plger commented 3 years ago

The functions included in this package were moved from the SEtools package (and will be afterwards removed from there), so as to increase granularity and reduce dependencies, as suggested by @hpages

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bioc-issue-bot commented 3 years ago

Hi @plger

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: sechm
Type: Package
Title: sechm: Complex Heatmaps from a SummarizedExperiment
Version: 0.99.2
Depends: R (>= 4.1)
Authors@R: person("Pierre-Luc", "Germain", email="pierre-luc.germain@hest.ethz.ch", role=c("cre","aut"), comment=c(ORCID="0000-0003-3418-4218"))
Description:
    sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package.
    It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, 
    and implements a number of features to make the generation of heatmaps easier and more flexible.
    These functionalities used to be part of the SEtools package.
Imports:
    S4Vectors,
    SummarizedExperiment,
    seriation,
    ComplexHeatmap,
    circlize,
    methods,
    randomcoloR,
    stats,
    grid,
    grDevices
Suggests:
    BiocStyle,
    knitr,
    rmarkdown
biocViews: GeneExpression, Visualization
VignetteBuilder: knitr 
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.1.1
BugReports: https://github.com/plger/sechm

bioc-issue-bot commented 3 years ago

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bioc-issue-bot commented 3 years ago

Dear Package contributor,

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bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5d777b39c3f7d1e367854846206bfd5dcd17428c

bioc-issue-bot commented 3 years ago

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, skipped". 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/sechm to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6af557f8696c9c3dc06f73387bea1fd6b9af6d61

bioc-issue-bot commented 3 years ago

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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/sechm to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LiNk-NY commented 3 years ago

Hi Pierre-Luc, @plger Thank you for your submission. Please see the review below.

Best, Marcel

sechm #2057

DESCRIPTION

Looks good.

NAMESPACE

Looks pretty compact.

vignettes

Remove the GitHub installation code upon acceptance.
Use a more descriptive dataset name rather than SE. You could even use the author's name and year of publication.
Everyhthing else looks good.

R

Avoid using eval(parse(...)) in resetAllSechmOptions. You can simply list and set them to NULL.
Would .getDef("assayName") return the value assay in the switch function? These should probably agree to avoid errors.
It may be better to create a package-wide environment / object for the various options. See here for an example: https://github.com/Bioconductor/SOUNDBoard/blob/master/R/zzz.R.
Deprecations in un-released packages are not usually necessary. If you wish, you can deprecate arguments with .Deprecated.
Describe what type of data can ses contain.
The code looks quite complicated and the number of arguments in sechm can overwhelm any user. Try to reduce the number of specifiable arguments in the function calls, if possible.

tests

We highly recommend adding unit tests to the package.

NEWS

Please add a NEWS file.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5e6387e73dace6bcf379d84f47c5437bd85c412d

bioc-issue-bot commented 3 years ago

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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to git@git.bioconductor.org:packages/sechm to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 3 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 3f32218bf70350a99e872cb41d48146d102d850b

bioc-issue-bot commented 3 years ago

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. This link will be active for 21 days.

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plger commented 3 years ago

Hi @LiNk-NY , thanks for the review and suggestions (neat idea with the package options!), I've included everything I think except i) unit tests, ii) I didn't reduce the arguments (while users typically need only a few of them, I've got many collaborators using the various functionalities regularly...)

LiNk-NY commented 3 years ago

Hi Pierre-Luc, @plger Please respond to the individual items in the review. It's helpful to see what has changed. Thank you. Best, Marcel

plger commented 3 years ago

Ok:

Vignette:

Remove the GitHub installation code upon acceptance. -> removed from vignette
Use a more descriptive dataset name rather than SE. -> renamed to AuthorYear as suggested

R:

Avoid using eval(parse(...)) in resetAllSechmOptions. -> replaced with explicit list
Would .getDef("assayName") return the value assay ... -> corrected to have the same argument name everywhere (thanks)
It may be better to create a package-wide environment / object for the various options -> did exactly that
Deprecations in un-released packages are not usually necessary. -> it is in this case, since this was moved: I need to nudge users into updating their scripts that were using the same function formerly in SEtools. I've however changed it to .Deprecated as suggested.
Describe what type of data can ses contain. -> I'll admit I didn't get what you meant there. Could it be that you didn't see it in the @param because of the linebreak? Or were you thinking of a more detailed description?
Try to reduce the number of specifiable arguments in the function calls -> I didn't, I'm afraid we need all of this from time to time (it's still quite small WRT to the underlying ComplexHeatmap::Heatmap)

tests:

We highly recommend adding unit tests to the package. -> I didn't. It'd be easy to add 2-3 tests just to pretend I've done it, but this doesn't make much sense unless it's done thoroughly, and at the moment I'm afraid I don't have time. But I do aim to get there eventually ;)

news:

Please add a NEWS file. -> added

LiNk-NY commented 3 years ago

Hi Pierre-Luc, @plger

Thanks for making those changes. Perhaps a bit more detail in @param ses would help new users. Are these typically gene expression SummarizedExperiment s? The package looks good to go. Thank you for your submission.

Best, Marcel

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Bioconductor / Contributions

sechm (moved) #2057

sechm #2057

DESCRIPTION

NAMESPACE

vignettes

R

tests

NEWS