[Bioc-devel] BiocCheck result

[Karim Mezhoud]

Dear Dr Dan,
Thanks,
With GUI package the vignette does not have chunks only for installation
paragraph.
Thanks
Karim

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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
> >
>

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