BEARscc

[seversond12]

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Repository: https://github.com/seversond12/BEARscc

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[bioc-issue-bot]

Hi @seversond12

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: BEARscc
Type: Package
Title: BEARscc (Bayesian ERCC Assesstment of Robustness of 
    Single Cell Clusters)
Version: 0.99.0
Author: David T. Severson <david.severson@ludwig.ox.ac.uk>
Maintainer: Benjamin Schuster-Boeckler 
    <benjamin.schuster-boeckler@ludwig.ox.ac.uk>
Description: BEARscc is a noise estimation and injection tool that is 
    designed to assess putative single-cell RNA-seq clusters in the 
    context of experimental noise estimated by ERCC spike-in controls.
License: GPL-3
Imports: ggplot2, data.table, stats, utils, graphics, parallel
Suggests: testthat, cowplot, 
    knitr,
    rmarkdown,
    BiocStyle,
    NMF
VignetteBuilder: knitr
RoxygenNote: 6.0.1
biocViews: SingleCell, Clustering, Transcriptomics

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

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]

Your package must be interoperable with other similar Bioconductor packages. This means that the main inputs / outputs must be SingleCellExperiment. While data.table may be used inside your package, the reference semantic and specialized syntax make it inappropriate as part of the interface exposed to users.

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/BEARscc_buildreport_20171210191208.html

[bioc-issue-bot]

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

1ca8874 - added version number after registering with leve...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/BEARscc_buildreport_20171210192455.html

[bioc-issue-bot]

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

dc15dcf - maintainer and author added themselves to devel ...

[bioc-issue-bot]

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 following build report for more details:

http://bioconductor.org/spb_reports/BEARscc_buildreport_20171210195147.html

[vobencha]

Before I do a full review please respond to issues raised in https://github.com/Bioconductor/Contributions/issues/574#issuecomment-350593739.

Valerie

[seversond12]

@mtmorgan No user interface inputs use data.table. Though it is used extensively internally. However, two functions do output melted data.tables; should these be altered to output data.frame objects instead? Furthermore is a requirement that all function inputs/outputs use a SingleCellExperiment objects, and if so where may I find documentation on SingleCellExperiment objects to facilitate making these changes?

[mtmorgan]

The class is defined in the SingleCellExperiment package, and there's a vignette including a section on creating / using these objects -- remember to use accessors, e.g., colData(), assay(), rather than direct slot access @. If the inputs / outputs consist of information of the appropriate structure (basically, 'features' x 'samples' matrix of counts, possibly with row and column annotations) then yes, the I/O should use SingleCellExperiment.

And yes, your functions should not expose data.table to the user.

[seversond12]

Thanks, @mtmorgan. @vobencha, I will work on addressing the SingleCellExperiment input changes over the next 10 days. Thanks!

[vobencha]

Are you planning to submit a new version?

[seversond12]

Yes, I am.

[bioc-issue-bot]

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

2c902dc -copied bitbucket files of updated package to GitH...

[bioc-issue-bot]

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]

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

a5953b6 - replaced sapply with vapply for better security ...

[bioc-issue-bot]

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.

[bioc-issue-bot]

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

401a58d -hopefuly repaired vignette build issue -updated v...

[bioc-issue-bot]

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]

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

2093f07 -fixed glitch where build source had recursively g...

[bioc-issue-bot]

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.

[bioc-issue-bot]

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

50f8ac9 -testing if windows fail is stochastic

[seversond12]

@vobencha I have addressed the issues raised concerning user interface with data.table (eliminated all user exposure) and made the primary input and object of use of BEARscc functions a SingleCellExpression object. However, the windows building of my vignette seems to be failing sporadically and I'm not sure if this error is a genuine problem with my code as on my last commit I made no changes to the vignette other than it rebuilding when I built the package, yet after a successful build it exited with a an ERROR.

[bioc-issue-bot]

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.

[seversond12]

FYI for the last commit I simply changed the version number and now we have ceased to have the error, so I suspect it's not something with my vignette syntax. At any rate, apologies for the delay of the new version, but I believe the package is now ready for review.

[vobencha]

Thanks. I'll try to get to this by the end of this week.

[vobencha]

The package looks good - nice job with the man pages. Just a few comments.

• In the vignette, instruct the user to load the package with biocLite(), not install.packages().
• Remove the pdf file from the vignettes directory.

[bioc-issue-bot]

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

f8d57ca Tidying up package for BioConductor -removed pdf ...

[bioc-issue-bot]

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.

[seversond12]

@vobencha, I believe I have addressed your comments. Thanks for your help.

[vobencha]

Looks good. Thanks.

[mtmorgan]

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

https://bioconductor.org/packages/BEARscc

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.