decontam - Githubissues

benjjneb commented 6 years ago

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

Repository: https://github.com/benjjneb/decontam

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

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[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.
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bioc-issue-bot commented 6 years ago

Hi @benjjneb

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: decontam
Type: Package
Title: Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
Version: 0.99.0
Date: 2018-03-05
Author: Benjamin Callahan <benjamin.j.callahan@gmail.com>, Nicole Marie Davis
Maintainer: Benjamin Callahan <benjamin.j.callahan@gmail.com>
Description: Simple statistical identification of contaminating sequence features in 
    marker-gene or metagenomics data. Works on any kind of feature derived from 
    environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...).
    Requires DNA quantitation data or sequenced negative control samples.
Depends:
    R (>= 3.3.1),
    methods (>= 3.3.1)
Imports:
    ggplot2 (>= 2.1.0),
    reshape2 (>= 1.4.1)
Suggests:
    BiocStyle,
    knitr,
    rmarkdown,
    phyloseq
License: Artistic-2.0
Encoding: UTF-8
VignetteBuilder: knitr
biocViews: Microbiome, Sequencing, Classification, Metagenomics
URL: https://github.com/benjjneb/decontam
BugReports: https://github.com/benjjneb/decontam/issues
LazyData: true
RoxygenNote: 6.0.1

bioc-issue-bot commented 6 years ago

A reviewer has been assigned to your package Learn What to Expect during the review process.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

bioc-issue-bot commented 6 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 build report for more details.

bioc-issue-bot commented 6 years ago

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

f340a3a html_document instead of html_document2

bioc-issue-bot commented 6 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 build report for more details.

dvantwisk commented 6 years ago

Just messaging you back to check in on your progress. This is just a two week notice. Are you still working on this package? Do you want to keep this issue open?

bioc-issue-bot commented 6 years ago

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

ef78c45 Bump for BiocCheck warnings Picky Namespace stuff

bioc-issue-bot commented 6 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 build report for more details.

benjjneb commented 6 years ago

@dvantwisk

There is still one remaining Warning * WARNING: Update R version dependency from 3.4.1 to 3.5.

Can this package be reviewed while leaving the R package req at 3.4.1? I know this is preferred for new package, but it's not needed at all here. And right now the manuscript is in review, and I'd strongly prefer to not push the package requirements to a not-yet release version of R at this point.

dvantwisk commented 6 years ago

That's fine. I'll have a look at your package now.

dvantwisk commented 6 years ago

Here's the review for your package. It looks very good and there are just a few things that need to be mentioned. Please message me back once you've addressed these issues.

.gitignore

[REQUIRED] Add decontam.Rproj to .gitignore.

R/decontam.R

[CONSIDER] L79: Use match.arg() to improve style of function declaration. For example, the parameter batch.combine can have three values "minimum", "product", and "fisher". The parameter in the function declaration can be written as batch.combine=c('minimum', 'product', 'fisher'). The value that the user uses can be obtained with batch.combine <- match.arg(batch.combine). The first value (in this case minimum) is the default argument. Using this method makes it clear to users what the allowed inputs to a function are and may also make error catching easier. There are many places in this function that you could use this.

R/plotting.R

[CONSIDER] L26, 31, 35, 38: Add \code{logical} like the other entries just to remain consistent in documentation.

tests

[CONSIDER] adding tests using the testthat pacakge.

vignettes

[REQUIRED] Remove Stangled file: decontam_intro.R

bioc-issue-bot commented 6 years ago

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

a097eae Address BioC review issues Changed to match.arg h...

bioc-issue-bot commented 6 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 build report for more details.

benjjneb commented 6 years ago

Here's the review for your package. It looks very good and there are just a few things that need to be mentioned. Please message me back once you've addressed these issues.

@dvantwisk These comments have been addressed in 0.99.3 which was just pushed and built: a097eae9837e1af5accc6d614df8b6d83905606e

[REQUIRED] Add decontam.Rproj to .gitignore. R/decontam.R

Done.

[CONSIDER] L79: Use match.arg() to improve style of function declaration. For example, the parameter batch.combine can have three values "minimum", "product", and "fisher". The parameter in the function declaration can be written as batch.combine=c('minimum', 'product', 'fisher'). The value that the user uses can be obtained with batch.combine <- match.arg(batch.combine). The first value (in this case minimum) is the default argument. Using this method makes it clear to users what the allowed inputs to a function are and may also make error catching easier. There are many places in this function that you could use this. R/plotting.R

Done. That is useful, I hadn't been aware of that functionality.

[CONSIDER] L26, 31, 35, 38: Add \code{logical} like the other entries just to remain consistent in documentation. tests

Done.

[CONSIDER] adding tests using the testthat pacakge. vignettes

Not done, although acknowledge that this would be a good idea in the future.

[REQUIRED] Remove Stangled file: decontam_intro.R

Done.

dvantwisk commented 6 years ago

All the changes look good! I'm going to move to accept the package now.

bioc-issue-bot commented 6 years ago

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!

benjjneb commented 6 years ago

Thanks @dvantwisk!

mtmorgan commented 6 years ago

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

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

https://bioconductor.org/packages/decontam

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.

Bioconductor / Contributions

decontam #666