[Bioc-devel] BiocCheck result

----- 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."

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