MultiBaC

[ManuelUgidos]

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• Repository: https://github.com/ConesaLab/MultiBaC

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[bioc-issue-bot]

Hi @ManuelUgidos

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: MultiBaC
Type: Package
Title: Multiomic Batch effect Correction
Version: 0.99.0
Author: person("Manuel", "Ugidos", email = "manuelugidos@gmail.com"), person("Sonia", "Tarazona", email = "sotacam@gmail.com"), person("María José", "Nueda", email = "mjnueda@ua.es")
Maintainer: The package maintainer <manuelugidos@gmail.com>
Description: MultiBaC is a strategy to correct batch effects from multiomic datasets distributed across different labs or data acquisition events. MultiBaC is the first Batch effect correction algorithm that dealing with batch effect correction in multiomics datasets. MultiBaC is able to remove batch effects across different omics generated within separate batches provided that at least one common omic data type is included in all the batches considered.
License: GPL-3
Encoding: UTF-8
biocViews: Software, StatisticalMethod, PrincipalComponent, DataRepresentation, GeneExpression, Transcription, BatchEffect
Imports: Matrix, ggplot2, MultiAssayExperiment, ropls, graphics
Suggests: knitr, rmarkdown, BiocStyle, devtools
VignetteBuilder: knitr
Collate:
    'auxfunctions.R'
    'ARSyNcomponents.R'
    'ASCA1f.R'
    'PCA-GENES.R'
    'ASCAfunres.R'
    'ASCAfun12.R'
    'ASCAfun1.R'
    'ASCA2f.R'
    'ARSyNbac.R'
    'MultiBaC.R'
    'createMbac.R'
    'plot-methods.R'
NeedsCompilation: no
RoxygenNote: 6.1.1

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[ManuelUgidos]

I have already created an SSH Key. What am I supposed to do with it?

[bioc-issue-bot]

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[mtmorgan]

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[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". 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:

c3bd4d6 version bumped

[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". 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:

52a9403 documentation updated

[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". 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:

3dc9328 runnables examples corrected

[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". 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:

8112545 runnables examples corrected

[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". 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:

c841947 removing latex encoding latin 10 from vignettes

[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.

[bioc-issue-bot]

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

52fb2e3 correction of a reference in vignette

[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.

[ManuelUgidos]

Dear reviewers, We would like to include our R package in our next publications. Is there any kind of link for reviewers even thought the package is in devel status? Thanks

[lshep]

I don't know what feedback @hpages will provide and your willingness to adapt the package to his review. As far as links, once accepted into Bioconductor the package could be linked with the shorturl link: https://bioconductor.org/packages/MultiBaC but it will not be active until officially accepted through the review process.

[hpages]

Hi @ManuelUgidos ,

Thanks for submitting MultiBaC. The package is in good shape and has a nice vignette. Only a few minor cosmetic issues:

1. The doc/ folder should be a subfolder of the inst/ folder. See section "1.1 Package structure" of the "Writing R Extensions" manual. In your case, the doc/ folder contains MultiBaC.html, MultiBaC.R, and MultiBaC.Rmd. Note that these files will be automatically generated by R CMD build and included in the resulting source tarball so they must not be included in the source tree. Please remove them. In other words, you need a doc/ folder only if you want to include a static document in your package (vignettes are dynamic documents). Since you don't have any static document (and most packages don't have and don't need one), you don't even need the inst/doc/ folder.

2. Also please remove MultiBaC.R and MultiBaC.html from the vignettes/ folder. Like the files you have in doc/, these are not needed and don't belong to the package source tree.

3. The code in the vignette produces a dozen of warnings e.g.

   ## Warning: 'info.txtC = NULL' argument value is deprecated; use 'info.txtC =
   ## 'none'' instead.

   Note that these warnings are displayed in the HTML version of the vignette. Also some man pages have examples that produce the same warnings e.g.

   > example(batchCorrection)
   ...
   There were 12 warnings (use warnings() to see them)
   > warnings()
   Warning messages:
   1: 'info.txtC = NULL' argument value is deprecated; use 'info.txtC = 'none'' instead.
   ...
   12: 'fig.pdfC = NULL' argument value is deprecated; use 'fig.pdfC = 'none'' instead.

4. Why do you have man pages for functions that are not available to the user? For example the code in the man page for getData fails with:

   > omicData <- getData (my_mbac$ListOfBatches)
   Error in getData(my_mbac$ListOfBatches) : 
     could not find function "getData"

   This will be the most confusing for your users, especially given the fact that this man page will be included in the reference manual of the package (we will display a link to the reference manual of the package on its landing page, see for example https://bioconductor.org/packages/Biobase). You basically have 2 options to address this:

   • (1) Don't document non exported functions.
   • (2) Exclude the man page from the reference manual. This is done by adding the \keyword{internal} line to the man page, usually at the bottom. Also you'll need to make sure that the code in the Examples section is valid and you shouldn't put it inside a \dontrun directive.

Don't hesitate to ask on the bioc-devel mailing list if you have concerns or questions about this.

Thanks

[bioc-issue-bot]

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

a25ced8 First corrections 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.

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

Please see the build report for more details.

[ManuelUgidos]

Hi @hpages,

Thanks for your feedback!. I made the changes and I think I addressed all your points:

1. doc/ folder has been removed.
2. Both files have been removed.
3. All the warnings I could see in the code were because of the function opls and its arguments. That function returns two warnings and, as it is invoked 6 times running the vignette, at the end it returns 12 warnings. This issue has been addressed modifying the arguments. Please, let me know if there are other warnings.
4. man pages for non-exported functions have been removed.

I hope that your requests have been met successfully.

[bioc-issue-bot]

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

c7b0ff1 PCA plot viz correction

[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". 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:

e2d6194 PCA plot viz correction.2

[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.

[ManuelUgidos]

Hi @hpages,

I have modified one argument in plot functions and I made an error but now is corrected. Please find my previous message bellow.

Thanks for your feedback!. I made the changes and I think I addressed all your points:

doc/ folder has been removed. Both files have been removed. All the warnings I could see in the code were because of the function opls and its arguments. That function returns two warnings and, as it is invoked 6 times running the vignette, at the end it returns 12 warnings. This issue has been addressed modifying the arguments. Please, let me know if there are other warnings. man pages for non-exported functions have been removed. I hope that your requests have been met successfully.

[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.

[ManuelUgidos]

Hi,

I already did a new push with corrected issues 28 days ago. Is there anything else I can/must do to finish the submission of the package?

Thanks in advance.

[hpages]

Hi @ManuelUgidos ,

Thanks for making the changes. Package is now ready for inclusion in Bioconductor.

Cheers, H.

[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.

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See further instructions at

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

https://bioconductor.org/packages/MultiBaC

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.