Dear Dr Dan, Thanks, With GUI package the vignette does not have chunks only for installation paragraph. Thanks Karim
Ô__ c/ /'_;~~~~kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Fri, Jan 2, 2015 at 6:55 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > > > ----- Original Message ----- > > From: "Karim Mezhoud" <kmezh...@gmail.com> > > To: bioc-devel@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@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
