[Bioc-devel] BiocCheck result

[Dan Tenenbaum]

----- 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]]
> 
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