(inactive) Dapar2

[samWieczorek]

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

• Repository: https://github.com/samWieczorek/Dapar2

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 instructions. My package is consistent with the Bioconductor Package Guidelines.

• [x] I understand Bioconductor Package Naming Policy 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 genomic data.

• [x] I am committed to the long-term maintenance of my package. This includes monitoring the support site for issues that users may have, subscribing to the 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 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 (optionally via GitHub).

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 @samWieczorek

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: Dapar2
Type: Package
Title: Tools for the Differential Analysis of Proteins Abundance with R
Version: 0.99.0
Date: 2021-07-15
Authors@R: c(person(given = "Samuel", family = "Wieczorek",
  email = "samuel.wieczorek@cea.fr",
  role = c("aut","cre")),
  person(given = "Thomas", family ="Burger",
  email = "thomas.burger@cea.fr",
  role = c("aut")),
        person(given = "Enora", family ="Fremy",
  email = "enora.fremy@cea.fr",
  role = c("ctb"))
  )
Author: Samuel Wieczorek [cre,aut],
    Thomas Burger [aut],
    Anais Courtier [ctb],
    Enora Fremy [ctb]
Maintainer: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Description: This package contains a collection of functions for the
    visualisation and the statistical analysis of proteomic data.
License: Artistic-2.0
VignetteBuilder: knitr
Depends: R (>= 4.1.0)
Suggests: 
    testthat, 
    BiocStyle, 
    knitr,
    MSnbase,
    DAPARdata2
Imports:
    Biobase,
    S4Vectors,
    QFeatures,
    methods,
    apcluster,
    diptest,
    cluster,
    base64enc,
    MsCoreUtils,
    SummarizedExperiment,
    MultiAssayExperiment,
    AnnotationFilter,
    openxlsx, 
    preprocessCore,
    lme4,
    vsn, 
    stringr,
    RColorBrewer,
    graph,
    FactoMineR, 
    factoextra,
    DT, 
    doParallel,
    dplyr,
    foreach,
    gplots,
    highcharter,
    tibble,
    tidyr,
    visNetwork, 
    Matrix,
    cp4p,
    grDevices,
    limma,
    vioplot,
    imp4p (>= 0.9),
    impute,
    dendextend,
    readxl,
    forcats,
    multcomp,
    purrr,
    ggplot2,
    reshape2,
    colourpicker,
    htmlwidgets,
    shiny,
    shinyBS,
    shinyWidgets,
    shinyalert,
    shinyjs,
    sos
biocViews: 
    Proteomics,
    Normalization,
    Preprocessing,
    MassSpectrometry,
    QualityControl,
    GO,
    DataImport
NeedsCompilation: no
Collate:
    AllGenerics.R
    palette.R
    metacell.R
    aggregation.R
    compute.t.tests.R
    DiffAnalysis.R
    group_ttest.R
    export_qfeatures.R
    import_2_qfeatures.R
    limmaAnalysis.R
    plots_mv_for_impute.R
    ConnectedComps.R
    Filtering.R
    normalize.R
    plots_boxplot.R
    plots_compare_normalization_plots.R
    plots_corr_matrix.R
    plots_CV_dist.R
    plots_density_plot.R
    plots_heatmap.R
    plots_mv_histo.R
    plots_mv_PerLinesHisto.R
    plots_mv_PerLinesHistoPerCondition.R
    plots_pca.R
    plots_violin.R
    plots_volcano.R
    utils.R
    missingValuesImputation_PeptideLevel.R
    missingValuesImputation_ProteinLevel.R
    pepa.R
    anova_analysis.R
    clustering.R
    misc.R
    hypothesis_test.R
    global.R
    mod_Protein.R
    mod_Protein_Description.R
    mod_Protein_Filtering.R
    mod_Protein_Normalization.R
    mod_all_plots.R
    mod_convert.R
    mod_format_DT.R
    mod_graph_pept_prot.R
    mod_plots_cc.R
    mod_plots_corr_matrix.R
    mod_plots_density.R
    mod_plots_group_mv.R
    mod_plots_heatmap.R
    mod_plots_intensity.R
    mod_plots_legend_colored_exprs.R
    mod_plots_mv_for_imputation.R
    mod_plots_pca.R
    mod_plots_se_explorer.R
    mod_plots_tracking.R
    mod_plots_var_dist.R
    mod_popover_for_help.R
    mod_settings.R
    zzz.R
RoxygenNote: 7.1.1
Packaged: 2017-10-13 11:13:04 UTC; sw175264
Encoding: UTF-8

[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.

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 Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR, 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. 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/Dapar2 to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

[lshep]

Please correct all ERROR's before @nturaga will do a formal review

[nturaga]

Hi, please explain the differences between DAPAR (which is already a package within Bioconductor) and Dapar2.

The DESCRIPTION file describes both of them is exactly the same.

Description: This package contains a collection of functions for the
    visualisation and the statistical analysis of proteomic data.

Bump the version number and make sure there are no ERROR messages for the review.

[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.