[Bioc-devel] release new package bioccheck failing

[Dan Tenenbaum]

----- 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*
> 
> 

Looks like a bug. I will take a look and report back.
Dan



> thanks in advance
> regards
> avi
> 
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> 
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