Closed scoetzee closed 9 years ago
BiocCheck out
Summary: REQUIRED count: 5 RECOMMENDED count: 1 CONSIDERATION count: 6 For detailed information about these checks, see the BiocCheck vignette, available at http://www.bioconductor.org/packages/3.0/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#Interpreting_BiocCheck_output BiocCheck FAILED. $requirements [1] "'vignettes' directory!" [2] "Valid package Version, see http://www.bioconductor.org/developers/how-to/version-numbering/" [3] "Add some biocViews!" [4] "Authors@R must evaluate to 'person' object!" [5] "At least 80% of man pages documenting exported objects must have runnable examples.The following pages do not:"
$recommendations [1] "Add non-empty \value sections to the following man pages:"
$considerations [1] "Clarifying how objects TRUESS.range, TRUEFs, TRUEF.meth.cor, TRUERange, upperOR, lowerOR (used in get.feature.probe, get.TFs, GetNearGenes, motif.enrichment.plot, scatter, TF.rank.plot) 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] "Adding unit tests.\n We strongly recommend them. See\n http://www.bioconductor.org/developers/how-to/unitTesting-guidelines/." [3] "Adding a NEWS file, so your package news will be included in Bioconductor release announcements." [4] "Shortening lines; 293 lines (7%) are > 80 characters long." [5] "Replacing tabs with 4 spaces; 82 lines (1%) contain tabs." [6] "Indenting lines with a multiple of 4 spaces; 1204 lines (29%) are not."
Also think about removing your ReadBed and ReadGFF functions.
There are built in functions in bioconductor from the rtracklayer package