cliqueMS

[osenan]

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• Repository: https://github.com/osenan/cliqueMS

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[bioc-issue-bot]

Hi @osenan

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: cliqueMS
Type: Package
Title: Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data
Version: 0.99.0
Date: 2019-09-10
Authors@R: c(
       person("Oriol", "Senan Campos", email = "oriol.senan@urv.cat", role = c("aut","cre")),
       person("Antoni", "Aguilar-Mogas", role = "aut"),
       person("Jordi", "Capellades", role = "aut"),
       person("Miriam", "Navarro", role = "aut"),
       person("Oscar", "Yanes", role = "aut"),
       person("Roger", "Guimera", role = "aut"),
       person("Marta", "Sales-Pardo", role = "aut")
       )
Description: Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.Guimerà and M. Sales-Pardo, Metabolomics Conference (2016), Dublin), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.
License: GPL (>= 2)
Depends: R (>= 3.6.0)
Imports: Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, qlcMatrix, methods
LinkingTo: Rcpp, BH, RcppArmadillo
URL: https://cliquems.seeslab.net
BugReports: https://github.com/osenan/cliqueMS/issues
biocViews: Metabolomics, MassSpectrometry, Network, NetworkInference
SystemRequirements: C++11
Encoding: UTF-8
RoxygenNote: 6.1.1
Suggests: knitr,
    rmarkdown,
    testthat, CAMERA
VignetteBuilder: knitr

[bioc-issue-bot]

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

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[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.

[mtmorgan]

Please revise your package to respond to the following comments, posting a brief summary fo your changes when ready for final review.

DESCRIPTION

• good

NEWS.md

• is this file formatted so that it is parsed by utils::news(), e.g., as created by usethis::use_news_md()?

vignettes

• looks really good

R

• Please use S4 classes and methods for more robust data structures and interoperabilty with Bioconductor infrastructure. This is not as big an ask as it might sound; define a class, constructor, accessors, and show method, as well as replacing S3 with S4 methods. Use the accessors throughout your own code, so that direct slot access is only present in the accessors.

.AnClique <- setClass(
    'AnClique",
    slots = c(
        peaklist = "data.frame",
        network = ...
    )

AnClique <-
    function(peaklist = data.frame(), ...)
{
    ...
    .AnClique(peaklist = peaklist, ...)
}

setGeneric("peaklist", function(x) standardGeneric("peaklist"))

setMethod("peaklist", "AnClique", function(x) slot(x, "peaklist"))

...

setMethod(
    "show", "AnClique",
    function(x)
{
    ...
})

...

• e.g., allClasses.R:160 Use message() rather than cat() to provide diagnostic information

• please use more standard formating (e.g., using formatR or the guidelines at http://bioconductor.org/developers/how-to/coding-style/). E.g., in buildNetwork.R:34 the use of } else { ... makes it very difficult to parse the limits of the if and else blocks

    if( sum(repeated.peaks) == 0 ) {
        nodes.delete = NULL
    } else {
        filtered.edges <- edges0.99[repeated.peaks,]
        if(sum(repeated.peaks) == 1) {
            ## only one peak filtered
            nodes.delete <- min(filtered.edges)
        } else {
            nodes.delete <- vapply(
                seq_len(nrow(filtered.edges)),
                function(x) { 
                    min(filtered.edges[x,])
                }, 
                numeric(1)
            )
        }
    }

• look carefully at your code for opportunities to vectorize (replace many R-level function calls with one function call. E.g., in the above code chunk the use of vapply(), which calls min() and [ nrow(filtered.edges) times, can be replaced with matrixStats::rowMins(nodes.deleted).

• use message() rather than cat() to communicate diagnostic messages to the user, e.g., buildNetwork.R:290

• it is usually sufficient to use warning(...) rather than warning(paste(...)), e.g., findIsotopes.R:235

man

• ok

[osenan]

Dear @mtmorgan,

Thank you very much for the comments. When all the corrections are made I will post a summary with the changes along with the new version.

Kind regards, Oriol

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

517d9d1 Changes in NEWS.md format to parse utils::news fun... 82897e1 remove 'cat' and improve WARNING messages 5cbc69a First build of S4 classes c4fcf07 complete substitution of S3 for S4 anClique classe... c898ef9 New S4 anClique class, new documentation 29ee5d7 correction on the const reference

[osenan]

Dear @mtmorgan ,

Here is a summary of the changes

• DESCRIPTION: New webpage, added a collate field, added a package to Imports.

• NEWS: The file could not be parsed by utils::news(). I changed and now it is.

• R Code:

  • I changed the main class of the package anClique from S3 to a S4 class. This means:

    1. New class, methods and functions with slots, accessors and setters.
    2. Changes in all the other functions to adapt to the new S4 class.
    3. Changes in the documentation, with new entries for the accessors and the setters and the own class.
    4. Changes in the vignette.

  • I changed all cat for message, and I removed paste from the warnings.

  • I reviewed the coding style so space indenting, if and else enclosures are clearer, and the code looks cleaner in general.

  • I tried to vectorize the loops in the places were I was using to much basic function calls. Many of them remained unchanged because they are too complex to be synthesized in one line.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

5d6b793 Include bump in version

[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.

[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.

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor Git repository and nightly builds. Additional information will be posed to this issue in the next several days.

Thank you for contributing to Bioconductor!

[mtmorgan]

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/osenan.keys is not empty), then no further steps are required. Otherwise, do the following:

1. Add an SSH key to your github account
2. Submit your SSH key to Bioconductor

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

https://bioconductor.org/packages/cliqueMS

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.

[mtmorgan]

@osenan unfortunately, when trying to add your package to the Bioconductor git repository the large *tgz files in the MacOS directory are flagged as too large. These need to be removed from the master branch of your repository before your package can be added to Bioconductor. To do this you might

0. Make a copy of your repository

1. Make a commit that removes the files

   git rm MacOS/*tgz git commit -am "remove large .tgz files" git push

2. Clean the repository following the instructions at https://rtyley.github.io/bfg-repo-cleaner/ using a maximum file size of 4.99M and push the results to github.

Please let me know when repository has been cleaned in this way. Once added to Bioconductor, your github repository can be managed in whatever way you like (though you will normally need to keep it in sync with the Bioconductor repository, and adding the large files back to the master branch would re-introduce problems).

[osenan]

Dear @mtmorgan , Those files *tgz files were necessary as the CRAN repository was not building the version for MacOS because the server did not have all the dependencies. Now they are not necessary anymore, I followed the instructions and commited the changes.

I also updated the DESCRIPTION and removed another doc file that only was needed for CRAN.

[mtmorgan]

thanks, but I think the files are still there?

[osenan]

Yes they were, I did not commit the local changes correctly. Now they are definitely not. Sorry for the inconvenience.