RcwlPipelines

[hubentu]

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• Repository: https://github.com/hubentu/RcwlPipelines

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[bioc-issue-bot]

Hi @hubentu

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: RcwlPipelines
Title: Bioinformatics pipelines based on Rcwl
Version: 0.99.0
Authors@R: 
    person(given = "Qiang",
 family = "Hu",
 role = c("aut", "cre"),
 email = "qiang.hu@roswellpark.org")
Description: A collection of Bioinformatics pipeline recipes based on Rcwl.
Depends: R (>= 3.6), Rcwl
License: GPL-2
Encoding: UTF-8
Suggests: 
    testthat,
    knitr,
    rmarkdown
VignetteBuilder: knitr
RoxygenNote: 6.1.1
biocViews: Software, WorkflowStep, Alignment, Preprocessing, QualityControl,
       Workflow, BasicWorkflow, GeneExpressionWorkflow, GenomicVariantsWorkflow
SystemRequirements: nodejs

[hubentu]

Hi, this is a data package for Rcwl. Thanks!

[bioc-issue-bot]

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[bioc-issue-bot]

Dear Package contributor,

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

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[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

a7247f2 ignore Windows OS af7a574 bump version

[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.

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[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

651b1b9 update biocViews

[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: "skipped, UNSUPPORTED, 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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[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

0be5e86 package structure changed; add cwlTools function; ...

[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: "skipped, UNSUPPORTED, 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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

57db5d2 fix typo

[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: "skipped, ERROR, UNSUPPORTED, 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.

[hubentu]

Hi @Kayla-Morrell , Any status update?

Thanks, Qiang

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

e3cebf9 change String to File for bwa ref

[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: "skipped, UNSUPPORTED, 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.

[hubentu]

Hi @Kayla-Morrell ,

1. This package is dependent on the package Rcwl, which is only compatible with Linux and MacOS, so a file .BBSoptions was added to skip the Windows system.
2. There are some build warnings from inst/mc3 and inst/GATK4. These files are from the project MC3 and GATK4 by git-submodules. To keep these files the same as the original project, I didn't clean or rename them.

   WARNING: directory RcwlPipelines/inst/mc3/backup_templates/utils/backup_templates is empty
   ...
   Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
   storing paths of more than 100 bytes is not portable:
   RcwlPipelines/inst/GATK4/gatk4-data-processing/processing-for-variant-discovery-gatk4.b37.wgs.inputs.json

Thanks, Qiang

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

744d902 fix bwa bug 664d9d4 add bowtie2 and bwa_index

[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: "skipped, UNSUPPORTED, 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.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

4dfae68 Add author

[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: "skipped, UNSUPPORTED, 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.

[hubentu]

Hi @Kayla-Morrell @mtmorgan ,

I got some build warnings as follows, which are from the git clones of other CWL pipelines. These scripts are imported and invoked in my package. Could you give me some suggestion for this warning? Do I need to clean and rename these files?

Thanks, Qiang

* checking for empty or unneeded directories
WARNING: directory RcwlPipelines/inst/mc3/backup_templates/utils/backup_templates is empty
WARNING: directory RcwlPipelines/inst/mc3/tools/indelocator-tool/backup_templates is empty
WARNING: directory RcwlPipelines/inst/mc3/tools/markfiles-tool/backup_templates is empty
WARNING: directory RcwlPipelines/inst/mc3/tools/tcgavcf-tool/backup_templates is empty
WARNING: directory RcwlPipelines/inst/mc3/tools/vcf-tools/backup_templates is empty
WARNING: directory RcwlPipelines/inst/mc3/tools/vcf2maf-tools/backup_templates is empty
WARNING: directory RcwlPipelines/inst/mc3/utils/backup_templates is empty
* looking to see if a data/datalist file should be added
* building RcwlPipelines_0.99.6.tar.gz
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  RcwlPipelines/inst/GATK4/gatk4-data-processing/processing-for-variant-discovery-gatk4.b37.wgs.inputs.json
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  RcwlPipelines/inst/GATK4/gatk4-data-processing/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.json
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  RcwlPipelines/inst/GATK4/gatk4-data-processing/processing-for-variant-discovery-gatk4.hg38.wgs.inputs.local.json
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  RcwlPipelines/inst/GATK4/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.hg38.inputs.local.json

[Kayla-Morrell]

Hello @hubentu,

I don't have any suggestions for the warnings because I'm not familiar with them. I'm sure Martin will be able to offer some help. Until then, I will ignore these warnings and continue with my initial review. It's my plan to have a review for you by the end of this week. Thank you for your patience.

Best, Kayla

[mtmorgan]

For these WARNING: directory RcwlPipelines/inst/mc3/backup_templates/utils/backup_templates is empty I guess the problem is that the git repository contains empty directories; you could add these to an .Rbuildignore file in the root of your package if you do not need these directories but they need to be in the git repository; of course removing them from the git repository is also possible...

The second problem is simply that the paths RcwlPipelines/inst/GATK4/gatk4-germline-snps-indels/haplotypecaller-gvcf-gatk4.hg38.inputs.local.json have too many characters for some versions of tar() (there are 101 characters == bytes in the path above). The solution is to use shorter path names.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

18da196 add .Rbuildignore

[hubentu]

Hi @mtmorgan ,

Thank you for your help! The .Rbuildignore works perfectly with the empty files.

The files with the long name are from git-submodules of the GATK workflow project. https://github.com/gatk-workflows/gatk4-data-processing It would be easier to keep those files consistent with the original git source for future update and maintain. Otherwise, I need to rename the files every time when the project updates. However, if it is necessary, I will rename these files to avoid the warning.

Thanks, Qiang

[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: "skipped, UNSUPPORTED". 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.

[Kayla-Morrell]

Hi @hubentu ,

Thank you for submitting to Bioconductor. Please see the inital review of your package below:

General Package Development

R CMD BiocCheck

• [ ] SUGGESTION: Recommended biocViews that can be added to the package (if applicable) "DNASeq" and "DataImport".

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

• [ ] SUGGESTION: For formatting reasons, consider shorter lines. There are 4 lines that are > 80 characters long.

  • R/multiqc.R, line 7
  • R/rnaseq_Sf.R, line 6
  • man/multiqc.Rd, line 10
  • man/rnaseq_Sf.Rd, line 9

• [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces instead of tabs, 5 lines contain tabs.

  • vignettes/RcwlPipelines.Rmd, line 157
  • vignettes/RcwlPipelines.Rmd, line 203
  • vignettes/RcwlPipelines.Rmd, line 204
  • vignettes/RcwlPipelines.Rmd, line 205
  • vignettes/RcwlPipelines.Rmd, line 206

• [ ] SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 53 lines that are not. See FormatR package (https://cran.r-project.org/web/packages/formatR/index.html) for formatting help.

Vignettes

• [ ] SUGGESTION: Line 53 and 54, I would seperate the last r code section into two so that you can use message=FALSE when loading the dplyr library.

• [ ] CLARIFICATION: Line 73, what is the reason to include invisible(sapply(scripts, source))?

• [ ] CLARIFICATION: Line 82, for the "type" should there be a question mark after "File"?

• [ ] REQUIRED: Line 137, "brief" is misspelled.

• [ ] REQUIRED: When going to the url for the DNA alignment pipeline example, the second section should be "Prepare data".

• [ ] REQUIRED: Line 231, remove the \ at the end of the line so that the bullet points following render correctly. Currently they are not being recognized as bullets.

• [ ] REQUIRED: Line 246, there should not be a space between "GATK" and "4".

Comment back here with updates that have been made and when the package is ready for a re-review.

Best, Kayla

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

9baa709 updates from Bioc review

[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: "skipped, UNSUPPORTED". 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.

[hubentu]

Hi @Kayla-Morrell ,

Thank you very much for your review. I have updated the package based on your comments. Please check.

Thanks, Qiang

R CMD BiocCheck

1. DNASeq, RNASeq, DataImport are added to the biocViews.
2. NEWS file added.
3. Formatted.

Vignettes

1. message=FALSE added.
2. The code is to source the Rscript tools to the session, which will be used in the next step for building pipelines.
3. File? means this argument is optional, so it can work for both single-end and pair-end reads.
4. Updated all the URLs to the Rcwl book. I will keep updating the draft. Thanks!
5. Removed.
6. Revised.

[Kayla-Morrell]

Hi @hubentu,

Thank you for the work done on your package. I have looked over the changes made and have just one final requirement before accepting your package. See this requirement below and comment back here when you are ready for me to look over the changes made.

NEWS file

• [ ] REQUIRED: See the documentation (https://bioconductor.org/developers/package-guidelines/#news) on how your NEWS file should be formatted. The content is fine, it just needs to be formatted properly.

Best, Kayla

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

dbfcef8 format NEWS

[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: "skipped, UNSUPPORTED". 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.

[hubentu]

Hi @Kayla-Morrell , Updated the NEWS file. Please check. Thanks, Qiang

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

[mtmorgan]

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/hubentu.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

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

https://bioconductor.org/packages/RcwlPipelines

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.