Thanks a lot Dan for quickly addressing this. BiocCheck is now passing for the package. I have integrated instruction to install ransampl and GSL. Is it obvious that user will include their library path to the GCC flags? In any case I have added an example Makevars too, to do this.
thanks avi On Tue, Jan 20, 2015 at 6:58 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > > > ----- Original Message ----- > > From: "avinash sahu" <avinash.s...@gmail.com> > > To: bioc-devel@r-project.org > > Sent: Tuesday, January 20, 2015 8:49:06 AM > > Subject: [Bioc-devel] release new package bioccheck failing > > > > Hi All, > > > > I am trying to release a package https://github.com/vinash85/GOAL in > > bioconductor. But BiocCheck is failing, however it only failing in > > linux > > and not in MAC. And I cannot figure out reason. The package is uses > > Rcpp. > > Both build, CHECK is passing in linux and mac. > > I am using latest R (3.1.2) > > The failing message from linux by BiocCheck is: > > > > * This is BiocCheck, version 1.2.1. > > * BiocCheck is a work in progress. Output and severity of issues may > > change. > > * Installing package... > > * This is a software package, checking vignette directories... > > * REQUIRED: vignette sources in vignettes/ directory. > > * Checking version number... > > * RECOMMENDED: y of x.y.z version should be even in release > > * Checking biocViews... > > * CONSIDER: Adding some of these automatically suggested > > biocViews: > > Epigenetics > > * Checking build system compatibility... > > * Checking unit tests... > > * CONSIDER: Adding unit tests. We strongly recommend them. See > > > http://www.bioconductor.org/developers/how-to/unitTesting-guidelines/. > > * Checking native routine registration... > > * RECOMMENDED: Register native routines! see > > > > > http://cran.r-project.org/doc/manuals/R-exts.html#Registering-native-routines > > * Checking for deprecated package usage... > > * Parsing R code in R directory, examples, vignettes... > > * Checking for T... > > * Checking for F... > > * Checking for browser()... > > * Checking for <<-... > > * Checking for library/require of GOAL... > > * Checking DESCRIPTION/NAMESPACE consistency... > > * Checking function lengths........ > > * The longest function is 87 lines long > > * The longest 5 functions are: > > * generate.epieQTL.logistic() (R/simulate.eQTL.R, line 4): 87 lines > > * fit.logit() (R/fit.logit.R, line 1): 27 lines > > * mvrnormArma() (R/RcppExports.R, line 4): 3 lines > > * find_correlation() (R/RcppExports.R, line 8): 3 lines > > * filterSNP() (R/RcppExports.R, line 12): 3 lines > > * Checking man pages... > > > > > > > > > > ** Checking exported objects have runnable examples...Error in if > > (line == > > "## No test: " || insideDontTest || line == "## End(No test)") { : > > missing value where TRUE/FALSE neededCalls: <Anonymous> ... > > checkExportsAreDocumented -> doesManPageHaveRunnableExample -> > > removeDontTestExecution halted* > > > > This was caused by a bug that was triggered by an empty \example{} section. > > Fixed in BiocCheck 1.3.5 which is now available via git or svn and will be > available > tomorrow via biocLite(). > > BTW, your package should mention its dependency on ransampl and GSL in the > SystemRequirements: field of the DESCRIPTION file and your documentation > (at a minimum, the README file) should explain how to install these > dependencies. > > Dan > > > > > > thanks in advance > > regards > > avi > > > > [[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
