cvanderaa commented 4 years ago

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

Repository: https://github.com/UCLouvain-CBIO/scp

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bioc-issue-bot commented 4 years ago

Hi @cvanderaa

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: scp
Title: Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
Version: 0.99.0
Authors@R:
    c(person("Christophe", "Vanderaa",
          email = "christophe.vanderaa@uclouvain.be",
          comment = c(ORCID = "0000-0001-7443-5427"),
          role = c("aut", "cre")),
      person("Laurent", "Gatto",
          email = "laurent.gatto@uclouvain.be",
          comment = c(ORCID = "0000-0002-1520-2268"),
          role = "aut"))
Description: Utility functions for manipulating, processing, and analyzing mass
    spectrometry-based single-cell proteomics (SCP) data. The package is an 
    extension to the 'QFeatures' package designed for SCP applications. 
Depends:
    R (>= 4.0),
    QFeatures
Imports:
    methods,
    stats,
    utils,
    SingleCellExperiment,
    SummarizedExperiment,
    MultiAssayExperiment,
    S4Vectors,
    dplyr,
    magrittr,
    rlang
Suggests:
    testthat,
    knitr,
    BiocStyle,
    rmarkdown,
    patchwork,
    ggplot2,
    matrixStats,
    impute,
    scater,
    sva,
    uwot
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
biocViews: 
    GeneExpression,
    Proteomics,
    SingleCell,
    MassSpectrometry,
    Preprocessing,
    CellBasedAssays
BugReports: https://github.com/UCLouvain-CBIO/scp/issues
URL: https://UCLouvain-CBIO.github.io/scp
Roxygen: list(markdown=TRUE)
RoxygenNote: 7.1.1

cvanderaa commented 4 years ago

Tagging @lgatto

bioc-issue-bot commented 4 years ago

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bioc-issue-bot commented 4 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. 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/scp to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: ee38b901d7ecee9cf95fc047d7b0a82360b77d75

cvanderaa commented 4 years ago

The changes introduced by the push are:

Maintainer subscribed to bioc-devel mailing list
Removed infIsNA, the implementation was moved to the QFeatures packages

bioc-issue-bot commented 4 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. 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/scp to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

LTLA commented 4 years ago

Wow, we have single-cell proteomics? I didn't even know that was a thing.

Guess I'm getting old. Back in my day, we just did MALDI-TOF/TOF.

cvanderaa commented 4 years ago

@nturaga any news ?

lshep commented 4 years ago

I'll have a review for you by tomorrow.

lshep commented 4 years ago

Thank you for your submission. We apologize for the delay in review. Please see minor comments below:

README

[ ] Please include the official repo location for stable download and github for development

Description

[ ] we recommend LazyData: true be removed from the DESCRIPTION file. We have rarely found it useful and that it can actually slow the installation process.

Data / man

[ ] scp1 can you include source information for the data files in the man pages for the data objects. I realize it is also in the vignette but would be good to include in the man page as well.

Vignette

[ ] PCA plot doesn't appear? See warning and transparency message?

Please address the above issues. When ready please do a version bump and leave a comment here that you are ready for a re-review. Cheers

lgatto commented 4 years ago

Thank you very much for the prompt review, Lori.

cvanderaa commented 4 years ago

Hi @lshep Thanks a lot for your rapidity! I have been struggling with replicating the PCA plot issue, but thanks to @lgatto we could solve the issue. Here is an update of your review.

README

[x] Please include the official repo location for stable download and github for development

Description

[x] we recommend LazyData: true be removed from the DESCRIPTION file. We have rarely found it useful and that it can actually slow the installation process.

Data / man

[x] scp1 can you include source information for the data files in the man pages for the data objects. I realize it is also in the vignette but would be good to include in the man page as well.

I added extra information about data collection in the Details section for the 3 datasets: scp1, mqScpData and sampleAnnotation

Vignette

[x] PCA plot doesn't appear? See warning and transparency message?

I removed the transparency

I bumped the version of scp to 0.99.3. Thank you for your time!

lshep commented 4 years ago

It does not appear you pushed these changes to bioconductor. Please update the repository as described here

lshep commented 4 years ago

I went ahead and looked at the changes on your gitub. Please update the stable instructions in the README to Bioconductor repository BiocManager::install('scp') not the github repository.

Everything else looks good. Please push the git.bioconductor.org repository to kick off the new build with this change. As long as the build report still looks good I will accept the package.

lgatto commented 4 years ago

Sorry about the installation instructions, this slid through the cracks. Fixed now, and I'm pushing to Bioc's git server.

lgatto commented 4 years ago

Would it be possible to give me write access to git@git.bioconductor.org:packages/scp.git - thanks.

lshep commented 4 years ago

@nturaga can you assist with this?

nturaga commented 4 years ago

@lgatto you should have access now.

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6e7181ed841091cecdbe5fdd605c9865f626ebd4

lgatto commented 4 years ago

Thank you @nturaga

bioc-issue-bot commented 4 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. 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/scp to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

bioc-issue-bot commented 4 years ago

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

mtmorgan commented 4 years ago

The master branch of your GitHub repository has been added to Bioconductor's git repository.

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See further instructions at

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for working with this repository. See especially

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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

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

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Bioconductor / Contributions

scp: Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data #1628

README

Description

Data / man

Vignette

README

Description

Data / man

Vignette