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GNOSIS #3132

Closed Lydia-King closed 8 months ago

Lydia-King commented 10 months ago

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

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

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

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 commented 10 months ago

Dear @Lydia-King,

The package version number, '1.99.0', does not start with 0. Expecting format: '0.99.z' for new packages. Starting with non-zero x of 'x.y.z' format is generally only allowed if the package has been pre-released.

We recommend fixing the version number. See Bioconductor version numbers Please also consider running BiocCheck::BiocCheck('new-package'=TRUE) on your package to look for other Bioconductor package requirements.

bioc-issue-bot commented 10 months ago

Hi @Lydia-King

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: GNOSIS
Type: Package
Title: Genomics explorer using statistical and survival analysis in R
Version: 1.99.0
Description: GNOSIS incorporates a range of R packages enabling users to 
    efficiently explore and visualise clinical and genomic data obtained
    from cBioPortal. GNOSIS uses an intuitive GUI and multiple tab panels 
    supporting a range of functionalities. These include data upload and initial 
    exploration, data recoding and subsetting, multiple visualisations, 
    survival analysis, statistical analysis and mutation analysis, in addition 
    to facilitating reproducible research.
Authors@R: c( 
    person("Lydia", "King", ,"l.king18@universityofgalway.ie",
      c("aut", "cre"), c(ORCID = "0000-0002-0696-9811")
    ),
    person("Marcel", "Ramos", ,"marcel.ramos@roswellpark.org", "ctb")
  )
License: MIT + file LICENSE
Imports:
    DT, 
    fontawesome, 
    shinycssloaders, 
    cBioPortalData, 
    shinyjs, 
    reshape2, 
    RColorBrewer,
    survival,
    survminer,
    stats,
    compareGroups,
    rpart,
    partykit,
    DescTools,
    car,
    rstatix,
    fabricatr,
    shinylogs
Depends: 
    shiny, 
    shinydashboard, 
    shinydashboardPlus, 
    dashboardthemes, 
    shinyWidgets, 
    shinymeta, 
    tidyverse,
    operator.tools,
    maftools
Suggests: 
    BiocStyle, 
    knitr, 
    rmarkdown
biocViews:
    Software, ShinyApps, Survival, GUI
BugReports: https://github.com/Lydia-King/GNOSIS/issues
URL: https://github.com/Lydia-King/GNOSIS/
Video: https://doi.org/10.5281/zenodo.5788544
VignetteBuilder: knitr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
vjcitn commented 10 months ago

Can the vignette provide some more concrete illustration of the capabilities? The link to the paper is useful but the package vignette is an opportunity to provide a concise illustration of major benefits achievable through the use of the package/app.

Lydia-King commented 10 months ago

I have updated the vignette to provide a brief overview of what you can do in GNOSIS, including screenshots. If additional information is needed, please let me know.

bioc-issue-bot commented 10 months ago

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 commented 10 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): GNOSIS_0.99.0.tar.gz macOS 12.6.5 Monterey: GNOSIS_0.99.0.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/GNOSIS to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 10 months ago

A reviewer has been assigned to your package for an indepth review. Please respond accordingly to any further comments from the reviewer.

bioc-issue-bot commented 10 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 0718e1423faba9244066d5a09341c7cd890b0ac4

bioc-issue-bot commented 10 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: macOS 12.6.5 Monterey: GNOSIS_0.99.1.tar.gz Linux (Ubuntu 22.04.2 LTS): GNOSIS_0.99.1.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/GNOSIS to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jianhong commented 9 months ago

Package 'GNOSIS' Review

Thank you for submitting your package to Bioconductor. The package passed check and build. However there are several things need to be fixed. Please try to answer the comments line by line when you are ready for a second review. Code: Note: please consider; Important: must be addressed.

The DESCRIPTION file

R code

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 5a4c04388d29c02543b37b70be07f7a87244886e

Lydia-King commented 8 months ago

Response to Review

Thank you @jianhong for the comments and suggestions. Please find my response below.

The DESCRIPTION file

Documentation

bioc-issue-bot commented 8 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: macOS 12.6.5 Monterey: GNOSIS_0.99.2.tar.gz Linux (Ubuntu 22.04.2 LTS): GNOSIS_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/GNOSIS to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 8 months ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 34a34c951115afb0c8ae51c0d71523f5ec9ebcfd

bioc-issue-bot commented 8 months ago

Dear Package contributor,

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

Your package has been built on the Bioconductor Build System.

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 Bioconductor Build System: Linux (Ubuntu 22.04.2 LTS): GNOSIS_0.99.3.tar.gz macOS 12.6.5 Monterey: GNOSIS_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/GNOSIS to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 8 months ago

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.

lshep commented 8 months ago

The default branch of your GitHub repository has been added to Bioconductor's git repository as branch devel.

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/Lydia-King.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("GNOSIS"). The package 'landing page' will be created at

https://bioconductor.org/packages/GNOSIS

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.