

Aug 27 '22 14:08 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: "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 [email protected]:packages/crisprViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Aug 27 '22 14:08 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: a18f5c7b255a2d6f075e3923702101812bbac3b1

Aug 27 '22 16:08 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.

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

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 [email protected]:packages/crisprViz to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Aug 27 '22 16:08 bioc-issue-bot

Hi Kayla @Kayla-Morrell, is there anything else that I need to do from my side for this review?

Best, JP

Sep 06 '22 15:09 Jfortin1

Hello JP @Jfortin1 - I'm currently wrapping up an initial review of a multiple package submission which has used up the majority of my time. I'll work on reviewing the changes you made and get back to you in the next couple days. Sorry for the delay.

Best, Kayla

Sep 06 '22 17:09 Kayla-Morrell

Thanks @Kayla-Morrell for the heads up!

Sep 06 '22 17:09 Jfortin1

@Jfortin1 - Thank you again for your patience and making the necessary changes. I have looked everything over and it all looks good. I'm more than happy to accept that package.

Best, Kayla

Sep 09 '22 14:09 Kayla-Morrell

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.

Sep 09 '22 14:09 bioc-issue-bot

Thank you @Kayla-Morrell !

Sep 09 '22 17:09 Jfortin1

Would it be possible to add the package to the nightly builds sometime this week? Thank you!

Sep 19 '22 18:09 Jfortin1

I'm very sorry for the delay. I will be ingesting packages later this afternoon and it should be on the nightly builds within 48 hours.

Sep 26 '22 12:09 lshep

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

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See further instructions at

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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("crisprViz"). The package 'landing page' will be created at

https://bioconductor.org/packages/crisprViz

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.

Sep 26 '22 13:09 lshep

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crisprViz

General package development

DESCRIPTION

Data

Vignette

Unit tests

R code

General package development

DESCRIPTION

Data

Vignette

Unit tests

R code

Contributions
Contributions copied to clipboard