IgGeneUsage

[snaketron]

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

• Repository: https://github.com/snaketron/IgGeneUsage

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.

[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]

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

e5a639c 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.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details.

[bioc-issue-bot]

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

ae7f971 SummarizedExperiment, better explained

[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.

[bioc-issue-bot]

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

c8f2b3e it is good to depend on StanHeaders

[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". 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:

dbe7909 R >= 3.6

[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.

[mtmorgan]

This package looks good, with a few minor suggestions below.

DESCRIPTION

• please provide a more complete Description: of what your package does, e.g., like an abstract

• Including a copy of the GPL license is not required, since it is distributed with R

• It is unlikely that the user directly interacts with Rcpp; this should be in 'Imports:' rather than 'Depends:'.

vignettes

• it's not clear how ModelOverview.Rmd represents a standalond vignette?

• IgUsageCaseStudies.Rmd seems mostly to use base R commands and ggplot; revise so it is clear how your package contributes to understanding. In particular the key function seems to be DGU(), but the use of this function is in code chunks presented without description of inputs or interpretation of outputs.

R

• e.g., Usage.R:49 use message() rather than cat() to communicate progress to the user

• Util.R:176 this 'copy-and-append' pattern is very inefficient, use sapply() or pre-allocate and fill a list followed by a single do.call("rbind", ...) instead

man

• ok

tests

• good

[bioc-issue-bot]

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

6bc7451 suggestions applied

[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". 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:

5885b09 effect size = es

[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.

[snaketron]

Thank you for your suggestions @mtmorgan .

This package looks good, with a few minor suggestions below.

DESCRIPTION

* please provide a more complete Description: of what your package does, e.g., like an abstract

• provided

  • Including a copy of the GPL license is not required, since it is distributed with R

• extra GPL license removed

  • It is unlikely that the user directly interacts with Rcpp; this should be in 'Imports:' rather than 'Depends:'.
• Rccp is necessary for runtime compilation of stan models

vignettes

* it's not clear how ModelOverview.Rmd represents a standalond vignette?

• removed vignette. Methods section describing the model was added in IgUsageCaseStudies.Rmd

  • IgUsageCaseStudies.Rmd seems mostly to use base R commands and ggplot; revise so it is clear how your package contributes to understanding. In particular the key function seems to be DGU(), but the use of this function is in code chunks presented without description of inputs or interpretation of outputs.
• vignette restructured with more focus on inputs/outputs of DGU
• all input parameters are explained in more detail

R

* e.g., Usage.R:49 use `message()` rather than `cat()` to communicate progress to the user

• all cat -> message
  • Util.R:176 this 'copy-and-append' pattern is very inefficient, use sapply() or pre-allocate and fill a list followed by a single do.call("rbind", ...) instead
• pre-allocated list followed by do.call("rbind", ...)

man

* ok

tests

* good

[bioc-issue-bot]

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

bf5ad70 logos, typos, gitignore, last commit 9f5d42f Merge branch 'master' of github.com:snaketron/IgGe...

[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]

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/snaketron.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("IgGeneUsage"). The package 'landing page' will be created at

https://bioconductor.org/packages/IgGeneUsage

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.