Including multiGSEA in Bioconductor

[boll3]

• Repository: https://github.com/yigbt/multiGSEA

Confirm the following by editing each check box to '[x]'

• [ x] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.

• [ x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.

• [ x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [ x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

• [ x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

I am familiar with the essential aspects of Bioconductor software management, including:

• [ x] The 'devel' branch for new packages and features.
• [ x] The stable 'release' branch, made available every six months, for bug fixes.
• [ x] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

[bioc-issue-bot]

Hi @boll3

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: multiGSEA
Type: Package
Title: Combining GSEA-based pathway enrichment with multi omics data integration
Version: 0.99.0
Date: 2020-03-05
Authors@R: c(
    person( "Sebastian", "Canzler", email = "sebastian.canzler@ufz.de", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7935-9582")),
    person( "Jörg", "Hackermüller", email = "joerg.hackermueller@ufz.de", role = "aut", comment = c( ORCID = "0000-0003-4920-7072")))
Description: Extracted features from patways derived from 8 different databases 
  (KEGG, Reactome, Biocarta, etc.) can be used on transcriptomic, proteomic, and/or
  metabolomic level to calculate a combined GSEA-based enrichment score.
License: AGPL-3
Depends: R (>= 3.6)
Imports: 
    magrittr,
    graphite,
    AnnotationDbi,
    dplyr,
    fgsea,
    metap,
    stringr,
    rappdirs,
    rlang,
    methods
VignetteBuilder: knitr
biocViews: GeneSetEnrichment, Pathways, Reactome, BioCarta
URL: https://github.com/yigbt/multiGSEA
BugReports: https://github.com/yigbt/multiGSEA/issues
Encoding: UTF-8
NeedsCompilation: no
RoxygenNote: 7.0.2
Suggests: 
    org.Hs.eg.db,
    org.Mm.eg.db,
    org.Rn.eg.db,
    org.Ss.eg.db,
    org.Bt.eg.db,
    org.Ce.eg.db,
    org.Dm.eg.db,
    org.Dr.eg.db,
    org.Gg.eg.db,
    org.Xl.eg.db,
    org.Cf.eg.db,
    knitr,
    rmarkdown,
    BiocStyle,
    testthat (>= 2.1.0)

Add SSH keys to your GitHub account. SSH keys will are used to control access to accepted Bioconductor packages. See these instructions to add SSH keys to your GitHub account.

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[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: "TIMEOUT". 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:

1b2827d Version bumbed.

[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: "ABNORMAL". 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:

7d8d222 Bugfix in test_pathway_features.

[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:

cb5d94e Metabolites mapping fixed in tests. acc546a Update package to 0.99.3

[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: "ABNORMAL". 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:

2174f98 Update R version dependency to 4.0

[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.

[boll3]

Apparently the build system on Windows was not able to clone the git repo. It worked smoothly on linux and the last time on windows. I didn't change anything that might cause this issue.

Any help is much appreciated.

[mtmorgan]

best guess is that this is a transient github failure; can you try a version bump again?

[bioc-issue-bot]

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

b6552fb Version Bump.

[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]

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.

[boll3]

Hi @mtmorgan,

we have now passed the build process without errors or warnings. We have only a few remaining notes regarding some coding style issues.

1) We added runnable examples for each function. To present some more function calls in those examples, we also add \donttest sections. We explicitly used the \donttest section, since these would significantly increase the building time of the package.

2) Line lengths longer than 80 characters and line indent with multiples of four. We tried to keep lines within 80 chars as often as possible, but especially in combination with multiple line indents this was not always to be accomplished. And for readability we would like to keep the remaining line the way they are.

Can we ignore these notes for now, or should we take care of all notes to accomplish a completely clean build report?

Thanks a lot for your help!

Cheers,

boll3

[mtmorgan]

DESCRIPTION

• Please spell check the Description: field, vignette, and man paages

vignettes

• please reconsider the merit of including conda installation instructions; using conda causes frequent confusion on the support site.

• please update teh Bioconductor installation instructions 'as if' the package were available on Bioconductor

• Please do not include the command-line installation instructions, since a major source of problem with Bioconductor packages is mixing packages from different Bioconductor releases.

• is it necessar to load several packages manually? Are these not loaded as part of your package Depends: and Imports: directives?

• since your package already depends on common 'tidyverse' packages, maybe the data() objects should be tibble for better and more modern display

• multiGSEA.rmd:317 please avoid long lines, even in echo=FALSE

  kable( 
      df %>% 
      dplyr::arrange( combined_padj) %>% 
      dplyr::select(c( 
          transcriptome_padj, proteome_padj, metabolome_padj, combined_padj
      )) %>% 
      dplyr::slice( 1:15), caption = caption
  )

R (comments on specific lines should be applied throughout the code base)

• functions.r:240 perhaps better than a long if () statement is along the lines of

  map <- c(hsapiens = "org.Hs.eg.db", rnorvegicus = "org.Rn.eg.db", ...)
  stopifnot(organism %in% names(map))
  pkg <- map[[organism]]

• functions.R:276 avoid parsing and evaluating text

  get(pkg, envir = getNamespace(pkg))

• functions.R:335 these are scalar logical operations, use &&

• functions.R:335 reduce code duplication

  if (returntype %in% c("DTXCID", "DTXSID", "HMDB") && length(map) > 0)
      map <- paset0(returntype, map)

• functions.R:416 does str_detect() provide meaningful improvement over base R string functions? if not avoid this package dependency.

• functions.R:451 avoid long lines with nested logic, which are hard to read

  dbs0 <- pDBs %>% 
      filter( .data$species == organism ) %>% 
      pull( .data$database) )
  dbs <- as.vector( dbs0 )

• functions.R:858 use file.path() rather than paste0() when constructing file paths

• functions.R:916 this line is evaluated when the package is built (on the build machine), but presumably requires evaluation on the user machine (in a .onLoad() function); it seems unlikely that this is needed now...

• consider refactoring functions.R into separate files containing logically related functions, so that it is easier to navigate the source code. Follow the 'one source file / one man page' model, where functions in a single file are documented on the same man page.

• consider using the styler package to format your code into a more standard foramt,

  style_pkg(".", transformers=tidyverse_style(indent = 4))

  data

• 'metabolitesMapping' is a large file; does it make sense to make this an ExperimentHub resource and package, both for better distribution and for re-use across packages?

tests

• thanks for including unit tests

[mtmorgan]

please let me know when you plan to have a revision available.

[boll3]

First of all, thanks for your comments! I'm done including all the suggestions you made. I also excluded the 'metabolitesMapping` table from this package and designed a stand-alone AnnotationHub package. As soon as this one is available, and I can use the data in the multiGSEA package, I will push the revison into the repo.

[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]

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/boll3.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("multiGSEA"). The package 'landing page' will be created at

https://bioconductor.org/packages/multiGSEA

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.