[Bioc-devel] BiocCheck result
kmezhoud at gmail.com
Fri Jan 2 13:22:44 CET 2015
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
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?
 "Evaluate more vignette chunks." "y of x.y.z version
should be even in release"
 "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
 "Shortening lines; 1227 lines (11%) are > 80 characters
 "Replacing tabs with 4 spaces; 6 lines (0%) contain
 "Indenting lines with a multiple of 4 spaces; 1752 lines (15%) are
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