reese3928 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/reese3928/NBAMSeq

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bioc-issue-bot commented 5 years ago

Hi @reese3928

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: NBAMSeq
Type: Package
Title: Negative Binomial Additive Model for RNA-Seq Data
Version: 0.99.0
Authors@R: c(
    person("Xu", "Ren", 
        email = "xuren2120@gmail.com", role = c("aut", "cre")),
    person("Pei Fen", "Kuan", 
        email = "peifen.kuan@stonybrook.edu", role = "aut"))
Description: High-throughput sequencing experiments followed by differential 
    expression analysis is a widely used approach to detect genomic biomarkers. 
    A fundamental step in differential expression analysis is to model the 
    association between gene counts and covariates of interest. NBAMSeq a 
    flexible statistical model based on the generalized additive model and 
    allows for information sharing across genes in variance estimation. 
License: GPL-2
Encoding: UTF-8
Imports:
    DESeq2,
    mgcv(>= 1.8-24),
    BiocParallel,
    genefilter,
    methods,
    stats,
Depends:
    R (>= 3.5),
    SummarizedExperiment,
    S4Vectors
Suggests:
    knitr,
    rmarkdown,
    testthat,
    ggplot2
RoxygenNote: 6.1.0
VignetteBuilder: knitr
biocViews: RNASeq, DifferentialExpression, GeneExpression, Sequencing

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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Kayla-Morrell commented 5 years ago

Hello @reese3928,

Thank you for submitting to Bioconductor. Please see the inital review of your package below. Comment back here with updates that have been made and when the package is ready for a re-review. Please keep in mind the deadline to accept packages into this release cycle is 4/24, therefore changes should be made in a timely manner so as to give enough time for a re-review and any additional changes.

This package was very well put together and very clean, kudos for that.

DESCRIPTION

[ ] SUGGESTION: We strongly encourage the addition of 'BugReports:' field with a relevant link to a GitHub for reporting Issues.

vignette

[ ] CLARIFICATION: Line 150, is there a reason you set this as eval = FALSE?

man pages

makeExample

[ ] REQUIRED: For 'Description' capitalize the first letter of the sentence.

NBAMSeq-methods

[ ] SUGGESTION: When looking up this man page, it is not clear what each sentence is referring to in the 'Description'. Could you make this clearer? Same with the return values. Maybe adding something like "For getDesign()...", "For getsf()...", that way the user knowns which description and return value is associated with which method.

NBAMSeqDataSet-class

[ ] CLARIFICATION: The only slot that is documented is 'design', is this correct?
[ ] SUGGESTION: You might consider adding in a reference for this man page since you talk about how it is inherited from 'SummarizedExperiment'.

R code

[ ] REQUIRED: AllClasses.R, line 185 should not use direct slot access with '@' but use an accessor method instead.

Best, Kayla

bioc-issue-bot commented 5 years ago

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

764d78a package review

bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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bioc-issue-bot commented 5 years ago

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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.

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bioc-issue-bot commented 5 years ago

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

f880ba5 updated

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reese3928 commented 5 years ago

Hi @Kayla-Morrell ,

Thanks very much for your review. We have addressed all of your comments and the package is ready for re-review. Here is our point-by-point response to your comments.

DESCRIPTION

SUGGESTION: We strongly encourage the addition of 'BugReports:' field with a relevant link to a GitHub for reporting Issues.

We have included the URL field and BugReports field in the DESCRIPTION file.

vignette

CLARIFICATION: Line 150, is there a reason you set this as eval = FALSE?

We have changed this as eval = TRUE. Previously we set this as eval = FALSE to meet the R CMD build time limit requirement. But it turns out that this option does not have a very huge impact on R CMD build time, so we set this as eval = TRUE.

man pages

makeExample REQUIRED: For 'Description' capitalize the first letter of the sentence.

Thanks for pointing out this typo, we have capitalized the first letter of the sentence.

NBAMSeq-methods

SUGGESTION: When looking up this man page, it is not clear what each sentence is referring to in the 'Description'. Could you make this clearer? Same with the return values. Maybe adding something like "For getDesign()...", "For getsf()...", that way the user knowns which description and return value is associated with which method.

Thanks for your suggestion, we have included "For getDesign()...", "For getsf()..." in the 'Description', 'return' and 'examples' to make it more clear for the users.

NBAMSeqDataSet-class CLARIFICATION: The only slot that is documented is 'design', is this correct?

Yes, because in our class design is the only extra slot compared to SummarizedExperiment.

SUGGESTION: You might consider adding in a reference for this man page since you talk about how it is inherited from 'SummarizedExperiment'.

Thanks for you suggestion. We have included the reference for this man page.

R code

REQUIRED: AllClasses.R, line 185 should not use direct slot access with '@' but use an accessor method instead.

We totally understand that direct slot access with '@' is not acceptable. However, this '@' happens when we are creating the accessor method. We used '@' when creating the accessor getDesign. getDesign itself is an accessor method. Just to clarify, do you mean we should use slot instead of '@' ?

We look forward to hearing from you.

Sincerely, Xu Ren

Kayla-Morrell commented 5 years ago

Hello @reese3928,

Thank you for all the work done on this package. I have looked over the changes made and everything looks good. In regards to the last requirement in AllClasses.R, this was my mistake and no change needs to be made.

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!

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/reese3928.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("NBAMSeq"). The package 'landing page' will be created at

https://bioconductor.org/packages/NBAMSeq

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

NBAMSeq #1073

DESCRIPTION

vignette

man pages

R code

DESCRIPTION

vignette

man pages

R code