HMP2Data - Githubissues

jstansfield0 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/jstansfield0/HMP2Data

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 @jstansfield0

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: HMP2Data
Title: 16s rRNA sequencing data from the Human Microbiome Project 2
Version: 0.99.1
Author:
    John Stansfield <stansfieldjc@vcu.edu>,
    Mikhail Dozmorov <mikhail.dozmorov@vcuhealth.org>
Maintainer: John Stansfield <stansfieldjc@vcu.edu>
Description: 
    HMP2Data is a Bioconductor package of the Human Microbiome
    Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as
    phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects.
    Individual matrices and data.frames used for building these S4 class 
    objects are also provided in the package.
Depends: R (>= 3.5.0)
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
Imports:
    AnnotationHub,
    assertthat,
    dplyr,
    ExperimentHub,
    kableExtra,
    knitr,
    magrittr,
    methods,
    readr,
    S4Vectors,
    SummarizedExperiment,
    phyloseq,
    MultiAssayExperiment,
    data.table
Suggests:
    Biobase,
    BiocCheck,
    BiocManager,
    BiocStyle,
    cowplot,
    devtools,
    ggplot2,
    gridExtra,
    haven,
    rmarkdown,
    roxygen2,
    stats,
    testthat,
    tibble,
    UpSetR
biocViews:
    ExperimentData,
    Homo_sapiens_Data,
    MicrobiomeData,
    ReproducibleResearch,
    SequencingData
RoxygenNote: 6.1.0
VignetteBuilder: knitr

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:

af1e366 fix class() checks

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.

Liubuntu commented 5 years ago

Hi @jstansfield0 ,

Thanks for your contribution to Bioconductor. Below is the initial review of your package. It is a very well written / organized package, with only several minor issues. please seek to address all / most of the issues, bump version, and make commit, and comment back here for updates or questions, or when ready for a 2nd look. Thanks!

Best, Qian

DESCRIPTION

LazyData: field: For packages that include data, we recommend not including LazyData: TRUE. This rarely proves to be a good thing. In our experience it only slows down the loading of packages with large data.
BugReports: field: It is encouraged to include the relevant links to Github for reporting Issues.
URL: field: This field directs users to source code repositories, additional help resources, etc; details are provided in “Writing R Extensions”, RShowDoc("R-exts").

NAMESPACE

Good!

R/

momspiMultiAssay.R & patient_table.R & table_two.R: remove unnecessary commented code (Suggested but not strictly required.). Could retain some comments for easy track. Check other files.

man/

Looks good.

data/

Good!

unit test

Good!

vignette

Prerequisites section, please add a little bit about installing BiocManager, and instruction for downloading the development version of the package, something like the following:

Download the package from Bioconductor.

{r getPackage, eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("pkgName")

Or install the development version of the package from Github.

{r, eval = FALSE}
BiocManager::install(“githubUserName/pkgname”)

bioc-issue-bot commented 5 years ago

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

cce469e address bioconductor comments

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.

jstansfield0 commented 5 years ago

Hi @Liubuntu

I have addressed your comments and pushed a new version of the package.

Liubuntu commented 5 years ago

Hi @jstansfield0 ,

Thanks for the quick updates. The package looks very nice, I'm accepting it right now.

Cheers, Qian

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!

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/jstansfield0.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("HMP2Data"). The package 'landing page' will be created at

https://bioconductor.org/packages/HMP2Data

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

HMP2Data #1123

DESCRIPTION

NAMESPACE

R/

man/

data/

unit test

vignette