RNASeqHelper

[mtekman]

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[bioc-issue-bot]

Hi @mtekman

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: RNASeqHelper
Type: Package
Title: Generate Heatmaps and Volcano Plots for your DESeq2 Genes of Interest
Version: 0.99.0
Authors@R: 
    c(person(given="Mehmet", family="Tekman",
        email = "mtekman89@gmail.com",
        role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4181-2676")),
        person(given="Sebastian", family="Arnold",
        email = "sebastian.arnold@pharmakol.uni-freiburg.de",
        role = c("fnd"), comment = c(ORCID = "0000-0002-2688-9210")))
Description:
    Perform a full DESeq2 analysis for your RNA-seq data, generating
    colourful Volcano and Kmeans-clustered Heatmaps, along with
    time-series gene plots for genes of interest. QC-metrics that such
    as PCA validation are built in, and the heatmaps generated show
    z-score scaled expression between contrasts for contrasted samples
    and all. Time series plots show gene trends on normalised,
    corrected, and scaled data, for varying cluster correlation
    thresholds.
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
VignetteBuilder: knitr
biocViews: RNASeq, QualityControl, GeneExpression
Imports:
    pheatmap (>= 1.0.12), patchwork (>= 1.1.3), DESeq2 (>= 1.40.2),
    dplyr (>= 1.1.3), readr (>= 2.1.4), tibble (>= 3.2.1),
    ggplot2 (>= 3.4.4), ComplexHeatmap (>= 2.16.0), ggrepel (>= 0.9.4),
    purrr (>= 1.0.2), tidyr (>= 1.3.0), grDevices, graphics,
    grid, stats, utils
Suggests:
    BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), svglite (>= 2.1.3)
Depends:
    SummarizedExperiment (>= 1.30.2)
URL: https://gitlab.com/mtekman/rnaseqhelper
BugReports: https://gitlab.com/mtekman/rnaseqhelper/issues
Config/testthat/edition: 3

[lshep]

Please use tempdir() to specify the temporary output directory instead of manually "/tmp" this ensure cross OS compatibility and write access by the user making the calls.

[mtekman]

Added changes:

• now uses tempdir()
• minor spacing fixes for other warnings

[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.

On one or more platforms, the build results were: "TIMEOUT, skipped".
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Remember: if you submitted your package after July 7th, 2020,
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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: 8cffbf9ba1202d8a2d1100548feb12715c30f246

[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: RNASeqHelper_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/RNASeqHelper 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: 8d787e511e4c283fc431cd2ffebcce187d840803

[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: RNASeqHelper_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/RNASeqHelper 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: 297e7fb08038a4708dd73dcbc076163263f3cd0a

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

[mtekman]

I keep hitting this error with svglite. It's definitely a required module for the svg device to work.

It builds fine locally on my machine, but it seems to fail on the CI. Any ideas?

[lshep]

I just did a quick check and the version is 2.1.2 on merdia1 but 2.1.3 is required. @jwokaty can you check why this CRAN package is not picking up the most recent version on CRAN; https://cran.r-project.org/web/packages/svglite/index.html. I will note I just restarted the linux builder and checked the version there and that is 2.1.3 so on the next try hopefully you would get farther on that OS check

[mtekman]

okay, I will push tomorrow just in case more time is needed, thanks!

[jwokaty]

@mtekman svglite 2.1.3 is installed on merida1 now. It wasn't installed automatically because the CRAN macOS binaries lag behind the source packages, so I had to manually update it.

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 24db05b29d1e244576bafeaee21a952e34b2d5c7

[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:
macOS 12.7.1 Monterey: RNASeqHelper_0.99.3.tar.gz
Linux (Ubuntu 22.04.2 LTS): RNASeqHelper_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/RNASeqHelper to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[mtekman]

Thanks all! The message I am getting now is:

WARNING: R CMD check exceeded 10 min requirement

My examples (and indeed the vignette) require at least 1000 features to function properly. Too small, the dispersion of the DESeq2 fitting become useless, and clustering produces nonsensical clustering that serves no educational purpose.

Is the 10min limit a hard requirement?

[lshep]

It will be important to try and cut back on the check time as much as possible.

[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.

[lshep]

In your vignette, you currently are writing to the home directory when you are doing ~/myanalysis/ and ~/myanalysis2; This is very problematic! Please do not write to the home directory and write all output to tempdir() instead of ~/ .

[mtekman]

Hi @lshep, thanks for the warning!

I've also noticed that my code falls apart if there is no "time" component in my phenotype data, so this is something I will fix before I ask you to review it again.

Cheers!

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 1ea73ad44b62b0a6a8dbbd13653dedd62e6a629d

[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): RNASeqHelper_0.99.7.tar.gz
macOS 12.7.1 Monterey: RNASeqHelper_0.99.7.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/RNASeqHelper to trigger a new build.
A quick tutorial for setting up remotes and pushing to upstream can be found here.

[mtekman]

Hello again, new version with:

• Changed ~/ → tempdir()
• Fix to phenotype data without time info
• Linting checks, default checks, biocchecks
• Reduced test time from 10m → 2m
• BiocStyle in Vignette

Hopefully this is the one!
Happily awaiting your review.

[DarioS]

I have evaluated the software and have major revisions to request, mainly about improved Bioconductor interoperability..

• Function and variable naming does not confirm to coding style requirements in Developer's Guide. camelCase not snake_case unlike tidyverse.
• Depends on tidyverse variable types such as tibble rather than Bioconductor variable types such as DataFrame. e.g.
  \item{long_data}{A tibble containing columns: gene, condition, value, and optionally time}. Please switch.
• Input RNA-seq data is required to be a plain numeric matrix.
  \item{tab}{a matrix of samples (columns) and genes (rows)}.
  Needs to support RangedSummarizedExperiment input to demonstrate improved interoperability with Bioconductor.
• Package is named RNASeqHelper but it only supports DESeq2 as back-end. How about edgeR? edgeR is 24th-ranked and DESeq2 is 26th-ranked based on monthly downloads, so such a pipeline should support both frameworks at a minimum. Don't instantly exclude about 50% of your future citations!
• The developers of DESeq2 have a special package named tximport for importing RNA-seq data. This is important for avoiding confounding by changes in gene length but not gene abundance. RNASeqHelper ignores this best-practice.
• All of the code is in a single file 1344 lines long. Please modularise into separate .R files to make finding functions easy.
• The vignette shows how RNASeqHelper operates on simulated data. Instead, please demonstrate how your package is useful for analysing a real data set. Please find a data set from Experiment Data view and use that instead. Also, note that using rnorm is unsuitable for simulating RNA-seq data. makeExampleDESeqDataSet from DESeq2 is ideal.
• Vignette needs to follow the sections of the Developer's Guide Vignettes section. In particuar, there is no Installation section.
• The unit tests seem incomplete. Most don't have expect or succeed or fail in them.

[mtekman]

Dear Dario,

Thank you for your comprehensive review, you have definitely given me a
lot to think about.

• RangedSummarizedExperiment, makeExampleDESeqDataSet, tximport,
  Installation, better unit tests.

Thanks for these hints, I will do these changes!

• edgeR

I do not have too much experience with edgeR, but I think you're right that it would be a huge win to incorporate it into the library, and it would even offer a nice "keepgenes" alternative method.

• tibble rather than DataFrame

I will remove tidyverse variable types, but can I at least keep dplyr %>% piping, or is that also bad?

• Function and variable naming does not confirm to coding style requirements in Developer's Guide. camelCase not snake_case unlike tidyverse.

All of my functions were previously camelCase, but I was told that I failed many linting checks, and so changed them all to snake_case at the behest of lintr.

Since the default lintr rules do not seem to be encouraged, may I ask which lintr rules are? I found this, but the rules do not seem to work with the current version of lintr.

• All of the code is in a single file 1344 lines long. Please
  modularise into separate .R files to make finding functions easy.

I find it much easier to keep things in a single R file, since I only need to mentally grapple with a single buffer. It also greatly helps when I produce a dependency map of my code (see image below). Is this a strict requirement?

Thanks again,
Mehmet

[DarioS]

The coding style requirements are in R Code chapter. You may keep functions in one file. How about base R pipe |> ?

[mtekman]

You just blew my mind about the base R pipe, I genuinely thought that was a dplyr implementation only.

I guess I will try formatR as a linter, cheers