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MSstatsTMT #882

Closed huang704 closed 5 years ago

huang704 commented 6 years ago

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

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bioc-issue-bot commented 6 years ago

Hi @huang704

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: MSstatsTMT
Title: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
Version: 0.99.0
Date: 2018-09-22
Description: Tools for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling.
Authors@R: c(person("Ting", "Huang", email = "thuang0703@gmail.com", role=c("aut","cre")),
    person("Meena", "Choi", email = "mnchoi67@gmail.com", role="aut"),
    person("Sicheng", "Hao", email = "hao.sic@husky.neu.edu", role = "aut"))
Maintainer: Ting Huang <thuang0703@gmail.com>
License: Artistic-2.0
Depends: R (>= 3.5)
Imports: limma, lme4, dplyr, tidyr, nlme, 
    reshape2, data.table, matrixStats, stats, utils, ggplot2, grDevices, graphics, MSstats
Suggests: BiocStyle, knitr, rmarkdown, testthat
VignetteBuilder: knitr
biocViews: MassSpectrometry, Proteomics, Software
Encoding: UTF-8
LazyData: true
URL: http://msstats.org
BugReports: https://groups.google.com/forum/#!forum/msstats
RoxygenNote: 6.1.0

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bioc-issue-bot commented 6 years ago

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.

mtmorgan commented 6 years ago

It's confusing to see the references to 'MSstats', including in URLs in the DESCRIPTION file, when this package does not seem to be related to the existing MSstats package.

bioc-issue-bot commented 6 years ago

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.

bioc-issue-bot commented 6 years ago

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

b0eba10 add examples for maxquant and spectromine converte...

bioc-issue-bot commented 6 years ago

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.

bioc-issue-bot commented 6 years ago

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

43a49f3 Delete system files that should not be git tracked

bioc-issue-bot commented 6 years ago

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

c90600a Delete system files that should not be git tracked

bioc-issue-bot commented 6 years ago

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.

bioc-issue-bot commented 6 years ago

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.

huang704 commented 6 years ago

It's confusing to see the references to 'MSstats', including in URLs in the DESCRIPTION file, when this package does not seem to be related to the existing MSstats package.

MSstatsTMT and MSstats are developed by the same lab and sibling packages. MSstatsTMT focuses on the statistical analysis for iTRAQ and TMT, while MSstats analyzes SRM, DIA(SWATH) and label-free DDA data.

MSstatsTMT and MSstats shares the same website. But to avoid the confusion, I have changed the URL to the specific address of MSstatsTMT webpage.

bioc-issue-bot commented 6 years ago

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

674e825 fix bug in groupComparison function

bioc-issue-bot commented 6 years ago

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: "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.

bioc-issue-bot commented 6 years ago

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

0d5d742 Reduce the checking time

bioc-issue-bot commented 6 years ago

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: "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.

bioc-issue-bot commented 6 years ago

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

28f7fb1 reduce the time of R CMD CHECK

bioc-issue-bot commented 6 years ago

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.

vobencha commented 5 years ago

Hi, Looks good. My only suggestion is to name the exported functions in a consistent manner. They are currently a combo of dots '.' and camelCase - please pick one or the other. Valerie

bioc-issue-bot commented 5 years ago

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

ae592b1 update of internal function name

bioc-issue-bot commented 5 years ago

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 commented 5 years ago

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

a66c093 Update exported function names

bioc-issue-bot commented 5 years ago

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: "ABNORMAL". 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.

bioc-issue-bot commented 5 years ago

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

f36d3dc Update vignettes

bioc-issue-bot commented 5 years ago

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.

huang704 commented 5 years ago

Hi @vobencha ,

Thank you for the comments. I have updated the package based on your comments. I named all the exported functions in camelCase.

vobencha commented 5 years ago

Thanks. The package is approved.

bioc-issue-bot commented 5 years ago

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 commented 5 years ago

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/huang704.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 biocLite(\"MSstatsTMT\"). The package 'landing page' will be created at

https://bioconductor.org/packages/MSstatsTMT

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.