netZooR

[marouenbg]

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Dear Package contributor,

This is the automated single package builder at bioconductor.org.

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Dear Package contributor,

This is the automated single package builder at bioconductor.org.

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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.

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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: "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/netZooR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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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: "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/netZooR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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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: "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/netZooR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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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: "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.

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/netZooR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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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". 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.

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/netZooR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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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.

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[Kayla-Morrell]

@marouenbg - 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: What is the purpose of the 'docs/' directory? This is normally not something we allow within Bioconductor packages.

DESCRIPTION

• [ ] SUGGESTION: Since you are using a standard license, the 'LICENSE' file doesn't need to be included in your package.

• [ ] REQUIRED: 'LazyData' should be set to false or removed.

• [ ] REQUIRED: There are packages listed in more than one of Depends, Imports, Suggests, Enhances: viridisLite, pandaR

• [ ] REQUIRED: There are trailing ',' after pandaR in 'Depends', yarn in 'Imports', and pkgdown in 'Suggests'. These should be removed.

• [ ] REQUIRED: Update R version dependency from 3.3 to 4.1.0.

• [ ] REQUIRED: There is a trailing ',' after the biocView GeneRegulation. This should be removed.

• [ ] SUGGESTION: Consider adding these automatically suggested biocViews: GeneExpression, Transcription, Microarray, GraphAndNetwork See http://bioconductor.org/developers/how-to/biocViews/

• [ ] SUGGESTION: We strongly encourage the use of the 'BugReports' field to include the relevant link to GitHub for reporting issues.

NAMESPACE

• [ ] REQUIRED: Exported functions should use camel case or underscoring and not include '.', which indicates S3 dispatch.

• [ ] SUGGESTION: Generally 'importFrom()' is encouraged over importing an entire package. However, if there are many functions from a single package, 'import()' can be acceptable.

NEWS

• [ ] SUGGESTION: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements.

Data

• [ ] REQUIRED: For exon.size, genes, monsterRs, and mut.ucec could you provide the actual reference to Kuijjer et al., similar to how you have a reference for small1976 and yeast.

• [ ] REQUIRED: Data in the 'inst/extdata/' directory need proper documentation in an 'inst/script/' directory. The scripts in the directory can vary but most importantly should clearly state how the data was generated. It should include source URLs and any key information regarding filtering or processing. It can be executable code, sudo code, or a text description. Users should be able to download and roughly reproduce the file or object that is present as data.

Vignettes

• [ ] REQUIRED: I think there needs to be thought into whether all the vignettes are needed in this package. The idea of a vignette is to demonstrate how to accomplish non-trivial tasks embodying the core functionality of your package, not other established packages. It is fine to explain packages and how they are relevant to yours but you should really be demonstrating the use of your package. It also might be better if all code was in one main vignette instead of many little ones. A user might not know which vignette to browse when looking for answers to questions or examples to run.

• [ ] REQUIRED: Whether you decide to go with one or many vignette each one must minimally include:

  • An Introduction section
  • An Installation section
  • Table of contents (though not necessarly required)
  • Evaluated code chunks - very few (if any) eval = FALSE code chunks
  • Session information section that includes sessionInfo()

• [ ] REQUIRED: There is a library(RColorBrewer) call in the yarn.Rmd file, but RColorBrewer isn't listed as a Suggests in the DESCRIPTION file. Please add to the DESCRIPTION file if usin in the vignette.

• [ ] REQURIED: All data used in vignette should come from the package itself or other CRAN/Bioconductor packages. You should avoid downloading files and external data from the web.

Man pages

• [ ] REQUIRED: Data used in examples should come from the package itself or other CRAN/Bioconductor packages. You should avoid downloading files and external data from the web.

• [ ] REQUIRED: Found '@' in man/monster.Rd. Use accessors; don't access S4 class slots via '@' in examples/vignettes.

• [ ] REQUIRED: All exported objects/functions need valid examples with them. For example, the alpaca function just has "a <- 1 # example place holder" as an example. This is not acceptable.

• [ ] REQUIRED: Add runnable examples to the following man pages which document exported objects: create.diff.panda.style.Rd create.panda.style.Rd sambar.convertgmt.Rd sambar.corgenelength.Rd sambar.desparsify.Rd sambar.Rd vis.diff.panda.in.cytoscape.Rd vis.panda.in.cytoscape.Rd

• [ ] REQUIRED: Usage of dontrun{} / donttest{} found in man page examples. Use donttest{} instead of dontrun{} if necessary. Found in the following files: vis.diff.panda.in.cytoscape.Rd vis.panda.in.cytoscape.Rd

Unit tests

• [ ] REQUIRED: Data used in tests should come from the package itself or other CRAN/Bioconductor packages. You should avoid downloading files and external data from the web.

R code

• [ ] REQUIRED: Function names should be camelCase or utilize the underscore and not have a dot.

• [ ] SUGGESTION: Consider clarifying how 2 objects are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within(). function (object) monster.monsterNI (yeast) runEgret (NA12878)

• [ ] REQUIRED: Avoid sapply(); use vapply() instead.

• [ ] REQUIRED: Avoid 1:...; use seq_len() or seq_along() instead.

• [ ] REQUIRED: Avoid use of direct slot access with '@' or slot(). Accessor methods should be created and utilized.

• [ ] REQUIRED: Avoid the use of 'paste' in condition signals. Found in files: R/panda.to.alpaca.R, line 49 R/panda.to.condor.object.R, line 72

• [ ] REQUIRED: Avoid redundant 'stop' and 'warn*' in signal conditions. Found in files: R/CONDOR.R, lines 375 and 581 R/MONSTER.R, lines 802, 828, and 835

• [ ] REQUIRED: Avoid system(); use system2() instead.

• [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 957 lines that are > 80 characters long.

• [ ] SUGGESTION: For formatting reasons, consider 4 spaces instead of tabs. There are 9 lines that contain tabs.

• [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 1990 lines that are not.

Best, Kayla

[marouenbg]

Hi @Kayla-Morrell ,

Thank for the great feedback, I am working on it at the moment. Regarding this point

• REQUIRED: For exon.size, genes, monsterRs, and mut.ucec could you provide the actual reference to Kuijjer et al., similar to how you have a reference for small1976 and yeast.

Where should I provide a reference to Kuijjer et al?

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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: "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.

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Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/netZooR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

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On one or more platforms, the build results were: "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.

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Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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Dear Package contributor,

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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: "skipped, WARNINGS, 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.

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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: "TIMEOUT, 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.

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