Add PolySTest

[veitveit]

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

• Repository: https://github.com/computproteomics/PolySTest

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[bioc-issue-bot]

Hi @veitveit

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: PolySTest
Title: PolySTest: Detection of differentially regulated features. Combined 
      statistical testing for data with few replicates and missing values
Version: 0.99.0
Authors@R: 
    person("Veit", "Schwämmle", , "veits@bmb.sdu.dk", role = c("aut", "cre"),
 comment = c(ORCID = "0000-0002-9708-6722"))
Description: The complexity of high-throughput quantitative omics
   experiments often leads to low replicates numbers and 
   many missing values. We implemented a new test to simultaneously 
   consider missing values and quantitative changes, which we combined
   with well-performing statistical tests for high confidence
   detection of differentially regulated features. The package contains
   functions to run the test and to visualize the results.
License: GPL-2
Encoding: UTF-8
biocViews: MassSpectrometry, Proteomics, Software, DifferentialExpression
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Imports:
    fdrtool (>= 1.2.15),
    limma (>= 3.44.3),
    matrixStats (>= 0.57.0),
    qvalue (>= 2.22.0),
    shiny (>= 1.5.0),
    SummarizedExperiment (>= 1.20.0),
    knitr (>= 1.33),
    plotly (>= 4.9.4),
    heatmaply (>= 1.1.1),
    circlize (>= 0.4.12),
    UpSetR (>= 1.4.0),
    gplots (>= 3.1.1),
    S4Vectors (>= 0.30.0),
    parallel (>= 4.1.0),
    grDevices (>= 4.1.0),
    graphics (>= 4.1.0),
    stats (>= 4.1.0),
    utils (>= 4.1.0)
Suggests: 
    testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Depends: 
    R (>= 4.3.0)

[lshep]

• Is it possible to move the Dockerfile and bitbucket-pipelines.yml and bioconda installation stuff to a different branch so that a clean R packages is submitted and distributed by Bioconductor

• The citation file is currently malformed

> readCitationFile("CITATION")
Error in tools:::.parse_CITATION_file(file, meta$Encoding) : 
  non-ASCII input in a CITATION file without a declared encoding

• 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.

• Rplots.pdf in the top level directory should be removed

[veitveit]

Thank you @lshep

I would prefer to keep docker file and bioconda files to avoid having to simultaneously maintain multiple branches. I moved everything to the inst folder. Would that be fine?

• The citation file should be fine now

• script file about data set has been added

• Rplots.pdf has been removed

[lshep]

FWIW: I still get the following

> readCitationFile("CITATION")
Error in tools:::.parse_CITATION_file(file, meta$Encoding) : 
  non-ASCII input in a CITATION file without a declared encoding

tools::showNonASCII(readLines("CITATION"))
5: author="Veit Schwmmle, Christian E. Hagensen, Adelina Rogowska-Wrzesinska, Ole N. Jensen",
14: author="Veit Schwmmle",

[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: "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.

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): PolySTest_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/PolySTest 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: 9b49c8d09f23b86a3b46d8c6bb0818e84d7ef850

[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): PolySTest_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/PolySTest to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.