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RTNsurvival: An R/Bioconductor package for survival analysis using transcriptional networks and regulons #363

Closed csgroen closed 7 years ago

csgroen commented 7 years ago

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bioc-issue-bot commented 7 years ago

Hi @csgroen

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: RTNsurvival
Type: Package
Title: Survival analysis using transcriptional networks inferred by the RTN package
Version: 0.9.9
Author: Clarice S. Groeneveld, Vinicius S. Chagas, Mauro A. A. Castro
Maintainer: Clarice Groeneveld <clari.groeneveld@gmail.com>, Mauro A. A. Castro <mauro.a.castro@gmail.com>
Depends: R (>= 3.3), methods, RTN
Imports: survival, RColorBrewer, grDevices, graphics, stats
Suggests: Fletcher2013b, pheatmap, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
Description: This package provides classes and methods to perform survival analysis using transcriptional networks inferred by the RTN package, including Kaplan-Meier and multivariate survival analysis using Cox's regression model.
License: Artistic-2.0
biocViews: NetworkEnrichment, Survival, GeneRegulation, GeneSetEnrichment, Regression, Preprocessing, Network, BiocViews, GeneExpression, GeneticVariability, NetworkInference, GraphAndNetwork, Preprocessing, Network
LazyData: TRUE
VignetteBuilder: knitr
RoxygenNote: 6.0.1
bioc-issue-bot commented 7 years ago

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

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bioc-issue-bot commented 7 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, 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.

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bioc-issue-bot commented 7 years ago

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

159bc31 Update DESCRIPTION

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/RTNsurvival_buildreport_20170510193238.html

bioc-issue-bot commented 7 years ago

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

a250437 Update DESCRIPTION

bioc-issue-bot commented 7 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: "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 following build report for more details:

http://bioconductor.org/spb_reports/RTNsurvival_buildreport_20170510201651.html

bioc-issue-bot commented 7 years ago

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

f7169e5 Update DESCRIPTION

bioc-issue-bot commented 7 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: "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 following build report for more details:

http://bioconductor.org/spb_reports/RTNsurvival_buildreport_20170510204843.html

bioc-issue-bot commented 7 years ago

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

e5a4354 Update DESCRIPTION

bioc-issue-bot commented 7 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: "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 following build report for more details:

http://bioconductor.org/spb_reports/RTNsurvival_buildreport_20170511195749.html

bioc-issue-bot commented 7 years ago

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

71b8a2a Update DESCRIPTION

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/RTNsurvival_buildreport_20170511210028.html

bioc-issue-bot commented 7 years ago

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

43342df Update DESCRIPTION

bioc-issue-bot commented 7 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: "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 following build report for more details:

http://bioconductor.org/spb_reports/RTNsurvival_buildreport_20170515153530.html

bioc-issue-bot commented 7 years ago

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

52e22aa Update DESCRIPTION

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/RTNsurvival_buildreport_20170515155229.html

nturaga commented 7 years ago

RTNsurvival Review

Build

R-release CMD build RTNsurvival: Ok

R-release CMD INSTALL RTNsurvival: Ok

DESCRIPTION

NAMESPACE

Vignette

man

R

General Comments

bioc-issue-bot commented 7 years ago

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

701bb29 Update DESCRIPTION

bioc-issue-bot commented 7 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: "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/RTNsurvival_buildreport_20170525120004.html

bioc-issue-bot commented 7 years ago

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

f7001fc Update DESCRIPTION

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/RTNsurvival_buildreport_20170530101153.html

bioc-issue-bot commented 7 years ago

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

c290614 Update DESCRIPTION

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/RTNsurvival_buildreport_20170602155941.html

bioc-issue-bot commented 7 years ago

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

7628e06 Update DESCRIPTION

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/RTNsurvival_buildreport_20170603155926.html

nturaga commented 7 years ago

Hi @csgroen ,

Should we review this package again? If not, please let us know in the comments when you are ready for us to review.

csgroen commented 7 years ago

Hi @nturaga,

We only saw your review last week and are still working on your comments. I'll let you know as soon as we address everything that has been remarked upon.

nturaga commented 7 years ago

Thanks. Keep me posted.

bioc-issue-bot commented 7 years ago

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

1e70a1e Add files via upload

bioc-issue-bot commented 7 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: "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 following build report for more details:

http://bioconductor.org/spb_reports/RTNsurvival_buildreport_20170619164931.html

bioc-issue-bot commented 7 years ago

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

69cc766 Update DESCRIPTION

bioc-issue-bot commented 7 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 following build report for more details:

http://bioconductor.org/spb_reports/RTNsurvival_buildreport_20170619165749.html

csgroen commented 7 years ago

Hi @nturaga. We have addressed all the comments and suggestions of your review. Please find our point-by-point reply to your comments below:

RTNsurvival Review

(1) REVIEWER: The DESCRIPTION should follow a paper abstract format. It should provide the reader a overview of what to expect in the package.

AUTHORS: We updated the package description with a more informative summary of the package.

(2) REVIEWER: biocViews : Too many biocViews. Emphasize most-specific terms

AUTHORS: We cut down on the number of biocViews. We can cut down more if needed.

(2) REVIEWER: Vignette is informative and well done.

AUTHORS: Thank you.

(3) REVIEWER: The markdown file in the vignette is not written according to "Rmarkdown" standards. The code section needs to start with "```{r}". If the code isn't written like this in the vignette then the R code is not evaluated. Bioconductor vignettes must have evaluated code chunks.

AUTHORS: All code sections now work as required and figures are evaluated and generated by the system.

(4) REVIEWER: You should not have a "figures" folder in your vignette. This should be generated as the build system runs your vignette. This is solved if you fix your markdown file.

AUTHORS: As suggested, we eliminated the figures folder by evaluating the vignette.

(5) REVIEWER: Consider putting .Rhistory in the .gitignore file of your repository

AUTHORS: .Rhistory file was removed

(6) REVIEWER: Good man pages, with examples for each function.

AUTHORS: Thank you.

(7) REVIEWER: It seems like the input to key functions could use the SummarizedExperiment package and class to represent data (see DESeq2's vignette). This greatly increases interoperability with other Bioconductor packages.

AUTHORS: We thank the Reviewer for the suggestion, SummarizedExperiment package is indeed a great tool and can increases interoperability and make data more consistent across different platforms. However, RTNsurivival requires a TNI class object. By the time SummarizedExperiment package was made available for the community, TNI class was 2 years on Bioconductor, so this would require updating an older Bioconductor class. Although it is possible, it requires considering the life cycle of another package. We are going to evaluate the possibility of implementing an alternative input format that includes SummarizedExperiment package. In the meantime, we have simplified the vignette of RTNsurvival in order to make the data type required clearer to run the current package, not exposing the implementations.

(8) REVIEWER: Always provide and use (including internally in the package) a constructor (e.g., TNS(...) instead of new("TNS", ...)) and accessors (e.g., tni() instead of object@tni) to avoid directly exposing implementation details (e.g,. new(), @) to the user.

AUTHORS: The same problem as described above, RTNsurvival requires a TNI class object. For RTNsurvival, there is no exposed implementations, all details hidden. We hope that the new examples in the vignette have clarified the input data format. Therefore, we changed the vignette and manual examples to provide the user with a processed TNI object. This makes the examples simpler and hides any implementation details from the user.

(9) REVIEWER: Consider: Use consistent code formatting and white space, e.g., use the formatR

AUTHORS: All code was cleaned up using formatR.

(10) REVIEWER: Functions like .survplot in the "AllSupplements.R" represent a plot, with too many 'magic numbers' that are likely to make the code very fragile, e.g., when the user changes the data set or size of the plotting device. But does make pretty plots

AUTHORS: Thank you. We now provide more graphical parameters for fine-tuning to functions like .survplot. As most of the 'magic numbers' are graphical parameters, we believe this will offset most plotting issues that users might have had.

(11) REVIEWER: Use message()instead of cat()so that diagnostic messages go to stderr rather than stdout.

AUTHORS: All cat() calls were replaced with message() calls.

(12) REVIEWER: Use e.g., seq_len(nSections) (AllSupplements.R:135) instead of 1:nSections for robust code (avoiding problems when nSections == 0).

AUTHORS: 1:nSections was changed toseq_len(nSections)

(13) REVIEWER: (AllMethods.R:448) Avoid 'copy-and-append', where resall is initialized and then at each iteration appended with rbind(). This is extremely inefficient. Either 'pre-allocate and fill' or use an lapply() to generate the data and then a single call do.call("rbind", result); some hints are here.

AUTHORS: The 'copy-and-append' problem has been solved using lapply()to generate resall.

(14) REVIEWER: Consider adding the existing code to the RTN package.

AUTHORS: We thank the Reviewer for the suggestion, however, the maintenance cycle of RTN is too complex to include new and not directly related methods as the ones provided by RTNsurvival. This new package provides concepts that cannot be easily integrated into the story around RTN. Therefore, we rather see RTN as a basic infrastructure to build regulatory networks. Whenever possible we want to spin off new methods if we see this opportunity. RTNsurvival brings a new method that we have recently described in our Nature Genetics study (doi: 10.1038/ng.3458), and we believe it can bring great value to the community that studies regulatory networks.

bioc-issue-bot commented 7 years ago

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

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