Package submission: scds

kostkalab commented 5 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/kostkalab/scds

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bioc-issue-bot commented 5 years ago

Hi @kostkalab

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: scds
Type: Package
Title: In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
Version: 0.99.0
Author: Dennis Kostka
Authors@R: c(person("Dennis", "Kostka", role=c("aut", "cre"),
        email="kostka@pitt.edu"), person("Bais", "Abha",
        role=c("aut"), email="abhabais@pitt.edu"))
Maintainer: Dennis Kostka <kostka@pitt.edu>
Description: More about what it does (maybe more than one line)
    Use four spaces when indenting paragraphs within the Description.
License: MIT + file LICENSE
Encoding: UTF-8
biocViews: SingleCell, RNASeq, QualityControl, Preprocessing,
        Transcriptomics, GeneExpression, Sequencing, Software, Classification
RoxygenNote: 6.1.1
Depends: R (>= 3.6.0)
Imports: 
    Matrix,
    S4Vectors,
    SingleCellExperiment,
    SummarizedExperiment,
    xgboost,
    methods,
    stats
Suggests: BiocStyle, knitr, rsvd, Rtsne, scater, cowplot
VignetteBuilder: knitr

bioc-issue-bot commented 5 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.

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:

35351b8 Version bump to trigger rebuild.

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.

lshep commented 5 years ago

Your Description is mal-formed. You'll have to fix it to get a build report.

https://github.com/kostkalab/scds/blob/master/DESCRIPTION

namely this section:

Description: In single cell RNA sequencing (scRNA-seq) data combinations of cells are sometimes considered a single cell (doublets). The scds package provides methods to annotate doublets in scRNA-seq data computationally.

More about what it does (maybe more than one line)
    Use four spaces when indenting paragraphs within the Description.
License: MIT + file LICENSE

bioc-issue-bot commented 5 years ago

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

4364453 Fixed DESCRCRIPTION format

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: "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.

kostkalab commented 5 years ago

Hi,

Have you started reviewing? The warnings are unrelated to code in the package.

Thanks a lot,

Dennis

lshep commented 5 years ago

Yes. I will have an official review before the end of the week.

kostkalab commented 5 years ago

Great thanks!

lshep commented 5 years ago

The package in general looks in good shape. Please find my review below:

Build Report

[ ] Please clean up coding notes about Avoiding 1:...

README

[ ] Include Bioconductor installlation instructions

LICENSE

[ ] (Optional) The MIT license is included with the R release so you do not strictly need to include it https://www.r-project.org/Licenses/

Description

[ ] Please use Authors@R (preferred) or Author/Maintainer fields but not both.

NEWS

[ ] We strongly encourage a news file so that updates to the package can be announced http://bioconductor.org/developers/package-guidelines/#news

Tests

[ ] We strongly encourage the use of unit tests http://bioconductor.org/developers/package-guidelines/#unittest

MAN OK

Vignette

[ ] Optional - It is much more intuitive to do vignette("scds") than it would be to do vignette("vignette-intro"). I would recommend renaming the vignette. Also with something generic like that, there is a chance the wrong vignette will be accessed by a user... for instance when I blindly did the vignette call without the package it actually gave me the one from scatter instead of yours.
```
> library(scds)
> vignette("vignette-intro")
starting httpd help server ... done
Warning message:
vignette 'vignette-intro' found more than once,
using the one found in '/home/lori/R/x86_64-pc-linux-gnu-library/3.6-BioC-3.9/scater/doc' 
```


- [ ] Include Bioconductor installation instructions
- [ ] Section 3.2, I feel like a brief indication of the difference between cxds
and bcds would be helpful. The link to the manuscript is good but not everyone
will follow it, so even just a few words to clarify the difference between the
two. And what exactly is gonig on with the cxds_bcds_hybrid -  The pipeline is
good but the clarification of what each step is really doing is somewhat
lacking. I would recommend just adding a few lines of more detail. 

**R code**
- [ ] I would put in a validation check on the sce object to make sure it is of
class SingleCellExperiment and that it has the needed assay matrix counts. 
- [ ] Update from using `cat` to using `message`. It is more appropriate for
printing status messages. 

Please update and perform a version bump to kick off a new build. When you are ready for a re-review please comment back here with what has been updated and I will look at the package again.  Cheers!

bioc-issue-bot commented 5 years ago

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

4edabf0 Addressed comments from Bioconductor review: seq_l...

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.

kostkalab commented 5 years ago

Thanks a lot for the comments, they've been helpful! Addressed them in an incremented version and the new package seems to build fine. It'd be great if you could take a second look. Here is what's changed in a bit more detail:

Now consistently using seq_len
Added NEWS file in ./inst/
DESCRIPTION now only uses Authors@R
Added Bioc installation instructions to README.md
Added Bioc installation instructions to vignette
Renamed vignette to "scds"
Expanded text in the doublet prediction section (3.2) of the vignette.
Checked that first argument for cxds and bcds functions: needs to be a SingleCellExperiment with "counts" in the assasys slot
Replaced cat with message
Used usethis::use_mit_license() to generate license files

lshep commented 5 years ago

Looks good. Thank you.

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/kostkalab.keys is not empty), then no further steps are required. Otherwise, do the following:

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

https://bioconductor.org/packages/scds

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.

Bioconductor / Contributions

Package submission: scds #1037