williazo commented 5 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/williazo/microbiomeDASim

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 commented 5 years ago

Hi @williazo

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: microbiomeDASim
Type: Package
Title: Microbiome Differential Abundance Simulation 
Version: 0.99.0
Author: Justin Williams, Hector Corrada Bravo, Jennifer Tom, Joseph Nathaniel Paulson
Maintainer: Justin Williams <williazo@ucla.edu>
Description: A toolkit for simulating differential microbiome data designed for
    longitudinal analyses. Several functional forms may be specified for the
    mean trend. Observations are drawn from a multivariate normal model. The objective of this
    package is to be able to simulate data in order to accurately compare different longitudinal
    methods for differential abundance.
License: MIT + file LICENSE
Imports:
    graphics, 
    ggplot2,
    MASS,
    tmvtnorm,
    Matrix,
    mvtnorm,
    pbapply,
    stats
Depends: 
    R (>= 3.6.0)
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 6.1.1
Suggests: 
    testthat (>= 2.1.0),
    knitr,
    devtools
VignetteBuilder: knitr
biocViews: Microbiome,
    Visualization,
    Software
BugReports: https://github.com/williazo/microbiomeDASim/issues
URL: https://github.com/williazo/microbiomeDASim

bioc-issue-bot commented 5 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 5 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: "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 5 years ago

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

6d844f5 fixing inline link from ggplot2::stat_smooth to gg... b56ed52 updating all documentation after fixing inline lin... 28af5e1 update BiocCheck comments to reflect indentation f... 6c9e7d6 bump version number

williazo commented 5 years ago

bumped the latest version with corrections to the inline function calling for ggplot2 as well as removed .Rproj from git files.

bioc-issue-bot commented 5 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.

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

Please see the build report for more details.

Kayla-Morrell commented 5 years ago

Hello @williazo,

Thank you for submitting to Bioconductor. Please see the initial review of the package below. The required changes must be made while the suggested changes do not have to be but we strongly encourage them. Comment back here with updates that have been made and when the package is ready for a re-review.

General package development

[ ] REQUIRED: The raw package directory should not contain unnecessary files, system files, or hidden files. These files may be present in your local directory but should not be commited to git. The 'BiocCheck-comments' and 'cran-comments' files, also the 'doc/' directory, don't seem necessary but please clarify if I am mistaken.
[ ] REQUIRED: Currently, the 'SIMULATION/' directory would not be distributed to users through your package. When we build packages we build off of specific things in the repo and this directory is not one of those things. If you want this to be apart of the Bioconductor package I suggest you put it within an 'inst/' directory. Even just placing the Jupyter notebook within an 'inst/script/' directory would be better, since this is where we ask developers to house scripts for creating extdata in their packages. This will insure that it is included since we keep things in this 'inst/' directory when building packages from GitHub.

DESCRIPTION

[ ] REQUIRED: 'LazyData:' should be set to false. This field being true can slow down the loading of the package.

Vignettes

[ ] SUGGESTION: The idea of the 'Introduction' section is to almost be an abstract to introduce the objective, models, unique functions, key points, etc that distinguish the package from other packages of similar type. The information you have currently is a good motive for using the package but I would add a bit more detail about the actual package.
[ ] REQUIRED: After the 'Introduction' section there should be an 'Installation' section that shows users how to download and the package from Bioconductor. The code should look something like this:

if(!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("microbiomeDASim")

[ ] REQUIRED: The last section of the vignette should be Session Info and should include sessionInfo().

man pages

[ ] SUGGESTION: Only functions that are exported need to have a man page. For those functions you have documented already that aren't exported, you can add the tag @keywords internal which will remove the function from the documentation index.

Unit tests

[ ] CLARIFICATION: What is the purpose of the 'Rplots.pdf' file in the 'test/testthat' directory?

Best, Kayla

bioc-issue-bot commented 5 years ago

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

c2fc670 version bump

bioc-issue-bot commented 5 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.

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

Please see the build report for more details.

williazo commented 5 years ago

Hi @Kayla-Morrell,

Thank you for your review comments above, I have gone through and updated the package based on your feedback and have included details for each of your points below.

General package Development

[x] REQUIRED: The raw package directory should not contain unnecessary files, system files, or hidden files. These files may be present in your local directory but should not be commited to git. The 'BiocCheck-comments' and 'cran-comments' files, also the 'doc/' directory, don't seem necessary but please clarify if I am mistaken.

I have removed the build comments (BiocCheck and cran) and 'doc/' directory from the package directory (commit a6d455d).

[x] REQUIRED: Currently, the 'SIMULATION/' directory would not be distributed to users through your package. When we build packages we build off of specific things in the repo and this directory is not one of those things. If you want this to be apart of the Bioconductor package I suggest you put it within an 'inst/' directory. Even just placing the Jupyter notebook within an 'inst/script/' directory would be better, since this is where we ask developers to house scripts for creating extdata in their packages. This will insure that it is included since we keep things in this 'inst/' directory when building packages from GitHub.

As suggested I moved the Jupyter notebook into an `inst/script/' directory to allow for it to be distributed. I think it provides a useful framework for a hands on introduction to using the package and some of the rationale (commit c2ad972).

Description

[x] REQUIRED: 'LazyData:' should be set to false. This field being true can slow down the loading of the package.

I have changed this to false in the Description file (commit 83adb13).

Vignettes

[x] SUGGESTION: The idea of the 'Introduction' section is to almost be an abstract to introduce the objective, models, unique functions, key points, etc that distinguish the package from other packages of similar type. The information you have currently is a good motive for using the package but I would add a bit more detail about the actual package.

As suggested I re-wrote the Introduction section to highlight the objective of the simulation package and some of the key functions involved in simulating the longitudinal differential abundance. I moved the previous Introduction section into a new Motivation section after the Installation section (commit 828cf40).

[x] REQUIRED: After the 'Introduction' section there should be an 'Installation' section that shows users how to download and the package from Bioconductor

The Installation section has been added (commit 828cf40).

[x] REQUIRED: The last section of the vignette should be Session Info and should include sessionInfo().

The Session Info section has been added (commit 828cf40).

man pages

[x] SUGGESTION: Only functions that are exported need to have a man page. For those functions you have documented already that aren't exported, you can add the tag @keywords internal which will remove the function from the documentation index.

I have added @keywords internal for all of the helper function that aren't exported (commit 7f089b1).

Unit tests

[x] CLARIFICATION: What is the purpose of the 'Rplots.pdf' file in the 'test/testthat' directory?

I believe that this Rplots.pdf file was created by accident as my test scripts had examples where the plot graphics were turned on. I have removed this file manually and have also changed the test scripts so that the graphics are turned off for all examples (commit 0149350).

I look forward to hearing additional comments and/or suggestions.

Best, Justin

Kayla-Morrell commented 5 years ago

Hi @williazo,

Thank you for making the changes and providing details for each point. Everything looks good and I'm happy to accept the package!

Best, Kayla

bioc-issue-bot commented 5 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!

williazo commented 5 years ago

Thanks @Kayla-Morrell! I will look out for further instructions and additional information in the coming days.

Best, Justin

mtmorgan commented 5 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/williazo.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 BiocManager::install("microbiomeDASim"). The package 'landing page' will be created at

https://bioconductor.org/packages/microbiomeDASim

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

microbiomeDASim #1216

General package development

DESCRIPTION

Vignettes

man pages

Unit tests

General package Development

Description

Vignettes

man pages

Unit tests