Contributions MsQuality

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Repository: https://github.com/tnaake/MsQuality

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Sep 20 '22 08:09 tnaake

Hi @tnaake

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: MsQuality
Type: Package
Title: MsQuality - Quality metric calculation from Spectra objects
Version: 0.99.2
Date: 2022-09-20
Authors@R: c(person(given = "Thomas", family = "Naake", 
		email = "[email protected]", role = c("aut", "cre"),
		comment = c(ORCID = "0000-0001-7917-5580")),
	person(given = "Johannes", family = "Rainer",
		email = "[email protected]", role = "aut",
		comment = c(ORCID = "0000-0002-6977-7147")))
Maintainer: Thomas Naake <[email protected]>
VignetteBuilder: knitr
Description: MsQuality enables to calculate quality metrics of mass spectrometry
	data. It is build upon Spectra objects.
Depends:
	R (>= 4.1.0)
Imports:
	ggplot2 (>= 3.3.5),
	htmlwidgets (>= 1.5.3),
	methods (>= 4.1.0),
	plotly (>= 4.9.4.1),
	ProtGenerics (>= 1.24.0),
	shiny (>= 1.6.0),
	shinydashboard (>= 0.7.1),
	Spectra (>= 1.2.0),
	stringr (>= 1.4.0),
	tibble (>= 3.1.4),
	tidyr (>= 1.1.3)
Suggests:
	BiocGenerics (>= 0.24.0),
	BiocStyle (>= 2.6.1),
	dplyr (>= 1.0.5),
	knitr (>= 1.11),
	msdata (>= 0.32.0),
	rmarkdown (>= 2.7),
	S4Vectors (>= 0.29.17),
	testthat (>= 2.2.1)
biocViews: Metabolomics, Proteomics, MassSpectrometry, QualityControl
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.2.0

Sep 20 '22 08:09 bioc-issue-bot

A reviewer has been assigned to your package. Learn what to expect during the review process.

IMPORTANT: Please read this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

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Sep 26 '22 14:09 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/MsQuality to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Sep 26 '22 14:09 bioc-issue-bot

Hi @tnaake - could you please address the issue mentioned in the build report. They should be easy to fix.

Just a few quick comments that you can already address before the more in-depth review:

You don't need to install devtools to install packages from GitHub, you only need remotes. You could also use BiocManager::install("tnaake/MsQuality") to install from GitHub, but you are asked to provide instructions to (also) install from Bioconductor. Your installation instructions could thus be:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")

## to install from Bioconductor
BiocManager::install("MsQuality")

## to install from GitHub
BiocManager::install("tnaake/MsQuality")

Could you also mention other packages that address MS quality control that are available in Bioconductor. proteoQC comes to mind, but there might be another or two, which you should be able to find with the biocViews.
Why does qualityMetrics() need an object of class Spectra as input? It only returns a vector of QC metric names. I tried with sps_sciex, sps_c_hilic, sps_c_rplc and the manually created sps, and I get the same set of metrics.
We already had the discussion about 1 sample or all samples per Spectra object in Heidelberg. In you sps_c_rplc and sps_c_hilic example objects seem to confirm that you don't limit yourself to one sample/file per Spectra object, which is good (the other would be wrong). Why to you have two in your vignette, and concatenate the metrics, as opposed to concatenating the Spectra object:

calculateMetrics(c(sps_c_hilic, sps_c_rplc))

Both are valid, just curious why you illustrate it explicitly, and making sure my understanding of the sample per Spectra is correct.

Oct 07 '22 14:10 lgatto

Received a valid push on git.bioconductor.org; starting a build for commit id: 90f179d3c7246aa4190fe8449af8d17f7125e051

Oct 11 '22 15:10 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, skipped". 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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/MsQuality to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 11 '22 15:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 8458d35883f1c64d9b20f5204ef8030dd2cbe387

Oct 11 '22 17:10 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

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. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/MsQuality to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 11 '22 17:10 bioc-issue-bot

Received a valid push on git.bioconductor.org; starting a build for commit id: 6fa1d4c62124058549bffe4e364fe68224b0a024

Oct 12 '22 11:10 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/MsQuality to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Oct 12 '22 11:10 bioc-issue-bot

Dear @lgatto

many thanks for this initial screen. I have now fixed the issues in the build report and addressed your comments.

devtools/remotes: I changed this accordingly in the vignette and the README.md file.
other packages: I have added a subsection in the vignette that mentions other packages in Bioconductor. proteoQC doesn't seem to be maintained any longer (at least it's only available via the RIKEN and TU Dortmund mirrors).
qualityMetrics(): We have implemented this in this way since we would like to get all available metrics for this kind of object. As you may know, we have also included some functionality for MsExperiment objects in another branch in the GitHub repository. We are planning to merge this branch into the main branch once MsExperiment is accepted in Bioconductor. The qualityMetrics() will allow us in future to get a vector of class-specific metrics either for Spectra, MsExperiment or other objects in future versions (e.g. Chromatogram).
calculateMetrics(c(sps_c_hilic, sps_c_rplc)): Good point, I think this has something to do with how the data of the article (Lee et al. 2019) we are using in the vignette is organized. This is basically a matrix with samples in columns and metabolites in rows. The metabolites have an appendix specifying if the metabolite was measured by RPLC or HILIC (the metabolites were measured via both methods, such that we have metabolite quanitifaction for each metabolite from both RPLC and HILIC). I understand that this might be a bit complicated for the reader and I show the creation of the Spectra object only in the Lee2019-data.R file. I have rewritten this such that we now creacte a new Spectra object (c()) in the beginning and pass to calculateMetrics the RPLC+HILIC-combined Spectra object. Do you think it's better this way? I thought that it might be nice to use a real-world data set to showcase the calculation rather than only with the data sets from msdata but this can be changed of course if you think this might be too complicated/confusing here.

Many thanks again for this initial (and future) review!

Oct 12 '22 11:10 tnaake

Following up from your previous replies, yes, I think the update in the vignette where you combine the Spectra first is nice and clean.

General package development

Please add .github to a .Rbuildignore file so that it doesn't end up in the package tar file.

The DESCRIPTION file

Here are a couple of notes from BiocCheck that you might want to address:

The Description field in the DESCRIPTION is made up by less than 3 sentences. Please consider expanding this field, and structure it as a full paragraph.
License 'GPL (>= 3)' is reported as unknown by BiocCheck. I think this would go away with GPL-3 which at the moment would be equivalent... and if one day there's a version 4, you might want to read it and update accordingly.
Update R version dependency from 4.1.0 to 4.2.0.

Some additional suggestions:

You could add a BugReports field in your DESCRIPTION file to point to your GitHub issues.
You could add a URL field in your DESCRIPTION file to point to your GitHub repo (or pkgdown if you plan to create one, which I recommend).

The NEWS file

Do you know that you can use markdown for your news and have NEWS.md. This plays well with a pkgdown site.

Package data

Installed package size is 7.5Mb, and data is 2.7Mb. Could you reduce the size of the data? An alternative would be to move Lee 2019 data to msdata (or better, later to MsDataHub that will put it on ExperimentHub).

Documentation

Lee_2019 documentation: the 'Source' section is a bit weird formatted as comments and code. If you want to keep it like that, I would suggest to remove the ## in front of the text, and you might be able to use markdown syntax for code chunks. A clean alternative would be to put the script in inst/scripts/ and point to it in the manual page.
You have a \dontrun{} in you shinyMsQuality example. You could also enclose shinyMsQuality(qc = qc) in an if (interactive()) so that the example is run by the user interactively.

Nov 27 '22 16:11 lgatto

Received a valid push on git.bioconductor.org; starting a build for commit id: c1556102bdfa43701feb209d7ac7b1b1f6b95b7d

Nov 29 '22 13:11 bioc-issue-bot

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the build report for more details. This link will be active for 21 days.

Remember: if you submitted your package after July 7th, 2020, when making changes to your repository push to [email protected]:packages/MsQuality to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

Nov 29 '22 13:11 bioc-issue-bot

Dear @lgatto,

many thanks again for the review! I have gone through your points and changed the package accordingly. Please see here for my responses:

.github: added to .Rbuildignore
Description in DESCRIPTION: I have extended the description.
License in DESCRIPTION: changed to GPL-3.
R version in DESCRIPTION: dependency bumped to 4.2.0.
BugReports and URL in DESCRIPTION: I added the links to the github repo.
NEWS file: changed to .md format package size: I have discussed this with @jorainer and we agreed to transfer the example data to MsDataHub once MsDataHub is ready. Could we transfer the dataset after acceptance of MsQuality and MsDataHub to Bioconductor ? As a side note, I was a bit astonished by the large file size of the doc part, which is due to plotly graphics. I have added partial_bundle to plotly graphics which reduced the file size substantially.
Lee2019: I have added a script in inst/scripts and am refering to it in the Lee2019-data.R file.
dontrun: I have changed this to if (interactive()) as suggested.

Many thanks again for having a detailed look into the package!

Best, tnaake

Nov 29 '22 13:11 tnaake

Great. Thank you for your contribution!

Dec 05 '22 16:12 lgatto

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.

Dec 05 '22 16:12 bioc-issue-bot

Thank you once more for your review!

Dec 06 '22 15:12 tnaake

The master branch of your GitHub repository has been added to Bioconductor's git repository.

To use the git.bioconductor.org repository, we need an 'ssh' key to associate with your github user name. If your GitHub account already has ssh public keys (https://github.com/tnaake.keys is not empty), then no further steps are required. Otherwise, do the following:

See further instructions at

https://bioconductor.org/developers/how-to/git/

for working with this repository. See especially

https://bioconductor.org/developers/how-to/git/new-package-workflow/ 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("MsQuality"). The package 'landing page' will be created at

https://bioconductor.org/packages/MsQuality

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.

Dec 19 '22 17:12 lshep