[Bioc-devel] BiocCheck result

[Dan Tenenbaum]

----- Original Message -----
> From: "Karim Mezhoud" <kmezhoud at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: bioc-devel at r-project.org
> Sent: Friday, January 2, 2015 12:15:31 PM
> Subject: Re: [Bioc-devel] BiocCheck result
> 
> 
> 
> 
> Dear Dr Dan,
> Thanks,
> 
> With GUI package the vignette does not have chunks only for
> installation paragraph.
> 

I'm not sure what you mean here, but I think you should just submit the package and these issues will be discussed during the review process.

Don't worry if your package does not pass BiocCheck the first time. We're here to help you through these things.

Thanks,
Dan


> Thanks
> 
> Karim
> 
> 
> 
> 
> 
> Ô__
> c/ /'_;~~~~kmezhoud
> (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ
> http://bioinformatics.tn/
> 
> 
> 
> 
> On Fri, Jan 2, 2015 at 6:55 PM, Dan Tenenbaum <
> dtenenba at fredhutch.org > wrote:
> 
> 
> 
> 
> ----- Original Message -----
> > From: "Karim Mezhoud" < kmezhoud at gmail.com >
> > To: bioc-devel at r-project.org
> > Sent: Friday, January 2, 2015 4:22:44 AM
> > Subject: [Bioc-devel] BiocCheck result
> > 
> > Dear all,
> > 
> > I have these comments and did not found solution for silencing
> > them.
> > 
> > 1 - What about Vignette?
> 
> The message (below) is saying you need to evaluate more vignette
> chunks, as mentioned in the BiocCheck vignette (
> http://www.bioconductor.org/packages/devel/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#Interpreting_BiocCheck_output
> ) at least 50% of vignette chunks need to be evaluated, otherwise
> you get this RECOMMENDation.
> 
> > 2 - The version is "package.0.99.0.tar.gz"
> > 
> 
> Looks like you are running BiocCheck under Bioconductor 3.0 (the
> release version). You should be developing your package under the
> devel version of Bioconductor (currently 3.1, requires R-devel
> (R-3.2)). If you do that you won't see this message.
> 
> 
> > 3 - In wich file can I clarify permanent objects. To avoid <<- I
> > create new
> > Environment with
> > myGlobalEnv <- new.env(parent = emptyenv())
> > 
> > I have many permanent objects because my package is a GUI. All
> > these
> > objects are useful for different functions and reduce the computing
> > time
> > and the multiple running of the same function.
> > 
> 
> This is something that is best looked at during the package review
> process.
> 
> > 4- Indenting, Tabs and long lines were not found.
> 
> As mentioned in the BiocCheck output and in the vignette, the
> formatting suggestions are just suggestions. Some of them are more
> important than others, for example, most reviewers will insist on
> lines shorter than 80 columns, for readability's sake.
> 
> > 
> > Can I submit with theses comments?
> 
> You can submit, and these issues will be looked at as part of the
> package review process.
> Dan
> 
> 
> 
> > Thanks
> > Karim
> > 
> > 
> > $requirements
> > character(0)
> > 
> > $recommendations
> > [1] "Evaluate more vignette chunks." "y of x.y.z
> > version
> > should be even in release"
> > 
> > $considerations
> > [1] "Clarifying how objects Li, A, ttCasesGenProfs, EventTime,
> > Category,
> > Continu, Category, ttMain, CasesStudies, curselectCases, fname.GCT,
> > fname.CLS, ttMain, GenesDetails, CaseChoice, mSigDB_SubName,
> > GenesDetails,
> > lenght, ttCasesGenProfs, myGlobalEnv (used in canceR , dialogMut ,
> > dialogOptionPhenoTest, dialogOptionPhenoTest ,
> > getClinicalDataMatrix,
> > geteSet, getGCTCLSExample, getGeneExpMatrix, getGenesClassifier,
> > getGenesTree_MultipleCases, getGSEAlm_Diseases,
> > getGSEAlm_Variables,
> > getMegaProfData, getMetDataMultipleGenes, getMSigDBExample ,
> > getMSigDBExample, GSEA, GSEA.Analyze.Sets, plot_1Gene_2GenProfs,
> > testCheckedCaseGenProf) were initialized. Maybe they are part of a
> > data set
> > loaded with data(), or perhaps part of an object referenced in
> > with()
> > or
> > within()."
> > [2] "Shortening lines; 1227 lines (11%) are > 80 characters
> > long."
> > 
> > [3] "Replacing tabs with 4 spaces; 6 lines (0%) contain
> > tabs."
> > 
> > [4] "Indenting lines with a multiple of 4 spaces; 1752 lines (15%)
> > are
> > not."
> > 
> > [[alternative HTML version deleted]]
> > 
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> 
>