miRSM - Githubissues

zhangjunpeng411 commented 6 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/zhangjunpeng411/miRSM

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bioc-issue-bot commented 6 years ago

Hi @zhangjunpeng411

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: miRSM
Type: Package
Title: Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
Version: 0.99.0
Author: Junpeng Zhang
Maintainer: Junpeng Zhang <zhangjunpeng_411@yahoo.com>
Description: The package aims to identify miRNA sponge modules by integrating expression data and miRNA-target binding information.
    It provides several functions to study miRNA sponge modules, including popular methods for inferring gene modules 
    (candidate miRNA sponge modules), and a function to identify miRNA sponge modules, as well as a function to conduct 
    functional analysis of miRNA sponge modules.
Depends: R (>= 3.4.3)
License: GPL-3
URL: <https://github.com/zhangjunpeng411/miRSM>
Encoding: UTF-8
LazyData: true
biocViews: GeneExpression, BiomedicalInformatics, 
 Clustering, GeneSetEnrichment, Microarray, 
             Software, GeneRegulation
RoxygenNote: 6.0.1
Imports: WGCNA,
    flashClust,
    dynamicTreeCut,
    GFA,
    igraph,
    linkcomm,
    MCL,
    NMF,
    biclust,
    runibic,
    iBBiG,
    fabia,
    BicARE,
    isa2,
    s4vd,
    BiBitR,
    rqubic,
    Biobase,
    varhandle,
    PMA,
    stats,
    miRsponge,
    Rcpp
Suggests:BiocStyle, 
    knitr,
    rmarkdown,
    testthat,
    org.Hs.eg.db
VignetteBuilder: knitr

bioc-issue-bot commented 6 years ago

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mtmorgan commented 6 years ago

please update the user-facing interface (argument and return values) to use a SummarizedExperiment and other standard objects instead of ad-hoc data representations.

bioc-issue-bot commented 6 years ago

Dear Package contributor,

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zhangjunpeng411 commented 6 years ago

@mtmorgan Thanks for you advice.

Junpeng

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

Dear Package contributor,

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

Dear Package contributor,

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Your package has been built on Linux, Mac, and Windows.

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bioc-issue-bot commented 6 years ago

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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: "ABNORMAL". 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.

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zhangjunpeng411 commented 6 years ago

Hi @lshep ,

How can I resolve the ABNORMAL status of the repository? I don't see anything particularly wrong in the build report, only the operating system is not showed in the OS/Arch field. In addition, only one operating system is runned.

Thanks and Regards, Junpeng

lshep commented 6 years ago

This was likely an issue on our end. I am rerunning the package now to generate the complete build report.

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lshep commented 6 years ago

Please let me know when you are finished updating user-facing interface (argument and return values) as @mtmorgan suggested. When you are finished with this update I will give a more formal review of the package.

zhangjunpeng411 commented 6 years ago

Hi @Ishep,

I have updated all functions by using a SummarizedExperiment object for arguments. Now, you can review it. Thanks for your hard work.

Regards, Junpeng

lshep commented 6 years ago

Sorry for the delayed response. Please see the following comments:

General:

[ ] Can you give a Comparison to existing ceRNAs, miRNA sponges or miRNA decoys packages. Like miRsponge SPONGE

README

[ ] Update installation instructions to use BiocManager

Description:

[ ] remove lazydata: true rarely proves a good thing in our experience.

NEWS:

[ ] not formatted quite right - please add delimiter for text under section - extend the below example to entire text

CHANGES IN VERSION 0.99.8-0.99.14
-------------------------
Update miRSM.Rmd

CHANGES IN VERSION 0.99.4-0.99.7
-------------------------
Update runnable examples

would become

CHANGES IN VERSION 0.99.8-0.99.14
-------------------------
o Update miRSM.Rmd

CHANGES IN VERSION 0.99.4-0.99.7
-------------------------
o Update runnable examples

Vignette:

[ ] you only need to load the data once instead of repeatedly
```
data(ceRExp)
data(mRExp)
```
[ ] So running your examples module_GFA is an empty list - is this intended?
[ ] All output are lists of character vectors? It seems as list of Genes - please look into formatting output to a GSEAbase::GeneSet or GeneSetCollection object
[ ] Are the lengths of the lists going to be consistent? What do the different elements of the list mean? Some better explanation of the output would be helpful as well as maybe labelling the list elements.
[ ] It seems like there is extra whitespace in the coding sections of Identification of miRNA sponge modules and Functional analysis of miRNA sponge modules causing it to display weirdly
[ ] Your last code section is eval=FALSE why?
[ ] So these modules are meant to be run separatly depending on which is appropriate or desired?

inst/script:

[ ] Please include a script in the above directory location that has the code used to generate your data objects and commented information like How were the samples selected? was there any filtering or formatting? etc...

Man files:

[ ] Data man files - either here or in the inst/script above please provide more details on how the samples were selected from teh cancergenome site.

R Code: Internal ProNet functions -

[ ] So I see that ProNet is temporarily removed from CRAN which is why I assume you are inlcuding these functions here? Have you reached out to the ProNet package maintainer to see if they plan on maintaining the package and having it back on CRAN?

[ ] It seems like this section of code outputs the resutls of each function. Maybe create a helper function for it instead so that if there are every updates it only needs to be updated in one instance

ceR_Num <- lapply(seq_along(Modulegenes), function(i) length(which(Modulegenes[[i]] %in%
    colnames(ceRExp))))
mR_Num <- lapply(seq_along(Modulegenes), function(i) length(which(Modulegenes[[i]] %in%
    colnames(mRExp))))

index <- which(ceR_Num >= num.ModuleceRs & mR_Num >= num.ModulemRs)
CandidateModulegenes <- lapply(index, function(i) Modulegenes[[i]])

return(CandidateModulegenes)

Please address the above issues and push changes. When you are ready please comment back here and I will re-review. Thank you for you submission - I look forward to working with you to get your package accepted

Cheers,

zhangjunpeng411 commented 6 years ago

Hi @lshep ,

Thanks for your comments.

Regards, Junpeng

bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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bioc-issue-bot commented 6 years ago

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Bioconductor / Contributions

miRSM #825