vmrseq

[nshen7]

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• Repository: https://github.com/nshen7/vmrseq

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[bioc-issue-bot]

Hi @nshen7

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: vmrseq
Type: Package
Title: Probabilistic Modeling of Single-cell Methylation Heterogeneity
Version: 0.99.0
Authors@R: person("Ning", "Shen", email = "ning.shen.wk@gmail.com",role = c("aut", "cre"))
Description: High-throughput single-cell measurements of DNA methylation allows studying inter-cellular epigenetic heterogeneity, but this task faces the challenges of sparsity and noise. We present vmrseq, a statistical method that overcomes these challenges and identifies variably methylated regions accurately and robustly.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
biocViews: Software, ImmunoOncology, DNAMethylation, Epigenetics, SingleCell,
  Sequencing, WholeGenome
Depends: 
    R (>= 3.5.0)
Imports: 
    bumphunter,
    dplyr,
    BiocParallel,
    DelayedArray,
    GenomicRanges,
    ggplot2,
    methods,
    tidyr,
    locfit,
    gamlss.dist,
    recommenderlab,
    HDF5Array,
    data.table,
    SummarizedExperiment,
    IRanges,
    S4Vectors
Suggests: 
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
URL: https://github.com/nshen7/vmrseq
BugReports: https://github.com/nshen7/vmrseq/issues

[lshep]

I'm getting the following ERROR when running R CMD check ?

* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'vmrseq-Ex.R' failed
The error most likely occurred in:

> ### Name: HDF5NAdrop2matrix
> ### Title: Coerce a NA-dropped HDF5 matrix back to regular matrix form
> ###   where NAs are not dropped to 0.
> ### Aliases: HDF5NAdrop2matrix
> 
> ### ** Examples
> 
> # load example data
> toy.se <- HDF5Array::loadHDF5SummarizedExperiment(system.file("extdata", "toy", package = "vmrseq"))
> 
> # run the function
> HDF5NAdrop2matrix(assays(toy.se)$M_mat)
Error in assays(toy.se) : could not find function "assays"
Calls: HDF5NAdrop2matrix ... <Anonymous> -> is -> as -> .class1 -> as -> .class1
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK

[lshep]

Could you also please remove the doc directory. These files should be generated interactively when the package is built.

[nshen7]

Hi @lshep, I have addressed your comments. Many thanks for reviewing my package!

[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.

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[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.

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.

The following are build products from R CMD build on the Single Package Builder:
macOS 12.7.1 Monterey: vmrseq_0.99.0.tar.gz
Linux (Ubuntu 22.04.3 LTS): vmrseq_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/vmrseq 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: c53eda552ad868b73c1d4808f4995c9c7f25c8e7

[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:
macOS 12.7.1 Monterey: vmrseq_0.99.1.tar.gz
Linux (Ubuntu 22.04.3 LTS): vmrseq_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/vmrseq 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.

[Kayla-Morrell]

@nshen7 - 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 (though 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 README file installation instructions should also demonstrate how to install from Bioconductor.

DESCRIPTION

• REQUIRED: LazyData field should be set to false or removed.
• REQUIRED: Update R version dependency from 3.5.0 to 4.4.0.

NAMESPACE

• REQUIRED: Function names should use camelCase or snake_case and not include '.' in the names.

NEWS

• SUGGESTION: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements.

Data

• REQUIRED: All data in the 'data/' directory need corresponding documentation man pages in the 'man/' directory.

Vignette

• REQUIRED: The Installation section should also include directions on how to install from Bioconductor.

Man pages

• REQUIRED: Add runnable examples to man pages that document exported objects.
• REQUIRED: Use donttest{} instead of dontrun{}.

Unit tests

• REQUIRED: If you are going to include tests, you need to actually test the functionality of your package and not just that multiplication works.

R code

• REQUIRED: Avoid sapply(); use vapply() instead.
• REQUIRED: Avoid 1:...; use seq_len() or seq_along() instead.
• SUGGESTION: Avoid the use of paste in condition signals.
• SUGGESTION: For formatting reasons, consider shorter lines. There are 208 lines that are > 80 characters long.
• SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 694 lines that are not.

Best,
Kayla

[lshep]

@nshen7 may we expected updates soon that address the review comments?

[nshen7]

@lshep Hi, yes! Apologies for not being able to get back sooner. I’ve been quite occupied with multiple priorities recently. I'll get these done ASAP.

[nshen7]

Hi @lshep @Kayla-Morrell, I have attempted to make necessary changes to address all the comments tagged as REQUIRED and some to those tagged as SUGGESTION. Would you mind reviewing again and let me know if I missed anything please?