[Bioc-devel] release new package bioccheck failing

[avinash sahu]

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 <dtenenba at fredhutch.org>
wrote:

>
>
> ----- 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]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>

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