GWENA

[Kumquatum]

Hello,

I would like to submit the GWENA package for inclusion in BioConductor release 3.11. It is a package containing a pipeline for gene co-expression analysis with biological and topological tools for further analysis included.

I hope you will find the package interesting enough to be included into Bioconductor.

Regards,
Gwenaëlle

---

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• Repository: https://github.com/Kumquatum/GWENA

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[bioc-issue-bot]

Hi @Kumquatum

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: GWENA
Title: Pipeline for augmented co-expression analysis
Version: 0.99.0
Authors@R: 
    person(given = "Gwenaëlle",
 family = "Lemoine",
 role = c("aut", "cre"),
 email = "[email protected]",
 comment = c(ORCID = "0000-0003-4747-1937"))
Description: Analyse transcriptomics data (either microarray or RNA-seq) through co-expression network analysis
   pipeline. Include filtration of the transcriptomic data, network build, gene clustering (modules), 
   biological integration (gene enrichment, phenotypic association), topological analysis, and modules comparison.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Depends: R (>= 3.6.0)
Suggests: 
    testthat (>= 2.1.0),
    knitr,
    rmarkdown
Imports: 
    WGCNA (>= 1.67),
    dplyr (>= 0.8.3),
    dynamicTreeCut (>= 1.63-1),
    ggplot2 (>= 3.1.1),
    gprofiler2 (>= 0.1.6),
    magrittr (>= 1.5),
    tibble (>= 2.1.1),
    tidyr (>= 1.0.0),
    NetRep (>= 1.2.1),
    igraph (>= 1.2.4.1),
    RColorBrewer (>= 1.1-2),
    purrr (>= 0.3.3),
    rlist (>= 0.4.6.1),
    matrixStats (>= 0.55.0)
VignetteBuilder: knitr
biocViews: Software, GeneExpression, Network, Clustering, GraphAndNetwork,
 GeneSetEnrichment, Pathways, Visualization, RNASeq, Transcriptomics, 
 mRNAMicroarray, Microarray, NetworkEnrichment
BugReports: https://github.com/Kumquatum/GWENA/issues

[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.

[mtmorgan]

Your package must be adapted to work with SummarizedExperiment and other standard Bioconductor data representations, for instance as inputs and outputs to your functions and as example data sets in your 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.

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.

[lshep]

Please fix the ERRORs in the report before @nturaga does a formal review. And make sure to take into account the comment from @mtmorgan above.

[bioc-issue-bot]

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

96aaa5a Incrementing version to 0.99.2 after corrections

[Kumquatum]

ERRORs in report were all corrected except for this one I couldn't reproduce :

Error: connections left open:
	<-TOKAY2:11632 (sockconn)
	<-TOKAY2:11632 (sockconn)
Execution halted

Could you give me more information on the test performed which returned this error ?

I also added compatibility with SummarizedExperiment

Also, I don't know if you're aware of this behavior (if so, sorry for the inconvenience) : when creating a branch to properly patch code, then incrementing the version in DESCRIPTION, and finally merging the branch, the @bioc-issue-bot doesn't seems to trigger new build. But if I look to the webhook, it is sent.

[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:

7d53d79 Fixed: Error in igraph::plot.igraph about vertex_l...
e893c7c Fixed: Error in .check_ncores(cores) : 19 simultan...
50df431 Fixed: Warning about '::' or ':::' import not decl...
75093fc Incrementing version to 0.99.3 after corrections

[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.

[Kumquatum]

Dear @mtmorgan
I made all the asked modifications. But it seems I can't reproduce the last two errors :

• The connection left open
• The test-net_and_modules.R fail with 'length(x) = 7 > 1' in coercion to 'logical(1)

Is there a way to have more information on them ?

Here is my session info if this can help :

> version
               _                                        
platform       x86_64-pc-linux-gnu                      
arch           x86_64                                   
os             linux-gnu                                
system         x86_64, linux-gnu                        
status         alpha                                    
major          4                                        
minor          0.0                                      
year           2020                                     
month          03                                       
day            26                                       
svn rev        78078                                    
language       R                                        
version.string R version 4.0.0 alpha (2020-03-26 r78078)
nickname

[bioc-issue-bot]

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

95d6aec Incrementing version to 0.99.4 after corrections

[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, 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:

f85d4bf Fixed: test fail for comparison
a16334e Fixed: test fail net build
f07578c Correction R version
b78a504 Incrementing version to 0.99.5 after corrections

[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:

640978e Trying fix for MS Windows error connection left op...
edc5caa Incrementing version to 0.99.6 after corrections

[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:

b894ce1 Correcting monothread
03ec384 Incrementing version to 0.99.7 after corrections

[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.

[Kumquatum]

Dear @nturaga,

Thank you. I addressed as much of your remarks as possible.
I prefer to keep the original functions like %sub_in% as they are since I copied them from the NetRep package. But if you insist I'll include them.
Regarding the use of the %>% operator, as much as I understand your concern, I think its use actually helps the readability of the code. Declaring a lot of single-use and short-living variable is confusing and requires more memory space.

However the package doesn't seem to pass the build on your server now. The function implied in the build report is plot_expression_profiles. I haven't changed the way it works since the last successful build on your servers. Still, I've been investigating :

• The only changes are a shortening of the lines to less than 80 char.
• You can see that with GitHub's blame windows or by doing git diff 516a2a6 b2f3c6f R/net_and_modules.R
• Since build/check/BiocCheck seems to pass on my station (Ubuntu 18.04) and my Windows VM, I've tried the R-hub tool. Here are the successful reports on each OS :
  • Windows
  • Linux
  • macOS

I can't reproduce the Can't convert <character> to <double>, do you have any idea how I could do it or correct it ?

[bioc-issue-bot]

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

aaf4a13 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.

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

Please see the build report for more details.

[bioc-issue-bot]

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

02db50c 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.

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:

4470f3e Updating accordingly to last version of pivot_long...
392e210 Merge branch 'dev'
112bcec 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.

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.

[bioc-issue-bot]

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

6941c20 Changing contingencyTable to internal
67e699d Changing compare_condition() example to do not run
f08e84e Merge branch 'dev'
de85a4e 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.

[nturaga]

Hi @Kumquatum

Even though your build report doesn't display any warning or error messages, you can notice some issues with it.

Error in !is_windows : invalid argument type
Error in !is_windows : invalid argument type

Another one is,

  * NOTE: Consider clarifying how 47 object(s) 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)
      build_graph_from_sq_mat (gene_from)
      build_graph_from_sq_mat (.)
      build_graph_from_sq_mat (gene_to)
      build_net (is)
      compare_conditions  (is)
      compare_conditions  (setNames)
      compare_conditions  (setNames)
      compare_conditions (.)
      detect_modules (is)
      detect_modules (as.dist)
      detect_modules (setNames)
      detect_modules (.)
      filter_low_var (is)
      filter_RNA_seq (is)
      get_fit.cor (SFT.R.sq)
      get_fit.cor (Power)
      get_fit.expr (is)
      get_hub_degree  (.)
      get_hub_high_co  (.)
      get_hub_kleinberg  (.)
      plot_comparison_stats (module)
      plot_comparison_stats (statistics)
      plot_comparison_stats (pvalue)
      plot_enrichment (query)
      plot_expression_profiles (is)
      plot_expression_profiles (stack)
      plot_expression_profiles (setNames)
      plot_expression_profiles (module)
      plot_expression_profiles (.)
      plot_expression_profiles  (prcomp)
      plot_expression_profiles  (.)
      plot_expression_profiles (gene)
      plot_expression_profiles (gene_gene)
      plot_expression_profiles (expression_gene)
      plot_expression_profiles (expression_eigengene)
      plot_expression_profiles (cor_sign)
      plot_module (.)
      plot_module (lsf.str)
      plot_module (vertex.size)
      plot_module (edge.width)
      plot_module (legend)
      plot_module (symbols)
      plot_modules_merge (stack)
      plot_modules_merge (before)
      plot_modules_phenotype (eigengene)
      plot_modules_phenotype (pval)
      plot_modules_phenotype (phenotype)

• Your DESCRIPTION file needs to contain a Description that is more like the abstract of a paper.

• Use donttest{} instead of dontrun{} for your examples if you insist on using it. At least it'll check for the validity of the R code.

These are easy fixes. I'm satisfied with the way your package has developed. If you are eager to get rid fo the NOTE for the coding style, take a look at http://bioconductor.org/developers/how-to/coding-style/.

I'll accept your package as soon as your next build report looks cleaner.

[bioc-issue-bot]

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

fbf681b Changing dontrun to donttest
9753f27 Changing package's description for a more abstract...
124fc31 Adding dplyr data-variables as globalCariables to ...
6bc1b47 Adding missing packages prefixes
152e6e3 Correcting !is_windows error
706fc63 Merge branch 'dev'
9227712 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]

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

c4a3f6b Modifying description again
d99823f Adding suggested biocViews by BiocCheck
66f88fc Adding NEWS file
37f0753 Changing first figure citation to real image
03159ee Trying to reset comparison example as runanble
7287216 Merge branch 'dev'
289191b 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.

[Kumquatum]

Hello @nturaga

All four corrections asked were implemented.
I tried the \donttest inclusion but it finally seems that it's not needed anymore (it was used in first place to avoid time out on the build). So good news.

[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/Kumquatum.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("GWENA"). The package 'landing page' will be created at

https://bioconductor.org/packages/GWENA

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.