broadSeq resubmission

[vondoRishi]

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

• Repository: https://github.com/dasroy/broadSeq

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

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[bioc-issue-bot]

Hi @vondoRishi

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: broadSeq
Title: broadSeq : for streamlined exploration of RNA-seq data
Version: 0.99.0
Authors@R: 
    person("Rishi", "Das Roy", , "rishi.dasroy@gmail.com", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0002-3276-7279"))
Description: This package helps user to do easily RNA-seq data analysis with multiple 
    methods (usually which needs many different input formats). Here the user will 
    provid the expression data as a SummarizedExperiment object and will get results 
    from different methods. It will help user to quickly evaluate different methods. 
License: MIT + file LICENSE
URL: https://github.com/dasroy/broadSeq
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews: GeneExpression, DifferentialExpression, RNASeq, 
        Transcriptomics
Suggests: 
    knitr,
    limma (>= 3.54.0),
    rmarkdown,
    stats (>= 4.2.2),
    samr
Depends: 
    dplyr,
    ggpubr,
    SummarizedExperiment 
Imports: 
    DELocal,
    EBSeq (>= 1.38.0),
    DESeq2 (>= 1.38.2),
    NOISeq,
    forcats (>= 1.0.0),
    genefilter,
    ggplot2,
    ggplotify,
    plyr,
    clusterProfiler (>= 4.8.2),
    pheatmap,
    sechm (>= 1.6.0),
    stringr,
    purrr (>= 0.3.5),
    edgeR (>= 3.40.1)
VignetteBuilder: knitr

[lshep]

Please include an inst/scripts that has a file that describes how the data in inst/extdata was generated. It can be text, psuedo-code, or code but should contain any relevant source and licensing information.

[bioc-issue-bot]

Your package has been added to git.bioconductor.org to continue the
pre-review process. A build report will be posted shortly. Please
fix any ERROR and WARNING in the build report before a reviewer is
assigned or provide a justification on why you feel the ERROR or
WARNING should be granted an exception.

IMPORTANT: Please read this documentation for setting
up remotes to push to git.bioconductor.org. All changes should be
pushed to git.bioconductor.org moving forward. It is required to push a
version bump to git.bioconductor.org to trigger a new build report.

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]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): broadSeq_0.99.0.tar.gz

Links above 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/broadSeq to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 2e5b3fb93f877359baac323374bf72b0c0ebd6fe

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): broadSeq_0.99.1.tar.gz

Links above 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/broadSeq to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[bioc-issue-bot]

A reviewer has been assigned to your package for an indepth review.
Please respond accordingly to any further comments from the reviewer.

[vondoRishi]

Looking forward to the reviewer's comments. :)

[lshep]

I'm so sorry for the long delay; I have been extremely backed up with post release tasks. I will have a review for you within the next day.

[lshep]

README

• Include Bioconductor installation instructions

man

• Please have a package level man page so that if a naive user does
  ?broadSeq they are directed appropriately how to get started.

DESCRIPTION

• When doing R CMD build the following occurs

  NB: this package now depends on R (>= 3.5.0)
  WARNING: Added dependency on R >= 3.5.0 because serialized objects in
  serialize/load version 3 cannot be read in older versions of R.
  File(s) containing such objects:
    'broadSeq/inst/extdata/rat_vole_mouseSE_salmon.rds'

We would appreciate a manual entry of R (>= 4.4.0) as this is the R value tested
against on our builders

BiocCheck

• Plesae correct coding NOTES

general

• We like to see endomorphism whenever possible. Curious your reasoning for
  taking in a SummarizedExperiment but then not returning it?

vignette
broadSeq.rmd

• Could you please provide an abstract/intro section in your vignette that
  provides motivation for inclusion in Bioconductor and when appropriate a
  review and comparison to existing Bioconductor packages with similar
  functionality or scope.

• This vignette shows no evaluated code. If I were a user I would not know
  where to start. Please include either references to the other vignettes or
  show/reference the main functions that can be used.

test

• We really strongly encourage tests to ensure functions are working
  correctly

NEWS

• We strongly advise a NEWS file. NEWS file not only make changes visible to
  end users, we collate the NEWS file for the Bioconductor relesae
  announcements. See example release announcement

[vondoRishi]

Hi,

Are all of these comments mandatory?

[lshep]

For the most part yes. You could justify why something shouldn't be implemented and if reasonable I could potentially make an exception.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 16391d5cb1aa374eb2a9339c83a18ee56b031e4d

[vondoRishi]

README

• Include Bioconductor installation instructions

man

• Please have a package level man page so that if a naive user does
  ?broadSeq they are directed appropriately how to get started.

DESCRIPTION

• When doing R CMD build the following occurs

Fixed the serialized object

  NB: this package now depends on R (>= 3.5.0)
  WARNING: Added dependency on R >= 3.5.0 because serialized objects in
  serialize/load version 3 cannot be read in older versions of R.
  File(s) containing such objects:
    'broadSeq/inst/extdata/rat_vole_mouseSE_salmon.rds'

We would appreciate a manual entry of R (>= 4.4.0) as this is the R value tested against on our builders

BiocCheck

• Plesae correct coding NOTES

There is no preprint or publication for this package yet

general

• We like to see endomorphism whenever possible. Curious your reasoning for
  taking in a SummarizedExperiment but then not returning it?

There are many functions which return SummarizedExperiment object , like
broadSeq::transformDESeq2 or broadSeq::normalizeEdgerCPM

vignette broadSeq.rmd

• Could you please provide an abstract/intro section in your vignette that
  provides motivation for inclusion in Bioconductor and when appropriate a
  review and comparison to existing Bioconductor packages with similar
  functionality or scope.
• This vignette shows no evaluated code. If I were a user I would not know
  where to start. Please include either references to the other vignettes or
  show/reference the main functions that can be used.

test

• We really strongly encourage tests to ensure functions are working
  correctly

At this moment, there is no manpower to write tests.

NEWS

• We strongly advise a NEWS file. NEWS file not only make changes visible to
  end users, we collate the NEWS file for the Bioconductor relesae
  announcements. See example release announcement

In future releases, news will be included.

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on the Bioconductor Single Package Builder.

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

Please see the build report for more details.

The following are build products from R CMD build on the Single Package Builder:
Linux (Ubuntu 22.04.3 LTS): broadSeq_0.99.2.tar.gz

Links above 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/broadSeq to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.