RIVER

[ipw012]

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• Repository: https://github.com/ipw012/RIVER

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[bioc-issue-bot]

Hi @ipw012

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: RIVERpkg
Date: 2017-01-06
Title: R package for RIVER (RNA-Informed Variant Effect on Regulation)
Description: An implementation of a probabilistic modeling framework that jointly 
        analyzes personal genome and transcriptome data to estimate the probability that 
        a variant has regulatory impact in that individual. It is based on a generative 
        model that assumes that genomic annotations, such as the location of a variant 
        with respect to regulatory elements, determine the prior probability that variant 
        is a functional regulatory variant, which is an unobserved variable. The functional 
        regulatory variant status then influences whether nearby genes are likely to 
        display outlier levels of gene expression in that person. See the RIVER website 
        for more information, documentation and examples.
Version: 0.99.0
Authors@R: c(person("Yungil", "Kim", role = c("aut", "cre"), email = "ipw012@gmail.com"),
        person("Damani", "Farhan", role = "ctb", email = "farhand7@gmail.com"),
        person("Alexis", "Battle", role = "aut", email = "ajbattle@cs.jhu.edu"))
Author: Yungil Kim [aut, cre], Alexis Battle [aut]
Maintainer: Yungil Kim <ipw012@gmail.com>
URL: https://github.com/ipw012/RIVERpkg
BugReports: https://github.com/ipw012/RIVERpkg/issues
Depends: R (>= 3.3.1)
biocViews: GeneExpression, GeneticVariability, SNP, Transcription, FunctionalPrediction, 
        GeneRegulation, GenomicVariation, BiomedicalInformatics, FunctionalGenomics, 
        Genetics, SystemsBiology, Transcriptomics, Bayesian, Clustering, 
        TranscriptomeVariant, Regression
Imports: dplyr, glmnet, pROC, ggplot2, graphics, stats
License: GPL (>= 2)
RoxygenNote: 5.0.1
LazyData: true
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown, testthat

[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.

[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 following build report for more details:

http://bioconductor.org/spb_reports/RIVERpkg_buildreport_20170109172527.html

[LiNk-NY]

Hi @ipw012,
I see that you are not using any Bioconductor resources. We want our packages to be inter-operable.
You should be able to support the use of an ExpressionSet, SummarizedExperiment or another Bioconductor class as input to your functions.

[bioc-issue-bot]

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

416f40b Modify an evaluation approach for fullly evaluatin...

[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 following build report for more details:

http://bioconductor.org/spb_reports/RIVERpkg_buildreport_20170128184322.html

[ipw012]

Hi @LiNk-NY,
I just updated my R package in several points:

1. ExpressionSet was incorporated as an input object of functions in my package.
2. Evaluation approach was changed so that related functions were revised accordingly.
3. A package version was changed from 0.99.0 to 0.99.1.

Could you please take a look at my package and see if it fits Bioconductor requirements?
I also have one question. What does "Update R version dependency from 3.3.1 to 3.4." mean? I am not sure how to fix that issue since the current version of R is 3.3.2 I believe. I had the same WARNING MESSAGES from all three OS environments.

[LiNk-NY]

Hi @ipw012,
Thanks for making that change. I will look at your package in the coming days.
"Updating your R version dependency" entails changing the Depends field to R (>= 3.3.2) in the DESCRIPTION. Ideally, you would have R (>= 3.4.0) since the Bioconductor 3.5 (devel) works R devel.
Regards,
Marcel

[LiNk-NY]

Hi @ipw012,
Can you bump the version?
Thanks.
-Marcel