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NBSplice #775

Closed gamerino closed 6 years ago

gamerino 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 @gamerino

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: NBSplice
Type: Package
Version: 0.99.0
Date: 2018-06-15
Title: Negative Binomial Models to detect Differential Splicing
Author: Gabriela A. Merino and Elmer A. Fernandez
Maintainer: Gabriela Merino <merino.gabriela33@gmail.com>
Description: The package proposes a differential splicing evaluation method
    based on isoform quantification. It applies generalized linear models with
    negative binomial distribution to infer changes in isoform relative
    expression. 
URL: http://www.bdmg.com.ar
License: GPL (>=2)
Depends:
    R (>= 3.5),
    methods
Imports:
    edgeR,
    stats,
    MASS,
    car,
    mppa,
    BiocParallel,
    ggplot2,
    reshape2
Suggests:
    knitr,
    RUnit,
    BiocGenerics
Collate:
    'NBSplice-package.R'
    'IsoDataSet.R'
    'IsoDataSet-getters.R'
    'IsoDataSet-show.R'
    'IsoDataSet-print.R'
    'IsoDataSet-buildLowExpIdx.R'
    'IsoDataSet-core.R'
    'NBSpliceRes.R'
    'NBSpliceRes-initialize.R'
    'NBSpliceRes-constructor.R'
    'NBSpliceRes-getters.R'
    'NBSpliceRes-show.R'
    'NBSpliceRes-print.R'
    'IsoDataSet-NBTest.R'
    'totalGeneCounts.R'
    'IsoDataSet-initialize.R'
    'IsoDataSet-constructor.R'
    'NBSpliceRes-getDSGenes.R'
    'NBSpliceRes-getDSResults.R'
    'NBSpliceRes-getGeneResults.R'
    'NBSpliceRes-plotRatiosDisp.R'
    'NBSpliceRes-plotVolcano.R'
    'NBSpliceRes-plotGeneResults.R'
    'NBSplice-isoCounts.R'
    'NBSplice-geneIso.R'
    'NBSplice-designMatrix.R'
    'NBSplice-myIsoDataSet.R'
    'NBSplice-myDSResults.R'
biocViews: Software, StatisticalMethod, AlternativeSplicing, Regression,
    DifferentialExpression, DifferentialSplicing, RNASeq
VignetteBuilder: knitr
RoxygenNote: 6.0.1
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

@lshep will review your package. Please update the vignette so that installation instructions assume the package has been accepted to Bioconductor -- biocLite("NBSplice)

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, 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:

9f0c4d1 Correcting packages errors

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:

5dd726b Registering at the support site

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:

b65bf22 Updating vignette assuming NBSplice has been accep...

gamerino commented 6 years ago

Hello!

I have updated the package vignette assuming that NBSplice has been accepted to Bioconductor.

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.

bioc-issue-bot commented 6 years ago

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

2ac3633 Correcting fitModel function

gamerino commented 6 years ago

I have updated the fitModel function to solve a problem found when the contrast parameter is specified by the user.

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.

lshep commented 6 years ago

General

Man Pages

Vignette

R code

Please make the adjustments above. When ready please do another version bump to kick off a new build and comment back here with updates and justifications.

Cheers

bioc-issue-bot commented 6 years ago

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

9d54629 NBSplice optimization following BioC team recommen...

gamerino commented 6 years ago

Hello Lori,

Thank you for all your comments about our package. I have pushed a new version of NBSplice fixing many of the issues you identified. I detailed below the changes and suggestions you made me and my responses, in bold text.

Please, let me know about any inconvenient or another change needed.

Cheers

General

Man Pages

Vignette

-If using expression counts, the functions can take in matrices but should also minimally take in SummarizedExperiment objects? could it take in both? I don't completely understand the question. Is about building an IsoDataSet from a summarizedExperiment object? NBsplice methods have been created based on kallisto and RSEM expression counts which are stored in tab files. For this reason, we have based the IsoDataSet constructor on matrixes or data.frames.

R code

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.

gamerino commented 6 years ago

Hi Lori,

I have updated NBSplice including the changes you recommended.

Should I push it again to avoid the warnings in the build report? I didn't see those on my laptop so I suppose they are a temporary warning.

Best

Gabriela

lshep commented 6 years ago

Yes please push it again to see if it resolves. Even if it remains I will review the package again but it would be nice to have the clean report.

bioc-issue-bot commented 6 years ago

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

f73f646 Fixing report warnings

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.

lshep commented 6 years ago

I'll ignore it for now and have a review for you soon.

gamerino commented 6 years ago

Thank you. I'm replicating the build, install and checks steps on my Mac, but I don't get those warnings.

lshep commented 6 years ago

Thank you. While I still strongly encourage expanding or utilizing SummarizedExperiment or MultiAssayExperiment class structure it is your decision as a maintainer.

Please update the installation instructions as we are currently in the process of updating this site wide. There is a new package on CRAN BiocManager that will install Bioconductor packages and avoid sourcing a script.

if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("NBSplice", version="devel")
bioc-issue-bot commented 6 years ago

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

7e626bd Updating information about package installation

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.

gamerino commented 6 years ago

Hi Lori,

I have updated the installation instructions as you suggested before.

Best

Gabriela

bioc-issue-bot commented 6 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 6 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/gamerino.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(\"NBSplice\"). The package 'landing page' will be created at

https://bioconductor.org/packages/NBSplice

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.