ramr

[oleksii-nikolaienko]

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

• Repository: https://github.com/BBCG/ramr

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.

• [x] I am familiar with the Bioconductor code of conduct and agree to abide by it.

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]

Hi @oleksii-nikolaienko

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: ramr
Title: Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
Version: 0.99.0
Authors@R: 
    person(given = "Oleksii",
 family = "Nikolaienko",
 role = c("aut", "cre"),
 email = "oleksii.nikolaienko@gmail.com",
 comment = c(ORCID = "0000-0002-5910-4934"))
Maintainer: Oleksii Nikolaienko <oleksii.nikolaienko@gmail.com>
Description: ramr is an R package for detection of low-frequency aberrant
    methylation events in large datasets obtained by methylation profiling
    using array or high-throughput bisulfite sequencing. In addition, package
    provides functions to visualize found aberrantly methylated regions (AMRs),
    and to generate sets of all possible regions to be used as reference sets
    for enrichment analysis.
Depends:
    R (>= 3.6.0),
    GenomicRanges,
    parallel,
    doParallel,
    foreach,
    matrixStats,
    methods
Imports:
    BiocGenerics,
    ggplot2,
    reshape2,
    EnvStats,
    ExtDist,
    S4Vectors
Suggests:
    RUnit,
    knitr,
    rmarkdown,
    gridExtra,
    annotatr,
    LOLA
License: Artistic-2.0
URL: https://github.com/BBCG/ramr
BugReports: https://github.com/BBCG/ramr/issues
Encoding: UTF-8
LazyData: true
biocViews: DNAMethylation, DifferentialMethylation, Epigenetics,
    MethylationArray, MethylSeq
RoxygenNote: 7.0.0
VignetteBuilder: knitr

[bioc-issue-bot]

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

[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: "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/ramr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 7eeec48b49c83c8331c762abace7d54bebfe08a4

[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. 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/ramr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[oleksii-nikolaienko]

Hi @lshep, I will probably ask the same question that many other people ask, but I couldn't find an explanation on Bioconductor's R version requirement. Warning in my build log suggests to increase it to R version 4.1, but it makes no sense, as the actual requirement for my package is 3.5.0, while the latest devel version is 4.0.3. I actually want people to use my package, reviewers of my paper to check it on their machines. If I put 4.1 no one would be able to install it. What should I do with this warning?

[lshep]

The current released version of R is 4.0.3 (not devel) which technically is linked with our Release Bioc 3.12 packages. We say R 4.1 because that is the current devel version of R which is what our devel Bioc 3.13 is currently building off of. We coordinate our Spring release with the R release so they stay in sync and it is actually possible to download the devel version of R. We have no way on our builders to guarantee that a package would work on a previous version of R (and therefore also potentially previous versions of packages which are sometime very closely tied to an R release). R had significant changes from the jump of 3.6 to 4.0. We would recommend minimally making the requirement 4.0.3 and I could ignore the warning.

[oleksii-nikolaienko]

Ok, thank you for the clarification. I'll change the requirement to 4.0.3 and resubmit on weekend

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: d05abef7b0b55bdf41ef29e413f1701f8e654682

[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. 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/ramr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[oleksii-nikolaienko]

Hi @lshep, the only warning is on R version. Hope the rest is OK in order to be included

[lshep]

Sorry for the delay. I was away for the holiday. I should have a review for you within the next few days.

[lshep]

Good use of Bioconductor GRanges class. Please see the following minor comments:

Build report

• [ ] Please use donttest instead of dontrun. donttest requires valid R code while dontrun does not.

• [ ] Another option instead of donttest/dontrun in man pages for options like graphing is using if(interactive())

DESCRIPTION

• [ ] Please remove LazyData: true. We have rarely found it useful and can actually slow installation of packages.

Vignette:

• [ ] R 4.1 has made changes to the default options for timeout for downloading files to 60 seconds. You might want to add a note before downloading and unpacking raw IDAT files that if users experience timeouts to adjust the options(timeout=)

• [ ] I'm not sure if you are using these internally or if they are coming from a dependent package. If they are in a dependent package you can ignore, however if this in your code you should not use deprecated functions

  Warning messages:
1: `distinct_()` is deprecated as of dplyr 0.7.0.
Please use `distinct()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 
2: `group_by_()` is deprecated as of dplyr 0.7.0.
Please use `group_by()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 

R code:

getAMR.R

• [ ] Please remove any non active commented out code and TODO comments

Please address the above issues. When ready perform a version bump for the new build report to generate and comment back here with an update.
Cheers!

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 01943ab61ddfff0282753314dab400b41be4f0b8

[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. 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/ramr to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[oleksii-nikolaienko]

Thanks for the review, @lshep. New version builds with the only warning on R version. Here are the comments:

Build report

• [x] Please use donttest instead of dontrun. donttest requires valid R code while dontrun does not.

have changed to donttest

DESCRIPTION

• [x] Please remove LazyData: true. We have rarely found it useful and can actually slow installation of packages.

removed LazyData

Vignette:

• [x] R 4.1 has made changes to the default options for timeout for downloading files to 60 seconds. You might want to add a note before downloading and unpacking raw IDAT files that if users experience timeouts to adjust the options(timeout=)

added note on the potential timeout issue

• [x] I'm not sure if you are using these internally or if they are coming from a dependent package. If they are in a dependent package you can ignore, however if this in your code you should not use deprecated functions

those are some internal dplyr warnings

R code: getAMR.R

• [x] Please remove any non active commented out code and TODO comments

have removed them

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

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/oleksii-nikolaienko.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("ramr"). The package 'landing page' will be created at

https://bioconductor.org/packages/ramr

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.