(inactive) prozor

[wolski]

Hi, I did run BiocCheck and I know that there are two errors: 1 "Package must be removed from CRAN."
2 "Maintainer must register at the support site; visit https://support.bioconductor.org/accounts/signup/ ."

Ad 1 I am happy to remove it from CRAN once it is accepted for Bioconductor. Ad 2 I am registered with https://support.bioconductor.org/accounts/signup/ with the e-mail provided in the package description.

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

• Repository: https://github.com/protViz/prozor

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

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

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[bioc-issue-bot]

Hi @wolski

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: prozor
Type: Package
Title: Minimal Protein Set Explaining Peptide Spectrum Matches
Version: 0.99.3
Authors@R: c(person("Witold", "Wolski",
        email = c("wew@fgcz.ethz.ch", "wewolski@gmail.com"),
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0002-6468-120X")))
Description: Determine minimal protein set explaining
    peptide spectrum matches. Utility functions for creating fasta amino acid databases with decoys and contaminants.
    Peptide false discovery rate estimation for target decoy search results on psm, precursor, peptide and protein
    level. Computing dynamic swath window sizes based on MS1 or MS2 signal distributions.
License: GPL-3
Imports:
    AhoCorasickTrie,
    docopt,
    Matrix,
    methods,
    purrr,
    readr,
    rlang,
    seqinr,
    stringr,
    dplyr
Suggests: knitr,
    rmarkdown,
    reticulate,
    ssh
URL: https://github.com/protviz/prozor
BugReports: https://github.com/protviz/prozor/issues
Repository: CRAN
RoxygenNote: 7.1.2
Depends: R (>= 4.1.0)
VignetteBuilder: knitr
Collate: 
    'annotatePeptides.R'
    'readjustWindow.R'
    'cdsw.R'
    'computeFDR.R'
    'createDecoyDB.R'
    'create_fgcz_fasta_db.R'
    'fgcz_helper.R'
    'greedy.R'
    'hello.R'
    'loadContaminantsFasta.R'
    'prepareMatrix.R'
    'readFasta.R'
    'removeSignalPeptides.R'
    'reverseSeq.R'
    'writeFasta.R'
    'zzz.R'
biocViews: Software, MassSpectrometry, Proteomics, ExperimentHubSoftware, 

[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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[lshep]

Please only have one email associated with your package maintainer.

[lshep]

Your BiocCredentials account was set up with wewolski@gmail.com

[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 git@git.bioconductor.org:packages/prozor to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[LiNk-NY]

Hi Witold, @wolski

On quick inspection, the package does not seem to be making use of the Bioconductor ecosystem and thus is not a candidate for Bioconductor. If you have plans to rework the package to use familiar Bioconductor classes and interfaces, you are welcome to resubmit the package.

Best regards, Marcel

[wolski]

@LiNk-NY Hi Marcel,

Is my guess correct that you refer to the usage of the "seqinr" CRAN package? Should I replace it with Biostrings readAAStringSet?

Is there anything else?

Best, Witek

[LiNk-NY]

Hi Witek, @wolski

I was referring to the overall functionality of the package. It does not look like a package that was created with Bioconductor functionality in mind. Perhaps it make use of the suite of functionality provided by MSnbase and friends?

Replacing seqinr with Biostrings would be a good starting point.

Best regards, Marcel

[lshep]

@wolski do you intend to follow up on submission. We like to see updates and changes within 3-4 weeks?

[wolski]

@lshep There is, as of today, only comment from one reviewer. Isn't there a second review pending?

[vjcitn]

Hi @wolski .... I don't know if there is a second review pending -- the package is still in an error state so it may get a lower priority than packages that are getting revised to an "OK" state. Several bits of advice were given in the previous comment and your responses are of interest. I noticed in the PeptideAnnotation... vignette there is a "TODO" section indicative of more work planned at your end. The graphic just before the TODO needs to have the axis labels adjusted as there are only two labels for four bars. Please attend to the previous comments, fix the error state, bump the version number, commit and push the corrections, and the review process will continue.

[lshep]

@wolski Bioconductor only assigns one reviewer per package. Please address @LiNk-NY Initial concerns and as @vjcitn pointed out clean up any ERROR/WARNING/Notes in the build reports produced. Once that occurs @LiNk-NY will do a more in-depth review of the package.

[wolski]

@lshep Thanks. I am on holiday for the next two weeks. I will look into addressing them once I am back.

[bioc-issue-bot]

This issue is being closed because there has been no progress for an extended period of time. You may reopen the issue when you have the time to actively participate in the review / submission process. Please also keep in mind that a package accepted to Bioconductor requires a commitment on your part to ongoing maintenance.

Thank you for your interest in Bioconductor.