rawDiag

[cpanse]

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

• Repository: https://github.com/cpanse/rawDiag

Confirm the following by editing each check box to '[x]'

[x] I understand that by submitting my package to Bioconductor,
the package source and all review commentary are visible to the
general public.

[x] I have read the Bioconductor [Package Submission](https://bioconductor.org/developers/package-submission/)
instructions. My package is consistent with the Bioconductor
[Package Guidelines](https://contributions.bioconductor.org/).

[x] I understand Bioconductor [Package Naming Policy](https://bioconductor.org/developers/package-submission/#naming) and acknowledge
Bioconductor may retain use of package name.

[x ] I understand that a minimum requirement for package acceptance
is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS.
Passing these checks does not result in automatic acceptance. The
package will then undergo a formal review and recommendations for
acceptance regarding other Bioconductor standards will be addressed.

[ x] My package addresses statistical or bioinformatic issues related
to the analysis and comprehension of high throughput omics data.

[ x] I am committed to the long-term maintenance of my package. This
includes monitoring the [support site](https://support.bioconductor.org/) for issues that users may
have, subscribing to the [bioc-devel](https://stat.ethz.ch/mailman/listinfo/bioc-devel) mailing list to stay aware
of developments in the Bioconductor community, responding promptly
to requests for updates from the Core team in response to changes in
R or underlying software.

[x ] I am familiar with the [Bioconductor code of conduct](https://bioconductor.org/about/code-of-conduct/) and
agree to abide by it.

I am familiar with the essential aspects of Bioconductor software management, including:

[x] The 'devel' branch for new packages and features.
[x] The stable 'release' branch, made available every six
months, for bug fixes.
[x] Bioconductor version control using [Git](http://bioconductor.org/developers/how-to/git/)
(optionally [via GitHub](http://bioconductor.org/developers/how-to/git/sync-existing-repositories/)).

For questions/help about the submission process, including questions about the output of the automatic reports generated by the SPB (Single Package Builder), please use the #package-submission channel of our Community Slack. Follow the link on the home page of the Bioconductor website to sign up.

[bioc-issue-bot]

Hi @cpanse

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: rawDiag
Type: Package
Title: Brings Orbitrap Mass Spectrometry Data to Life; Fast and Colorful 
Version: 0.99.0
Authors@R: c(person(given = "Christian", family = "Panse", email = "cp@fgcz.ethz.ch", role = c("aut", "cre"),
    comment = c(ORCID = "0000-0003-1975-3064")),
    person(given = "Christian", family = "Trachsel", email = "Christian.Trachsel@fgcz.ethz.ch", role = "aut"),
    person(given = "Tobias", family = "Kockmann", email = "Tobias.Kockmann@fgcz.ethz.ch", role = "aut"))
Depends:
  R (>= 4.3)
Imports:
  dplyr,
  ggplot2 (>= 3.4),
  grDevices,
  rawrr (>= 1.10),
  rlang,
  reshape2,
  scales,
  shiny,
  stats
Suggests:
  BiocStyle (>= 2.28),
  ExperimentHub,
  tartare,
  knitr,
  testthat
Description: Optimizing methods for liquid chromatography coupled to mass
  spectrometry (LC–MS) poses a nontrivial challenge. The rawDiag package
  facilitates rational method optimization by generating MS operator-tailored
  diagnostic plots of scan-level metadata. The package is designed for use on
  the R shell or as a Shiny application on the Orbitrap instrument PC.
License: GPL-3
URL: https://github.com/cpanse/rawDiag/
BugReports: https://github.com/cpanse/rawDiag/issues
Encoding: UTF-8
NeedsCompilation: no
RoxygenNote: 7.2.3
VignetteBuilder: knitr
biocViews: MassSpectrometry, Proteomics, Metabolomics

[lshep]

It looks like the set up for the rawrr package needs to be run in order to use your package. I highly suggest referencing the https://github.com/fgcz/rawrr/blob/devel/INSTALL in an INSTALL file of your own and making note of it perhaps in the package level man page?

[lshep]

I ran

rawrr::installRawFileReaderDLLs()
rawrr::installRawrrExe()

and when I still try to build your package locally I am getting an ERROR

lorikern@jbcj433:~/PkgReview$ R CMD build rawDiag 
* checking for file 'rawDiag/DESCRIPTION' ... OK
* preparing 'rawDiag':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘rawDiag.Rmd’ using rmarkdown
trying URL 'https://bioconductor.org/packages/3.19/data/experiment/src/contrib/tartare_1.17.0.tar.gz'
Content type 'application/x-gzip' length 314914 bytes (307 KB)
==================================================
downloaded 307 KB

* installing *source* package ‘tartare’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tartare)

The downloaded source packages are in
    '/tmp/RtmpzC3q1y/downloaded_packages'

Quitting from lines 65-68 [readOrbitrap] (rawDiag.Rmd)
Error: processing vignette 'rawDiag.Rmd' failed with diagnostics:
no lines available in input
--- failed re-building ‘rawDiag.Rmd’

SUMMARY: processing the following file failed:
  ‘rawDiag.Rmd’

Error: Vignette re-building failed.
Execution halted

[cpanse]

Dear @lshep,

I added an INSTALL file; SystemRequirements @DESCRIPTION and a note in the ?rawDiag man page. https://github.com/cpanse/rawDiag/commit/7db172841ef420168ced14f48578bfdca8825ebd C

[lshep]

I still get an ERROR when I try to build locally but I'll pass it into the build system for now and see if it reproduces there.

[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.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. All changes should be pushed to git.bioconductor.org moving forward. It is required to push a version bump to git.bioconductor.org to trigger a new build report.

Bioconductor utilized your github ssh-keys for git.bioconductor.org access. To manage keys and future access you may want to active your Bioconductor Git Credentials Account

[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: "skipped, 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: ERROR before build products produced.

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

[cpanse]

@lshep OK; I copied the part from the MsBackendRawFileReader vignette. Thanks, Christian

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 583266280133a3bd818745b298bd685fd8b0c897

[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: "skipped, 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: rawDiag_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/rawDiag 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: 66c9f8e97bde3a563c6c02d8ce40996e5c76317d

[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: "skipped, 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: rawDiag_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/rawDiag 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: fa294084544d72ab88f36aad717c8a5f227b9450

[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: "skipped, 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: rawDiag_0.99.4.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/rawDiag to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

Please fix all ERROR, Warning, Notes before a reviewer is assigned for an in depth review. thank you

[cpanse]

@lshep; I don’t know how to fix the error. One way is that rawrr is working (meaning having all the libraries installed) or I need to fetch the proprietary vendor libraries when rendering the vignette. Thanks and best wishes, C

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: 560894cb6ce3224676cb31e5f72b2b8115a522d8

[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 22.04.2 LTS): rawDiag_0.99.5.tar.gz macOS 12.7.1 Monterey: rawDiag_0.99.5.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/rawDiag 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: 9405d7399e0743f3f2ebf104f1f536b39d12f3bd

[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 22.04.2 LTS): rawDiag_0.99.6.tar.gz macOS 12.7.1 Monterey: rawDiag_0.99.6.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/rawDiag 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: a165c454c39dfa13b0ad015b0231fc89acddca51

[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: "skipped, 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: rawDiag_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/rawDiag 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: 2fb4d7c0b0c51ef23f6d5c7c81d01455b4402479

[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: "skipped, WARNINGS, 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: rawDiag_0.99.8.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/rawDiag 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: 7951e523d38e110ab600682ae904203645bd8214

[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: "skipped, 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: rawDiag_0.99.9.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/rawDiag 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: a8bd72bb2da99eebb3c40f453a92d1c95ec05977

[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: rawDiag_0.99.10.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/rawDiag to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[cpanse]

ERROR: Subscribe to the Bioc-devel mailing list by going to I get emails sent to bioc-devel@r-project.org

[lshep]

We can ignore this error for now as there seems to be an issue with the BiocCheck for the bioc-devel mailing list. I did confirm you are registered. Is there a way to reduce the package size as there is still a warning concerning package size?

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: dcf34774f0b2b9d16e8bbc6e747d2eb78a909718

[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: rawDiag_0.99.11.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/rawDiag to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[cpanse]

Dear @lshep; I could reduce the output of the vignette. Thanks, Christian

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: a6437831a156179b105bf044fca0e14e451caa13

[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: rawDiag_0.99.12.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/rawDiag 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: aab285fdf5301393365e78526aa66b929fc37f45

[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 22.04.2 LTS): rawDiag_0.99.13.tar.gz macOS 12.7.1 Monterey: rawDiag_0.99.13.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/rawDiag 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: 8f6f36fb620a80cbbc2e2da31c37184eb4cf4bf4

[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 22.04.2 LTS): rawDiag_0.99.14.tar.gz macOS 12.7.1 Monterey: rawDiag_0.99.14.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/rawDiag 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: 0b89f3f3c5251dd5a544ff35de954c93ee11c25b

[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: rawDiag_0.99.15.tar.gz Linux (Ubuntu 22.04.2 LTS): rawDiag_0.99.15.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/rawDiag 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: 563c4ade85010a8700e759fa63079a502c762bbc

[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 22.04.2 LTS): rawDiag_0.99.16.tar.gz macOS 12.7.1 Monterey: rawDiag_0.99.16.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/rawDiag 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: c30a4e5bea8db792f433a8424ff4fa3a56823250

[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 22.04.2 LTS): rawDiag_0.99.17.tar.gz macOS 12.7.1 Monterey: rawDiag_0.99.17.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/rawDiag 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.

[lazappi]

Hi @cpanse

Thanks for submitting rawDiag :tada:! Below is my review of your package. Please reply here if anything is unclear or needs any further explanation.

What next?

Please address the comments as best as you can. When you are ready for me to check the package again please reply to let me know with a summary of changes you have made or any other responses. You can use the "Quote reply" option in the ... menu on this comment to reply directly to my points below.

Luke

Review

Key: :rotating_light: Required :warning: Recommended :green_circle: Optional :question: Question

General package development

• [ ] :warning: Please address notes from R CMD build
• [ ] :warning: Please address notes and warnings from BiocCheck::BiocCheck()
  • Specifically the WARNING about using .Deprecated
• [ ] :warning: Please address notes from R CMD check
  • The check failed for me locally. If it passes on the build system it's probably fine though.

NAMESPACE file

• [ ] :rotating_light: Please rename read.raw to be consistent with the other functions

The NEWS file

• [ ] :green_circle: Remember to update the NEWS file when you make changes to the package

Documentation

Vignette

• [ ] :rotating_light: Please add an Introduction section. This should:
  • [ ] Introduce your package
  • [ ] Include motivation for inclusion in Bioconductor
  • [ ] Include comparison to similar packages (if applicable)
• [ ] :rotating_light: Please add an Installation section that includes:
  • [ ] Bioconductor installation instructions (not evaluated)
  • [ ] Instructions for installing additional system dependencies
• [ ] :warning: The vignette is very brief, I think it can be expanded to better explain the package and its functionality
• [ ] :warning: In general echo = TRUE is preferred in vignettes to show the code that is being run
• [ ] :rotating_light: Please remove commented code that isn't run

• [ ] :green_circle: I got an error when I tried to run the plotting chunk:

  Error in `ggplot()`:
  ! `mapping` should be created with `aes()`.
  ✖ You've supplied a <character> object

Man pages

• [ ] :warning: It is recommended to add a package man page
• [ ] :green_circle: I noticed some unrendered code in the documentation, you might want to check what the rendered output looks like

Unit tests

• [ ] :warning: The context() function is superseded in recent {testthat} versions
• [ ] :warning: The tests can be better organised into files for different parts of the package, usually they match the structure of the R/ directory
• [ ] :warning: The current tests are minimal, please consider adding more tests

Code

R

• [ ] :rotating_light: Using paste in message(), warning(), stop() is not needed
• [ ] :warning: Consider adding checks that function arguments are valid
  • For several of the function you could easily use match.arg
• [ ] :rotating_light: Parallelisation should use the BiocParallel package
• [ ] :rotating_light: Please remove commented code that isn't used
• [ ] :warning: The name of the shiny() function is very generation, I would recommend changing it to something more specific to the package
• [ ] :warning: I'm not sure about the need for the appDir argument in the shiny() function, I don't think a user would ever need to set this
• [ ] :warning: It might be better not to have a default value for the rawDir argument in the shiny() function. The default value is unlikely to work for most users and making it required would be clearer.
• [ ] :rotating_light: Please give the .f() function a more descriptive name

Third-party code

• [ ] :rotating_light: Please check the inclusion of third-party code follows the guidelines

[bioc-issue-bot]

Received a valid push on git.bioconductor.org; starting a build for commit id: edbda4b1e92f009b79239ed4f0e323d8d648c689

[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, skipped, 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): rawDiag_0.99.18.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/rawDiag 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: 803a86a2c9b5f88055606f13e398da10081e5932