jleechung 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/GoekeLab/proActiv

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

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bioc-issue-bot commented 4 years ago

Hi @jleechung

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: proActiv
Title: Estimate Promoter Activity from RNA-Seq data
Version: 0.99.0
Authors@R: c(
    person(given = "Deniz",
 family = "Demircioglu",
 role = c("aut"),
 email = "ddemircioglu@gis.a-star.edu.sg",
 comment = c(ORCID = "0000-0001-7857-0407")),
    person(given = "Jonathan",
family = "Göke",
role = c("aut"),
email = "gokej@gis.a-star.edu.sg"),
    person(given = "Joseph",
 family = "Lee",
 role = c("cre"),
 email = "joseph.lee@u.nus.edu"))
Description: Estimate promoter activity using RNA-Seq data. 
  This package uses BAM files or junction files from Tophat2
  or STAR and estimates promoter activity. The promoters of each 
  gene can be identified by providing a txdb object for the input 
  annotation version. 
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0.0)
RoxygenNote: 7.1.1
Imports: 
    dplyr,
    GenomicRanges,
    GenomicFeatures,
    GenomicAlignments,
    GenomeInfoDb,
    IRanges,
    S4Vectors,
    methods,
    rlang,
    SummarizedExperiment,
    AnnotationDbi,
    DESeq2,
    data.table,
    tibble,
    Gviz,
    BiocParallel
Suggests: 
    testthat,
    mockery,
    BSgenome,
    BiocManager,
    BSgenome.Hsapiens.UCSC.hg38,
    knitr,
    rmarkdown,
    DEXSeq,
    Rtsne,
    ggplot2,
    tidyr,
    vdiffr
URL: https://github.com/GoekeLab/proActiv
biocViews:
    RNASeq,
    GeneExpression,
    Transcription,
    AlternativeSplicing,
    GeneRegulation,
    DifferentialSplicing,
    FunctionalGenomics,
    Epigenetics,
    Transcriptomics,
    Preprocessing
VignetteBuilder: knitr

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 this documentation for setting up remotes to push to git.bioconductor.org. It is required to push a version bump to git.bioconductor.org to trigger a new build.

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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: "skipped, 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/proActiv to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

jleechung commented 4 years ago

Hi @nturaga! I looked at the build report and the errors on the Linux and macOS systems seem to be related to the Gviz package and its dependencies (biovizBase, rtracklayer). Gviz is listed in the imports so I would think that its dependencies would be installed too? Do you know why this might be the case and how I can fix it?

lshep commented 4 years ago

This does seem odd. I will kick off a manual build of your package to see if the issue has resolved; It might have caught the package when it was trying to reinstall on the builders.

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, skipped". 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/proActiv 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: 02cb8835b1bf9c2954512f85910396b3339b4e99

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/proActiv to trigger a new build. A quick tutorial for setting up remotes and pushing to upstream can be found here.

nturaga commented 4 years ago

proActiv review

DESCRIPTION

elaborate Description, it should be like a paper abstract.

NAMESPACE

ok

R

cat() or print() are used only when displaying an object to the user, e.g., in a show method. message() communicates diagnostic messages (e.g., progress during lengthy computations) during code evaluation.

This is done in multiple points of your code, please change.
What is the purpose of reexports.R ? Why can't these functions be used directly when being called where they are used?
This is a well written package in general! Good work.

vignette

There are quite a few eval=FALSE code chunks in the vignette. Is there any way to make the vignette fully evaluated, or come as close to it as possible?

man

ok

Good package over all!

bioc-issue-bot commented 4 years ago

Received a valid push on git.bioconductor.org; starting a build for commit id: 6f36e2f35eebe899b6ae86b2c3b4d1c3185e8119

jleechung commented 4 years ago

Hi @nturaga thanks for the comments! I've made changes summarized below and bumped the version to 0.99.2:

DESCRIPTION

Elaborated upon

R

print() statements replaced with message()
reexports.R exports functions from other packages that users might find useful for processing input or downstream analysis. For example, since proActiv returns a SummarizedExperiment object, users can simply load proActiv and have access to accessors such as assays, rowData, and colData from the SummarizedExperiment package, without explicitly loading SummarizedExperiment into namespace. I think this is examplified in the vignette, where we need only call library(proActiv), without, say, library(SummarizedExperiment), library(AnnotationDbi)... (this practice was inspired from dplyr) Does this make sense?

vignette

Out of the four chunks with eval=FALSE, three of the chunks are functions already run but demonstrated with different types of inputs, or already demonstrated in other sections (e.g. quickstart). Hope this is fine!

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.

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/jleechung.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("proActiv"). The package 'landing page' will be created at

https://bioconductor.org/packages/proActiv

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

proActiv #1602

proActiv review

DESCRIPTION

NAMESPACE

R

vignette

man