TMSig

[TylerSagendorf]

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• Repository: https://github.com/EMSL-Computing/TMSig

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[bioc-issue-bot]

Hi @TylerSagendorf

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: TMSig
Type: Package
Title: Tools for Molecular Signatures
Version: 0.99.0
Date: 2024-08-23
Authors@R: 
    c(
      person(given = "Tyler", family = "Sagendorf", 
   email = "tyler.sagendorf@pnnl.gov",
   comment = c(ORCID = "0000-0003-1552-4870"),
   role = c("aut", "cre")),
      person(given = "Di", family = "Wu", role = "ctb"),
      person(given = "Gordon", family = "Smyth", role = "ctb")
    )
Description: The TMSig package contains tools to prepare, analyze, and visualize
    named lists of sets, with an emphasis on molecular signatures (such as gene
    or kinase sets). It includes fast, memory efficient functions to construct
    sparse incidence and similarity matrices and filter, cluster, invert, and 
    decompose sets. Additionally, bubble heatmaps can be created to visualize 
    the results of any differential or molecular signatures analysis.
License: GPL (>= 3)
URL: https://github.com/EMSL-Computing/TMSig
BugReports: https://github.com/EMSL-Computing/TMSig/issues
Encoding: UTF-8
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
biocViews: Clustering, GeneSetEnrichment, GraphAndNetwork, Pathways, Visualization
Depends:
    R (>= 4.4.0),
    limma
Imports:
    circlize,
    ComplexHeatmap,
    data.table,
    grDevices,
    grid,
    lifecycle,
    Matrix,
    stats,
    utils
Suggests: 
    BiocStyle,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
Config/testthat/edition: 3

[lshep]

Please include an inst/script/ directory that has a file that can be code,
psuedo code, or text but that describes how the data in inst/extdata was
generated. minimally containing source/licensing information. A user should be
able to get an idea of how to recreate the data if necessary.

Given this package seems to be working with geneSets. It will be necessary to
also include functionality to the common Bioconductor classes for gene sets by
also making functions compatible with BiocSet::BiocSet or the GSEABase::GeneSet
or likely more appropriate GSEABase::GetSetCollection. See
https://contributions.bioconductor.org/important-bioconductor-package-development-features.html#commonclass

[TylerSagendorf]

@lshep I will get this taken care of. Since this doesn't have the pre-review tag, should I make these changes to the existing TMSig repo under EMSL-Computing?

[TylerSagendorf]

Functions sparseIncidence, filterSets, and invertSets have been converted to S4 generics to support objects of class GeneSet and GeneSetCollection from GSEABase. I have also added a .txt file to inst/script/ that explains how c5.go.v2023.2.Hs.symbols.gmt.gz was generated.

[lshep]

thank you. we will take a re-evaluation soon.

[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
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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:
Linux (Ubuntu 22.04.3 LTS): TMSig_0.99.0.tar.gz
Linux (Ubuntu 24.04.1 LTS): TMSig_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/TMSig 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: f35e1feab4612ac8a48cb0365beca90cc0dc0a10

[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 24.04.1 LTS): TMSig_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/TMSig 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]

@TylerSagendorf - 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: Package files exceed the 5MB size limit.

DESCRIPTION

• SUGGESTION: Consider adding these automatically suggested biocViews:
  GeneExpression, Transcription, Sequencing, ATACSeq, Microarray, Metabolomics,
  Proteomics, Epigenetics, Cheminformatics, Transcriptomics,
  DifferentialExpression, ExperimentalDesign, Normalization, Preprocessing,
  Bayesian, Regression, ExonArray, RNASeq, OneChannel, TwoChannel, MicroRNAArray,
  mRNAMicroarray, ProprietaryPlatforms, CellBiology, BiomedicalInformatics,
  FunctionalGenomics, SystemsBiology, ImmunoOncology, AlternativeSplicing,
  DifferentialSplicing, BatchEffect, MultipleComparison, QualityControl,
  TimeCourse, DataImport

NAMESPACE

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

R code

• SUGGESTION: For formatting reasons, consider shorter lines. There are 4 lines that are > 80 characters long.
• SUGGESTION: For formatting reasons, consider multiples of 4 spaces for line indents. There are 257 lines that are not.

Best,
Kayla

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 6f6c9c27e18790644926a42005b7c40465cdf7b6

[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 24.04.1 LTS): TMSig_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/TMSig 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: 1c4cf03b82fc1700252730509afde58daa624142

[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 24.04.1 LTS): TMSig_0.99.3.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/TMSig to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[TylerSagendorf]

@Kayla-Morrell Thank you for taking the time to review the package. I have either addressed these points in the latest changes or provided reasoning as to why they weren't addressed below.

1. DESCRIPTION: these biocViews are not strongly related to the TMSig package. My guess is they got suggested because of the limma dependency or some packages in the Imports field.
2. NAMESPACE: cameraPR.matrix is an S3 method (not S4 only because limma::cameraPR is not), so I don't believe I'll be able to remove the '.'
3. Multiples of 4 spaces for line indents: the 257 lines flagged are all cases like those below. If possible, I would like to keep them as-is since the extra blank space at the beginning significantly improves my ability to read the code, and it somewhat reduces the number of lines

Best,
Tyler

[Kayla-Morrell]

@TylerSagendorf - Thank you for making the necessary changes and/or providing reasoning. I have looked over everything and it all looks good. I'm more than happy to accept the package.

Best,
Kayla

[bioc-issue-bot]

Your package has been accepted. It will be added to the
Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor
community. If you are interested in becoming a Bioconductor package
reviewer, please see Reviewers Expectations.

[lshep]

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See further instructions at

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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("TMSig"). The package 'landing page' will be created at

https://bioconductor.org/packages/TMSig

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.