pathwrap

[Elizaddh]

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• Repository: https://github.com/Kannapolis-Bioinformatics/pathwrap

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[bioc-issue-bot]

Hi @Elizaddh

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: pathwrap
Title: Wrapper for Automated RNASeq Data analysis and pathway visualization
Version: 0.99.0
Authors@R: 
    person("Eliza", "Dhungel","", "elidhungel@gmail.com", 
    role = c("aut", "cre"),
    comment = c(ORCID = "0000-0002-7246-9452"))
Description:
    Pathwrap is a RNASeq analysis tool that provides a wrapper
    for the processing of RNASeq datasets from quality control of raw
    reads to the visualization of enriched pathways obtained from processing 
    the datasets. This tool runs all the essential steps of RNASeq processing
    from quality control, filtering out low quality reads, trimming adapters,
    sequence alignment, alignment count, differential analysis, enrichment 
    analysis and pathway visualization. It is the first tool that combines 
    all essential steps of RNASeq analysis till pathway visualization. It has
    the ability to continue the analysis if it is halted at any stage and 
    generate quality pictures and generate comprehensive analysis of the data.
    Results of metabolomics experiment generating quantitative compound 
    information can be integrated with RNAseq data analysis and pathway 
    visualization.
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
URL: https://github.com/Kannapolis-Bioinformatics/pathwrap
BugReports: https://github.com/Kannapolis-Bioinformatics/pathwrap/issues
RoxygenNote: 7.3.1
Imports:
    stats,
    utils,
    grDevices, 
    methods,
    DESeq2,
    EnhancedVolcano,
    edgeR,
    fastqcr,
    gage,
    GenomicFeatures,
    ggplot2,
    parallel,
    Rfastp,
    ShortRead,
    pathview,
    QuasR,
    tools,
    Rsamtools,
    Rhisat2,
    AnnotationDbi,
    stringr,
    S4Vectors,
    ComplexHeatmap,
    SummarizedExperiment,
    KEGGREST
Depends: 
    R (>= 4.3.0)
License: MIT + file LICENSE
biocViews: 
    Alignment,
    Pathways,
    QualityControl, 
    Sequencing, 
    RNASeq,
    ChIPSeq,
    GeneExpression, 
    Transcription,
    ExperimentalDesign,
    Metabolomics
Suggests:
    RUnit,
    BiocManager,
    BiocStyle, 
    knitr,
    rmarkdown,
    BiocGenerics
VignetteBuilder: knitr
VignetteEngine: knitr, rmarkdown

[lshep]

You should not be trying to install system requirements for a user. Anything
that is needed to should be assumed to be installed by the user. If a system
dependency is needed please include an INSTALL file for installation
instructions http://contributions.bioconductor.org/sysdep.html and make sure it
is listed in the DESCRIPTION file.

[Elizaddh]

Hi,
It looks like some scripts in the readme.md file were trying to install packages. I commented them out. My packages only prompts/messages user to install the required package when reference directory is not provided as an argument. I updated the DESCRIPTION file with reference and annotation packages for mouse in the Suggests section. Also I updated the code to include proper name of pathways for compound sets analysis without which there was a bug in the result table generation. Please let me know if any other things triggered this issue or other issues.
Thanks,

[lshep]

Is there a reason to change the user's options in mktxdbobj.R options(cache_size = NULL, synchronous = NULL) ; it is not advisable to change user options without their permission?

Why are you looking in the working directory for files when it seems like file paths are specified by the user in plotpathways.R?

[bioc-issue-bot]

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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.

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): pathwrap_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
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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.

[vjcitn]

Thanks for this submission. We've discussed it internally and have some concerns. First, the vignette includes (I substitute dots for backtick)

...r installation, eval = FALSE}
library(pathwrap)
data(anntpkglist, package = "pathwrap")
#replace Homo sapiens with scientific name of mouse, Mus musculus for mouse data
genomepkg <- anntpkglist$genome[which(anntpkglist$species == "Homo sapiens")]
anntpkg <- anntpkglist$annotate[which(anntpkglist$species == "Homo sapiens")]
#BiocManager::install(genomepkg)
#BiocManager::install(anntpkg)

So no code is being run or tested. This is not how vignettes are intended to work ... They really should put mileage on your code so that any bit-rot can be exposed when vignette computations fail. Is it possible to construct a modest working example with running code in the vignette? It might be more appropriate to submit this as a workflow package.

[vjcitn]

I am setting the flag to "pre-review" changes needed.

[Elizaddh]

Hi,
Thank you for the comments and concerns. I plan to rewrite vignettes and get some test codes running moving forward. I will update the package soon in github and let you know.
Eliza.

[lshep]

Just wanted to check in to see if we may expect any updates soon?

[Elizaddh]

Hi,
sorry for late response. I got occupied with other issues.I will probably work on this in July. Please expect an update after July 10 on early.