[Bioc-devel] BiocCheck result

[Karim Mezhoud]

Dear all,

I have these comments and did not found solution for silencing them.

1 - What about Vignette?
2 - The version is "package.0.99.0.tar.gz"

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.

4- Indenting, Tabs and long lines were not found.

Can I submit with theses comments?
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]]