AMARETTO new package submission

[ogevaert]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/gevaertlab/AMARETTO

Confirm the following by editing each check box to '[x]'

• [X] I understand that by submitting my package to Bioconductor, the package source and all review commentary are visible to the general public.

• [X] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.

• [X] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.

• [X] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.

• [X] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the bioc-devel mailing list to stay aware of developments in the Bioconductor community, responding promptly to requests for updates from the Core team in response to changes in R or underlying software.

I am familiar with the essential aspects of Bioconductor software management, including:

• [x] The 'devel' branch for new packages and features.
• [X] The stable 'release' branch, made available every six months, for bug fixes.
• [X] Bioconductor version control using Git (optionally via GitHub).

For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.

[jayendrashinde91]

Dear reviewers @mtmorgan @lwaldron @LiNk-NY Thank you for your suggestions. We added most of your suggested edits and made critical changes with the coding style for the package to be compliant with the Bioconductor submission.

• DESCRIPTION

• [x] Consider a more extensive Description: field, like a paper abstract.

• [x] The License: field says that the package is licensed under MIT but the LICENSE file is Apache. Please clarify.

• vignette

• [x] please remove vignette 'build' products, i.e., the pdf file, from the vignettes directory; these are created when the package is installed.

• [x] the vignette needs to contain evaluated R code chunks, rather than static code. Most code in the vignette should be evaluated, with the exception of package installation instructions.

• [x] Use TargetDirectory <- tempfile() for temporary file locations.

• R

• [x] Consider using BiocFileCache so that both your user and the build system only download large files once.

• [x] e.g., amaretto_download.R:21 use message() rather than cat() when providing informative messages to users. Note that message() pastes its arguments together, so that cat(paste0("foo ", bar)) becomes message("foo ", bar)

• [x] e.g., amaretto_download.R:42 this command is only executed if there are no prior errors, otherwise the user is surprised to find their directory changed 'behind their backs'. At the start of the function, ensure that the original directory is restored no matter what happens by using

• amaretto_download.R:59 I'm not an expert on TCGA, but am concerned that your efforts duplicate those available in other Bioconductor packages; maybe @LiNk-NY or @lwaldron can comment further.

We had some discrepancy in the downloads using curatedTCGA for certain cancer types. The number of samples varied using curatedTCGAData() and AMARETTO_Download()

• [x] amaretto_download.R:104 use httr instead of getURL()

• [x] amaretto_functions.R:185 use seq_len(AMARETTOresults$NrModules) to avoid surprise when AMARETTOresults$NrModules == 0

• [x] amaretto_functions.R:209 use 'pre-allocate and fill' or simply lappy() and friends.

• [x] amaretto_functions.R:217 use vectorized (one call to an R function) rather than iterative (one call per element) calculations, e.g., colMeans() rather than apply(., 2, mean).

• [x] amaretto_htmlreport.R:88 this and other code in this file is basically unreadable!

• [x] amaretto_preprocess.R: 674 Another (of many!) examples where a simple lapply would be both easier to read and more efficient

• man

• [x] pay attention to line widths, especially in examples, where many environments present man pages formatted to a width of 80 characters.

• [x] most man pages should have runnable code (not just loading a data set like AMARETTO_EvaluateTestSet.Rd!)

• other

• [x] please 'clean up' the master branch of the repository to include only files necessary for your package, e.g., removing AMARETTO-manual.pdf and files/.

• [x] usually only a single .gitignore file (in the top-level directory) is required.

[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/ogevaert.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("AMARETTO"). The package 'landing page' will be created at

https://bioconductor.org/packages/AMARETTO

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.