consensusDE - Githubissues

awaardenberg 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/awaardenberg/consensusDE

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

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[x] I have read the Bioconductor Package Submission instructions. My package is consistent with the Bioconductor Package Guidelines.
[x] I understand that a minimum requirement for package acceptance is to pass R CMD check and R CMD BiocCheck with no ERROR or WARNINGS. Passing these checks does not result in automatic acceptance. The package will then undergo a formal review and recommendations for acceptance regarding other Bioconductor standards will be addressed.
[x] My package addresses statistical or bioinformatic issues related to the analysis and comprehension of high throughput genomic data.
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bioc-issue-bot commented 5 years ago

Hi @awaardenberg

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: consensusDE
Type: Package
Title: An extensible package for RNA-seq analysis using multiple algorithms 
Version: 0.99.1
Author: Ashley J. Waardenberg
Maintainer: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Description: This package allows users to perform automatic DE analysis. It 
    seeks consensus by performing DE analysis using multiple algorithms. 
    Currently it supports "Voom", "EdgeR" and "DESeq", but can be easily 
    extended. It uses RUV-seq (optional) to remove batch effects.
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: 
    knitr,
    rmarkdown,
    TxDb.Dmelanogaster.UCSC.dm3.ensGene,
    airway
VignetteBuilder: knitr
biocViews: 
    Transcriptomics,
    MultipleComparison, 
    Clustering
Depends: 
    R (>= 3.5)
Imports:
    limma,
    AnnotationDbi,
    Biobase,
    edgeR,
    BiocParallel,
    GenomicAlignments,
    EDASeq,
    RColorBrewer,
    GenomicFeatures,
    SummarizedExperiment,
    DESeq2 (>= 1.20.0),
    pcaMethods,
    dendextend,
    RUVSeq,
    Rsamtools,
    S4Vectors,
    stats

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: "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 5 years ago

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

47e0b04 Addressing Bioconductor time requirements Change t...

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: "TIMEOUT, 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 5 years ago

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

0a44df5 Addressing Bioconductor time requirements

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.

bioc-issue-bot commented 5 years ago

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

e1209f2 Addressing Bioconductor time requirements

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.

awaardenberg commented 5 years ago

Hi @hpages - besides taking a lot of the running examples out of the vignette, I'm not sure about getting the build time further? Are we able to start the review process?

bioc-issue-bot commented 5 years ago

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

edcd300 Updating dependencies

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, 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.

awaardenberg commented 5 years ago

Hi @hpages, the Error seems to be an error with BioC check itself, as I'm certainly registered. I just wanted to see where you were up to or if there is something that I should be doing?

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.

hpages commented 5 years ago

Hi Ashley,

Thanks for your submission and sorry for the late review. Here are a few things that need your attention before we can add consensusDE to Bioconductor:

All the examples in your man pages are wrapped in \dontrun statements. As a consequence none of them gets executed by R CMD check. This is bad practice and against Bioconductor guidelines.
Please stick to the spelling of "summarized" as in "SummarizedExperiment", especially in a function name like read.summarised().
The name of the read.summarised() function does not reflect what the function does. This is not just an import function. The input are BAM files and a TxDb object and the function uses GenomicAlignments::summarizeOverlaps() internally to count reads. Please pick a more appropriate name for this function.

Thanks, H.

bioc-issue-bot commented 5 years ago

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

48e7abf removing dontruns from examples cc90298 changing function name 54ebabc change read.summarised to buildSummarised, change ... 2208100 version bump, adding workflow BioC abf173f replacing . with _ in functions and code 167dab3 Updating verbose message

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.

bioc-issue-bot commented 5 years ago

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

8231f06 version bump

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: "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 5 years ago

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

beec57e version bump examples updated adding biostrings im...

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: "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 5 years ago

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

cdc5250 version bump example update

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.

awaardenberg commented 5 years ago

Hi @hpages,

I've made all the changes that you've suggested. I've removed the dontruns, changed the summarised spellings to summarized and renamed the function to buildSummarized.

Now I'm getting a build time exceed 5 minutes with what I think is the i386 build only. What can we do to combat this?

Best, Ashley

awaardenberg commented 5 years ago

Hi @hpages I'm just seeing if you get this? The contributions github doesn't seem to be tracking with the build reports. I've changed everything you requested and the build report is here: http://bioconductor.org/spb_reports/consensusDE_buildreport_20181022011647.html#tokay1_check_anchor

hpages commented 5 years ago

Hi Ashley,

Thanks for making these changes. The "Citing results that use consensusDE" section in the vignette only contains:

When using this package, please cite the following when you use the results:

and doesn't actually provide the citation.

Cheers, H.

bioc-issue-bot commented 5 years ago

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

efee4e6 version bump adding citations

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.

awaardenberg commented 5 years ago

Hi @hpages, I've added in the citations. I've noticed the same warning for the build-time again, but on two systems. I'm guessing this is related to server usage? I.e. sometimes it builds within the 5 minutes for all the systems, and sometime not... Thanks, Ash.

hpages commented 5 years ago

Thanks for the quick fix. No worries about the warnings. Package is ok now.

Thanks for your contribution to the project.

Cheers, H.

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/awaardenberg.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(\"consensusDE\"). The package 'landing page' will be created at

https://bioconductor.org/packages/consensusDE

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

consensusDE #888