dorothea - Githubissues

christianholland 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/saezlab/dorothea

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bioc-issue-bot commented 4 years ago

Hi @christianholland

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: dorothea
Type: Package
Title: Collection Of Human And Mouse TF Regulons
Version: 0.99.0
Author: Christian H. Holland, Luz Garcia-Alonso, Alberto Valdeolivas, Minoo 
    Ashtiani, Attila Gabor 
Maintainer: Christian H. Holland <cholland2408@gmail.com>
Description: This package contains human and mouse TF regulons.
    The human regulons were curated and collected from different types of 
    evidence such as literature curated resources, ChIP-seq peaks, TF binding 
    site motifs and interactions inferred directly from gene expression. The 
    mouse regulons were constructed by mapping the human gene symbols to their 
    orthologs in mice.
URL: https://github.com/saezlab/dorothea
BugReports: https://github.com/saezlab/dorothea/issues
Depends: R (>= 3.6.0)
License: GPL-3 + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.0.2
VignetteBuilder: knitr
biocViews: ExperimentData, Homo_sapiens_Data, Mus_musculus_Data
Imports:
    dplyr,
    magrittr,
    bcellViper
Suggests:
    BiocStyle,
    knitr,
    pheatmap,
    Seurat,
    testthat (>= 2.1.0),
    tibble,
    tidyr,
    utils,
    viper

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bioc-issue-bot commented 4 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 4 years ago

It seems from a quick look at the vignette that this package should interact (accept as inputs / return as outputs) with SingleCellExperiment and other common Bioconductor classes and methods

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.

christianholland commented 4 years ago

Hi @mtmorgan,

thanks for your feedback. In the current state this package can interact with the classes "ExpressionSet" and "Seurat". Based on your suggestion I am adding also the ability to interact with "SingleCellExperiment" class in the development branch. Hope to push it to the master branch today

bioc-issue-bot commented 4 years ago

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

f3d9794 Added .Rproj to gitignore 123da80 Delete dorothea.Rproj 87d9ff5 Revert "Delete dorothea.Rproj" This reverts commi... 0de1c38 removed .rproj d28a8c0 add project file to gitignore 01952b2 Added citation 22611f1 Fixing link warnings 329a414 BioC class in, BioC class out 2bb3150 Added suggestion and bumped version 22ca51d Updated Namespace 083b955 updated news bbd8f6f Updated citation b8c024d Added method for SingleCellExperiment 8aaf680 Added test for singleCellExperiment method 24c323f Minor change 26da00a Added testdata of SingleCellExperiment 223bca5 attemp to fix link warning 8bf09bc Merge pull request #6 from saezlab/devel Upgrade ...

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.

bioc-issue-bot commented 4 years ago

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

5023671 Version bump and increased R dependency to 4.0

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.

bioc-issue-bot commented 4 years ago

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

41d3fdb Went back to Depends R>=3.6

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.

bioc-issue-bot commented 4 years ago

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

6bbe1f2 Updated to R4.0 fd9a4ee Created expected eset on the fly

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: "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 4 years ago

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

b481f04 T/F -> TRUE/FALSE 94ab66f Bumped version 148721a Removed link to ExpressionSet

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.

christianholland commented 4 years ago

Hi @mtmorgan,

please note that I have removed in my latest commit a link the to the Bioconductor class Biobase::ExpressionSet. The link raises only on windows machines the following warning:

dorothea/man/run_viper.Rd:13: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic.

With respect to this issue there is currently no solution for this warning. Hence, I removed the link to avoid this warning.

mtmorgan commented 4 years ago

I believe the problem with the link can be understood from https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Cross_002dreferences where the [] is a link to the help page file name. You had \link[Biobase:ExpressionSet]{ExpressionSet} but the page name is 'class.ExpressionSet'. You could have \link[Biobase:class.ExpressionSet]{ExpressionSet}, but this seems like getting too much into the internals of the package, and I think the solution should be to allow R to resolve the reference itself, dynamically at run-time \link{ExpressionSet}.

I have no other comments on your package, and will mark it as accepted. You can update the link as above after the package has been added to the Bioconductor git repository.

bioc-issue-bot commented 4 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 4 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/christianholland.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("dorothea"). The package 'landing page' will be created at

https://bioconductor.org/packages/dorothea

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

dorothea #1466