[Bioc-devel] release new package bioccheck failing

Dan Tenenbaum dtenenba at fredhutch.org
Tue Jan 20 18:58:23 CET 2015



----- Original Message -----
> From: "avinash sahu" <avinash.sahu at gmail.com>
> To: bioc-devel at 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]]
> 
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