enrichplot

[GuangchuangYu]

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• Repository: https://github.com/GuangchuangYu/enrichplot

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[bioc-issue-bot]

Hi @GuangchuangYu

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: enrichplot
Title: Visualization of Functional Enrichment Result
Version: 0.99.0
Authors@R: person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6485-8781"))
Description: This package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. All the visualization methods are developed based on 'ggplot2' graphics.
Depends: R (>= 3.4.2)
Imports:
    AnnotationDbi,
    cowplot,
    DOSE,
    ggplot2,
    ggraph,
    ggridges,
    GOSemSim,
    graphics,
    grDevices,
    grid,
    igraph,
    reshape2,
    utils
Suggests:
    clusterProfiler,
    knitr,
    org.Hs.eg.db,
    prettydoc
VignetteBuilder: knitr
License: Artistic-2.0
biocViews: Annotation, GeneSetEnrichment, GO, KEGG,
    Pathways, Software, Visualization
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

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: "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 following build report for more details:

http://bioconductor.org/spb_reports/enrichplot_buildreport_20171128100917.html

[bioc-issue-bot]

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

60fe1b4 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.

On one or more platforms, the build results were: "WARNINGS, 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 following build report for more details:

http://bioconductor.org/spb_reports/enrichplot_buildreport_20171128104458.html

[bioc-issue-bot]

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

2dc9456 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.

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 following build report for more details:

http://bioconductor.org/spb_reports/enrichplot_buildreport_20171128105855.html

[GuangchuangYu]

* checking for file enrichplot/DESCRIPTION ... OK
* preparing enrichplot:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
      -----------------------------------
ERROR: dependency ggraph is not available for package enrichplot

That's the problem of the build system.

[hpages]

Hi @GuangchuangYu,

For some reason the graph package was missing on Mac builder merida2. It should be installed by now. Can you please bump the version of enrichplot in order to trigger a new build? I'll start reviewing the package right after that.

Thanks, H.

[bioc-issue-bot]

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

8201014 bump version up

[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 following build report for more details:

http://bioconductor.org/spb_reports/enrichplot_buildreport_20171214213738.html

[GuangchuangYu]

Thanks, @hpages. It seems the issue is still exists.

[hpages]

Hi @GuangchuangYu,

My bad: It's ggraph that's causing problems, not graph. I misread the name sorry. CRAN doesn't provide Mac binary packages for R 3.5 yet. Problem is that ggraph depends (indirectly) on udunits2 which is one of those packages that the build system fails to install from source. This is a known issue, let's ignore it for know.

I'll take a first look at enrichplot in the next few days. Thanks for your patience!

Best, H.

[hpages]

Hi @GuangchuangYu,

Here is some feedback:

• The cnetplot(), dotplot(), gseaplot(), and ridgeplot() functions are already defined as generic functions in the DOSE package. Why would you redefine them as regular functions in the enrichplot package? The fact that enrichplot depends on DOSE and that you are also an author of DOSE makes this choice even more surprising/confusing.

• The vignette is plot gallery i.e. a collection of plots with no text. Would be nice to make it look like a real vignette e.g. by adding an introduction that provides some context and by providing some short explanation and/or comment about each plot.

• The man pages are also too minimalist. For example the title and description in ?mapplot are

  mapplot

  and

  Enrichment Map

  Having a title that is just the name of the function doesn't really help, especially when the user is navigating the man pages via the HTML browser interface. The description needs to be a full sentence (i.e. with a verb).

• Use of capitalization could be more consistent. For example the description and author in ?mapplot are

  Enrichment Map

  and

  Guangchuang Yu

  But in ?cnetplot they are

  gene-concept network

  and

  guangchuang yu

Please address at your earliest convenience, thanks!

H.

[bioc-issue-bot]

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

3d97d53 v 0.99.5

[GuangchuangYu]

Thanks @hpages for your feedback.

The cnetplot(), dotplot(), gseaplot(), and ridgeplot() functions are already defined as generic functions in the DOSE package. Why would you redefine them as regular functions in the enrichplot package? The fact that enrichplot depends on DOSE and that you are also an author of DOSE makes this choice even more surprising/confusing.

I have defined all of the visualization functions as generic functions in enrichplot and removed the dependency of DOSE. I will update DOSE to use methods implemented in enrichplot.

The reasons I split the visualization methods from DOSE to enrichplot are that some of the methods are re-implemented using ggplot2 (now all of them are ggplot2-based) and new methods were added.

The vignette is plot gallery i.e. a collection of plots with no text. Would be nice to make it look like a real vignette e.g. by adding an introduction that provides some context and by providing some short explanation and/or comment about each plot.

I have updated the vignette with explanation of each plot.

The man pages are also too minimalist. For example the title and description in ?mapplot are

mapplot

and

Enrichment Map

Having a title that is just the name of the function doesn't really help, especially when the user is navigating the man pages via the HTML browser interface. The description needs to be a full sentence (i.e. with a verb).

I have updated the man pages.

Use of capitalization could be more consistent. For example the description and author in ?mapplot are

Enrichment Map

and

Guangchuang Yu

But in ?cnetplot they are

gene-concept network

and

guangchuang yu

All man pages were updated and consistent now.

[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:

9ab2ec1 fixed BiocCheck

[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.

[GuangchuangYu]

any progress?

[hpages]

Hi @GuangchuangYu, Thanks for the update. Note that it is not a good idea to define S3 generics and methods to dispatch on S4 objects. Please define cnetplot(), dotplot(), gseaplot(), and ridgeplot() as S4 generics. The rest of your changes look good, especially the improvements to the vignette. Thanks! H.

[bioc-issue-bot]

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

5c78fc4 S4 methods

[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:

750da60 remove bioccheck error

[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.

[GuangchuangYu]

the error looks like another issue of the build server.

[bioc-issue-bot]

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

f638c9f upsetplot method

[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.

[GuangchuangYu]

@hpages do you have any further comments?

It took more than 2 months and I think it was hanged up too much due to the build system issue.

https://bioconductor.org/developers/package-submission/#review:

The entire review process typically takes between 2 and 5 weeks.

[bioc-issue-bot]

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

d61a56a bump up 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.

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.

[GuangchuangYu]

Error : package udunits2 was installed by an R version with different internals; it needs to be reinstalled for use with this R version

the build system issue is still not fixed.

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be sent to the maintainer email address in the next several days.

Thank you for contributing to Bioconductor!

[hpages]

Thanks @GuangchuangYu for the updated package.

Let's ignore the error on the Mac builder for now (which is a problem on our side).

Note that you shouldn't put curly braces around the call to standardGeneric() in the definition of your generic functions:

> heatplot
nonstandardGenericFunction for "heatplot" defined from package "enrichplot"

function (x, showCategory = 30, foldChange = NULL) 
{
    standardGeneric("heatplot")
}

This makes them look as non-standard generic functions and I don't think that's what you want.

Other than that everything looks fine and I'm labeling the package as "accepted".

Cheers, H.

PS: Yes, "the entire review process typically takes between 2 and 5 weeks". But please note that we don't promise anything. Sometimes it takes longer... That's just the way it is.

[GuangchuangYu]

Thanks @hpages.

I will update the generic function definition directly to the bioconductor git repo.

However, I don't have the permission:

FATAL: R any packages/enrichplot g.yu DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
error: Could not fetch upstream

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

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See further instructions at

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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 biocLite(\"enrichplot\"). The package 'landing page' will be created at

https://bioconductor.org/packages/enrichplot

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.