DrugDiseaseNet

[azampvd]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/azampvd/DrugDiseaseNet

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

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• [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]

Hi @azampvd

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: DrugDiseaseNet
Type: Package
Imports: ROntoTools,igraph,graph,methods,stringr
Title: A Systems Biology Approach for Drug Repurposing
Suggests: RUnit,BiocGenerics,
    knitr,
    rmarkdown
Version: 0.99.0
Author: Azam Peyvandipour, Sorin Draghici
Maintainer: Azam Peyvandipour <azam.peyvandipour@wayne.edu>
Description: Generates a drug-disease network (DDN) composed of the genes that are most likely perturbed by a drug. By performing a system-level analysis on this network using disease gene expression signatures and drug-exposure gene expression signatures, the amount of perturbation caused by a drug on the genes can be estimated. This can help to identify the associations to a disease of interest.
License: GPL (>=3)
biocViews: Network, Microarray, GraphAndNetwork, Pathways, KEGG,GeneExpression, SystemsBiology
RoxygenNote: 6.0.1
VignetteBuilder: knitr

[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]

No need to include vignette build products in the vignettes/ directory, just the Rnw and bib files.

[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/DrugDiseaseNet_buildreport_20170806120406.html

[bioc-issue-bot]

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

fe57f26 New version

[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 following build report for more details:

http://bioconductor.org/spb_reports/DrugDiseaseNet_buildreport_20170806161010.html

[bioc-issue-bot]

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

97f6725 Error fixed

[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/DrugDiseaseNet_buildreport_20170806164127.html

[vobencha]

Hi,

Package looks good. Just a few suggestions.

1) Convert the vignette over to use BiocStyle. There are examples of how to produce html or pdf output in the BiocStyle vignette.

2) Consistent naming of function arguments I would suggest using either underscores or camelCase but not mixing the two if possible:

edgeData_keggPathwaygraphs(edge_from, edge_to, updateKEGG = FALSE)

updateGlobalGraph(globalGraph, edgesToremove = list(c("hsa:6657", "hsa:79923")))

3) updateGlabalGraph.Rd needs an /examples section.

4) More descriptive examples on man pages For example, on keggGlobalGraph.Rd instead of just creating 'gg', show it:

> gg<-keggGlobalGraph()
> gg
A graphNEL graph with directed edges
Number of Nodes = 5593
Number of Edges = 28371 

Same with nodeData_keggPathwaygraphs.Rd. Show a little of what the result is.

> class(pathways)
[1] "character"
> head(pathways)
                path:hsa04010                 path:hsa04012
     "MAPK signaling pathway"      "ErbB signaling pathway"
                path:hsa04062                 path:hsa04066
"Chemokine signaling pathway"     "HIF-1 signaling pathway"
                path:hsa04150                 path:hsa04151
     "mTOR signaling pathway"  "PI3K-Akt signaling pathway" 

Valerie

[vobencha]

Checking in. Are you planning to submit an updated version? Valerie

[bioc-issue-bot]

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

e22e416 Updated version

[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/DrugDiseaseNet_buildreport_20170905164211.html

[azampvd]

Thank you very much for your message. I am confused about the issue/suggestion 1: "Convert the vignette over to use BiocStyle. There are examples of how to produce html or pdf output in the BiocStyle vignette." Other issues got resolved.

[vobencha]

Please use the BiocStyle package to create your vignette. Instructions for using BiocStyle are here: http://www.bioconductor.org/packages/release/bioc/html/BiocStyle.html

[vobencha]

Are you planning to submit a new version or should I close this issue?

[azampvd]

Hi,

I am sorry. I am gonna submit it ASAP.

Thanks,

Azam

---

From: vobencha notifications@github.com Sent: Monday, October 2, 2017 8:50:07 AM To: Bioconductor/Contributions Cc: Azam Peyvandipour; Mention Subject: Re: [Bioconductor/Contributions] DrugDiseaseNet (#443)

Are you planning to submit a new version or should I close this issue?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/Bioconductor/Contributions/issues/443#issuecomment-333524510, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AdVbY9kgC2M2b_IJd8Q9ECcVt7n2mLCaks5soNv-gaJpZM4Oul-S.

[vobencha]

Closing this issue. If you decide to submit a new version we can re-open this.