cTRAP #906

nuno-agostinho · 2018-10-05T12:30:38Z

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bioc-issue-bot · 2018-10-05T12:30:39Z

Hi @nuno-agostinho

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: cTRAP
Title: Identification of potential transcriptome perturbations
Version: 0.99.1
Authors@R: c(person("Nuno", "Agostinho", 
        email="nunodanielagostinho@gmail.com", role=c("aut", "cre")),
        person("Bernardo", "de Almeida", role="aut"),
        person(c("Nuno", "Luís"), "Barbosa-Morais", role=c("aut", "led")))
Description: Compare differential gene expression results with those from known
    cellular perturbations (such as gene knock-down, overexpression or small 
    molecules) derived from the Connectivity Map. Such analyses allow not only 
    to infer the molecular causes of the observed difference in gene expression 
    but also to identify small molecules that could drive or revert specific 
    transcriptomic alterations.
Depends: R (>= 3.5.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
biocViews: DifferentialExpression, GeneExpression, RNASeq, Transcriptomics,
    Pathways
URL: https://github.com/nuno-agostinho/cTRAP
BugReports: https://github.com/nuno-agostinho/cTRAP/issues
Suggests: testthat
RoxygenNote: 6.1.0
Imports: data.table,
    limma,
    stats,
    fgsea,
    pbapply,
    plyr,
    biomaRt,
    cowplot,
    ggplot2,
    rhdf5,
    R.utils,
    httr,
    methods,
    piano,
    readr,
    utils,
    graphics

bioc-issue-bot · 2018-10-05T19:03:07Z

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bioc-issue-bot · 2018-10-05T19:10:26Z

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bioc-issue-bot · 2018-10-09T11:01:51Z

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

cc87e27 Fix issue in Windows build

bioc-issue-bot · 2018-10-09T11:10:36Z

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bioc-issue-bot · 2018-10-09T12:46:40Z

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

ccbfada Change mode depending on downloading a compressed ...

bioc-issue-bot · 2018-10-09T12:57:57Z

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nuno-agostinho · 2018-10-10T13:34:38Z

Hello @vobencha, I have now fixed all issues with the package, but I am having trouble with running R CMD check within 5 minutes. The problem is that many examples/tests make use of data that is downloaded on demand.

I asked the question at bioc-devel, to which Lori Shepherd replied to check BiocFileCache. Still, wouldn't this make the build fail since it has to download everything the first time to create the cache?

bioc-issue-bot · 2018-10-10T13:44:46Z

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

0c232ca Avoid testing function to improve speed when runni...

bioc-issue-bot · 2018-10-10T13:45:27Z

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598419e Avoid testing function to improve speed when runni...

bioc-issue-bot · 2018-10-10T14:12:14Z

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bioc-issue-bot · 2018-10-10T14:13:28Z

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bioc-issue-bot · 2018-10-10T14:16:40Z

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bioc-issue-bot · 2018-10-10T14:30:18Z

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vobencha · 2018-10-10T15:00:43Z

Hi @nuno-agostinho ,

I'd recommend creating small sample data files for the man pages and vignette. Put them in cTRAP/data/ or cTRAP/inst/extdata. Documentation on what type of file goes where is here:
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Data-in-packages

Once this is done you can load the file with system.file() or data() - there is no need to create your own function, loadInternalData().

This solution assumes you're downloading data in man pages or vignette, not internally with your package functions. The package functions should avoid downloading on the fly - they will be broken when the user has no internet access.

Valerie

vobencha · 2018-10-17T15:00:12Z

We have until Oct 24th if you want this in Bioc 3.8:
https://www.bioconductor.org/developers/release-schedule/

Otherwise the package will only be available in devel (Bioc 3.9) until the Spring 2019 release.

bioc-issue-bot · 2018-10-20T00:43:30Z

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

009a160 Use smaller datasets for examples and vignettes

bioc-issue-bot · 2018-10-20T00:52:53Z

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bioc-issue-bot · 2018-10-20T09:44:14Z

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

2a306e0 Fix errors in R CMD check

bioc-issue-bot · 2018-10-20T09:54:59Z

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bioc-issue-bot · 2018-10-20T11:07:32Z

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

afef174 Add more runnable examples

bioc-issue-bot · 2018-10-20T11:18:46Z

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bioc-issue-bot · 2018-10-20T11:24:00Z

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bioc-issue-bot · 2018-10-20T11:34:08Z

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vobencha · 2018-10-22T18:14:31Z

@nuno-agostinho If the package is ready for re-review please articulate what changes were made wrt
#906 (comment)

nuno-agostinho · 2018-10-22T23:06:58Z

Hey @vobencha, as per the comparison between commit 5c8c972 and the current master (commit 6257e75), the following changes were made:

Data files are now stored in cTRAP/data (for external use) instead of cTRAP/R/sysdata.rda (for internal use)
As you suggested, small sample data files were created for the man pages and vignette; they are stored in the cTRAP/data folder and their respective documentation (including code on how to obtain the same sample data) is in the cTRAP/R/cTRAP-package.r file
As you suggested, internal data is loaded using the built-in data()function instead of the loadInternalData() function that was created for a redundant purpose
Code to download and filter/process data was isolated into new functions (downloadENCODEsamples(), downloadL1000data(), filterL1000metadata() and prepareENCODEgeneExpression()), so users are able to explicitly use the output of those functions as input for downstream functions
Changes were made to function examples, test units and vignette to reflect and leverage the new small data samples and functions, among the other changes reported here

Bug fixes, copy-editing and minor changes

The file cTRAP/R/l1000-package.r was renamed to cTRAP/R/cTRAP-package.r as the name of the package was changed cTRAP (I apologise for this as I forgot to rename this file before sending this for review)
performDifferentialExpression() returned a single mean-aggregate result of differential gene expression statistic for all genes whose ENSEMBL identifier did not match any gene symbol; the mean-aggregate value of such genes is now removed before returning the results
Function/variable names with L1000 were uniformed: any letter in a function/variable after L1000 is now lowercase for consistency purposes (e.g. getL1000Conditions() is now getL1000conditions())
Expanded the examples for the plotL1000comparison() function

vobencha · 2018-10-23T13:06:33Z

@nuno-agostinho

Excellent. Thanks for making the changes.

Just a few things left:

All man pages need running examples if possible; if there are exceptions please explain.
Remove vignettes/tutorial.R; only the vignette and graphic files should be in there.
Consider renaming the vignette to something more descriptive related to the package name.

We have until COB Oct 24 to get this in Bioc 3.8. These last issues shouldn't take much time - we should be able to make it.

Thanks.
Valerie

nuno-agostinho · 2018-10-23T14:07:50Z

Hey @vobencha, thank you for the quick reply. I would like to make the following comments on your points:

All man pages need running examples if possible; if there are exceptions please explain.

Do man pages for internal functions also need examples?

Regarding exported functions with no runnable examples, there are 3: downloadENCODEsamples() and downloadL1000data() have no runnable examples as they take time to download the data; loadL1000perturbations() requires the data downloaded from those functions and I thought it would be more useful to the user to have a non-runnable example with the code to download the needed files and running the function in question.

Consider renaming the vignette to something more descriptive related to the package name.

The vignette (previously named CTRAP: tutorial) will be renamed to cTRAP: differential expression comparison with cellular perturbations.

vobencha · 2018-10-23T17:27:23Z

Runable examples are only needed on man pages of exported functions.

WRT the download functions, I agree you don't want to download during the nightly builds. You could put a code chunk there and wrap in interactive():

if (interactive()) {
  # run the example
 }

Re: vignette name, I was specifically thinking of the R code file name. Currently the filename is tutorial.Rmd.

nuno-agostinho · 2018-10-23T17:58:00Z

You could put a code chunk there and wrap in interactive()

I will replace the \dontrun{ with if (interactive() ) { in the examples of the functions downloadENCODEsamples(), downloadL1000data() and loadL1000perturbations().

Re: vignette name, I was specifically thinking of the R code file name. Currently the filename is tutorial.Rmd.

I will rename the vignette to comparing_DGE_with_perturbations.Rmd.

As you suggested in your previous comment, I will also remove the vignettes/tutorial.R file. Do you agree with these changes?

bioc-issue-bot · 2018-10-23T17:58:37Z

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

2611ec8 Minor changes - Update vignette title - Fix docum...

bioc-issue-bot · 2018-10-23T18:13:41Z

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vobencha · 2018-10-23T19:03:14Z

Looks good! Thanks.

bioc-issue-bot · 2018-10-23T19:03:28Z

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 · 2018-10-23T19:09:05Z

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/nuno-agostinho.keys is not empty), then no further steps are required. Otherwise, do the following:

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

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mtmorgan closed this as completed Oct 23, 2018

cTRAP #906

cTRAP #906

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vobencha commented Oct 22, 2018 • edited Loading

nuno-agostinho commented Oct 22, 2018

Bug fixes, copy-editing and minor changes

vobencha commented Oct 23, 2018 • edited Loading

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