VplotR - Githubissues

js2264 commented 4 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/js2264/VplotR

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 4 years ago

Hi @js2264

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: VplotR
Type: Package
Title: Set of tools to make V-plots and compute footprint profiles
Version: 0.99.0
Date: 2020-05-03
Encoding: UTF-8
Authors@R: 
    c(person(given = "Jacques",
 family = "Serizay",
 role = c("aut", "cre"),
 email = "jacquesserizay@gmail.com",
 comment = c(ORCID = "0000-0002-4295-0624")))
Description: The pattern of digestion and protection from DNA nucleases such 
    as DNAse I, micrococcal nuclease, and Tn5 transposase can be used to 
    infer the location of associated proteins. This package contains useful 
    functions to analyze patterns of paired-end sequencing fragment density. 
    VplotR facilitates the generation of V-plots and footprint profiles 
    over single or aggregated genomic loci of interest.
URL: https://github.com/js2264/VplotR
BugReports: https://github.com/js2264/VplotR/issues
RoxygenNote: 7.1.0
Depends:
    R (>= 4.0)
Imports: 
    ggplot2,
    cowplot,
    magrittr,
    GenomeInfoDb,
    GenomicAlignments,
    GenomicRanges,
    IRanges,
    RColorBrewer,
    zoo,
    Rsamtools,
    S4Vectors,
    parallel,
    reshape2,
    methods, 
    graphics,
    stats
Suggests: 
    testthat,
    covr,
    knitr,
    rmarkdown,
    pkgdown
VignetteBuilder: knitr
biocViews:
    NucleosomePositioning,
    Coverage,
    Sequencing, 
    BiologicalQuestion, 
    ATACSeq, 
    Alignment
License: GPL-3 + file LICENSE

bioc-issue-bot commented 4 years ago

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 commented 4 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, skipped, TIMEOUT". 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/VplotR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 28e0cc1a34f7e053544bedce1109a6f155dfe851

bioc-issue-bot commented 4 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. 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/VplotR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: fd8523b8b7e143e4ca38b1282e6eb6e0d0988fee

bioc-issue-bot commented 4 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. 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/VplotR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: b6873a58a286d1f71a523bf1c7931eb0a580c967

bioc-issue-bot commented 4 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. 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/VplotR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

js2264 commented 4 years ago

Dear @dvantwisk, I've addressed the different error/warning messages obtained from initial build/check runs. I am now left with only minor "Note" messages. Let me know if the package seems to be ready for review or if you want me to do anything else before that! Best, Jacques

js2264 commented 4 years ago

Hi @dvantwisk, Any idea of when the review would be done? Best, J

Kayla-Morrell commented 4 years ago

Hello @js2264 - Thank you for your patience, I will be posting the initial review here within the next couple days.

Kayla-Morrell commented 4 years ago

@js2264 -

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 TODO file should be removed.

DESCRIPTION

[ ] SUGGESTION: The GPL-3 is a standard license so you don't have to include the LICENSE file.
[ ] REQUIRED: I see GenomicAlignments listed under 'Imports:' but I don't see it listed in the NAMESPACE file. Please either remove from 'Imports:' or be sure it is included in the NAMESPACE.

Data

[ ] REQUIRED: I was able to find the use of all the data files, whether that be in the vignette, in R code/examples, or in tests, but I wasn't able to locate where 'seqinfos' is used? Is this file necessary? If not, please remove it.

Vignettes

[ ] REQUIRED: There should be an 'Introduction' section that serves as an abstract to introduce the package and functionality of it.
[ ] REQUIRED: There should be an 'Installation' section that demonstates to the user how to install/download the package from Bioconductor. The code should look like the following and include eval = FALSE,

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

[ ] SUGGESTION: We strongly encourage the use of table of contents.
[ ] REQUIRED: All code chunks should be executable and therefore should not include eval = FALSE. Having this option defeats the purpose of having a reproducable vignette.
[ ] REQUIRED: Line 72, data should not be accessed from a website, there is no guarantee that the user will be able to access this data. The data should either be included in the package or be included in a seperate experiment data package.
[ ] REQUIRED: Line 225, if this a static plot for the vignette you can include the figure in the vignette directory. This will bypass having to get it from GitHub.

Man pages

[ ] REQUIRED: The 'figures' directory does not belong here. You should create an 'inst/figures/' directory and move them there.
[ ] SUGGESTION: For all of the function you have documented that are not exported I would suggest adding the tag @keywords internal. This will remove the function from the documentation index.
[ ] REQUIRED: There should be a runnable example for the following man pages since it documents and exported object:
- importPEBamFiles.Rd

Unit tests

[ ] REQUIRED: Tests should be testable, therefore you should remove any skip() use in the tests. Ideally broken tests should be fixed, but if that isn't possible they should be removed.

Best, Kayla

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 8925eae5affa7fbe3eaf37882e043a21eb3c7541

bioc-issue-bot commented 4 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. 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/VplotR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0a8a38d06c614a83ade05b0c5e09967941b5af46

bioc-issue-bot commented 4 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. 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/VplotR to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

js2264 commented 4 years ago

@Kayla-Morrell -

Thank you very much for your comments. I have addressed all the required comments and suggestions. I bumped the version and the checks only return Notes messages.

Let me know if there is something else you'd like me to change/improve. Best, Jacques

@js2264 -

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

[x] REQUIRED: The TODO file should be removed.

DESCRIPTION

[x] SUGGESTION: The GPL-3 is a standard license so you don't have to include the LICENSE file.
[x] REQUIRED: I see GenomicAlignments listed under 'Imports:' but I don't see it listed in the NAMESPACE file. Please either remove from 'Imports:' or be sure it is included in the NAMESPACE.

Data

[x] REQUIRED: I was able to find the use of all the data files, whether that be in the vignette, in R code/examples, or in tests, but I wasn't able to locate where 'seqinfos' is used? Is this file necessary? If not, please remove it.

Vignettes

[x] REQUIRED: There should be an 'Introduction' section that serves as an abstract to introduce the package and functionality of it.
[x] REQUIRED: There should be an 'Installation' section that demonstates to the user how to install/download the package from Bioconductor. The code should look like the following and include eval = FALSE,

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

[x] SUGGESTION: We strongly encourage the use of table of contents.
[x] REQUIRED: All code chunks should be executable and therefore should not include eval = FALSE. Having this option defeats the purpose of having a reproducable vignette.
[x] REQUIRED: Line 72, data should not be accessed from a website, there is no guarantee that the user will be able to access this data. The data should either be included in the package or be included in a seperate experiment data package.
[x] REQUIRED: Line 225, if this a static plot for the vignette you can include the figure in the vignette directory. This will bypass having to get it from GitHub.

Man pages

[x] REQUIRED: The 'figures' directory does not belong here. You should create an 'inst/figures/' directory and move them there.
[x] SUGGESTION: For all of the function you have documented that are not exported I would suggest adding the tag @keywords internal. This will remove the function from the documentation index.
[x] REQUIRED: There should be a runnable example for the following man pages since it documents and exported object:
- importPEBamFiles.Rd

Unit tests

[x] REQUIRED: Tests should be testable, therefore you should remove any skip() use in the tests. Ideally broken tests should be fixed, but if that isn't possible they should be removed.

Best, Kayla

Kayla-Morrell commented 4 years ago

@js2264 - Thank you for making the necessary changes. I have reviewed them and they look good. I am more than happy to accept the package.

Best, Kayla

bioc-issue-bot commented 4 years ago

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

Thank you for contributing to Bioconductor!

mtmorgan commented 4 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/js2264.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("VplotR"). The package 'landing page' will be created at

https://bioconductor.org/packages/VplotR

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

VplotR #1547

General package development

DESCRIPTION

Data

Vignettes

Man pages

Unit tests

General package development

DESCRIPTION

Data

Vignettes

Man pages

Unit tests