[Bioc-devel] FW: Package build error

Hervé Pagès hpages at fredhutch.org
Fri Oct 27 08:01:20 CEST 2017

Hi Ioannis,

The links to the build results generated  during the submission
process are permanent (or at least remain valid for several months),
so it's easier to provide the link to the particular results:


As a special bonus, we all get the color version ;-)

R uses its own markup language for man pages, called the Rd format.
\insertRef is not a valid tag in that format. See the "2 Writing R
documentation files" section of the "Writing R Extensions" manual for
more information:


Note that "Writing R Extensions" is the primary documentation for R
package developers.

If your code is C++11 and you don't have a src/Makevars or src/Makefile
file, then you need to add

   SystemRequirements: C++11

in the DESCRIPTION file. This will invoke the correct compiler. This
is also explained in "Writing R Extensions" in a subsection dedicated
to "Using C++11 code":


Finally, pushing changes to GitHub will automatically start the next
build/check only if you've properly set up the web hook and if you bump
the version of your package, as explained on the Contributions page:


Hope this helps,

On 10/26/2017 06:44 PM, Ioannis Vardaxis wrote:
> Hey,
> Yesterday I submitted an R package to Bioconductor and today I got the build results with some error end warnings. Please find the build results attached.
> The file is quite long and there are a lot of things there. However when I run R-check and BiocCheck on my MAC I don't get any and the package runs fine.
> We don't need to go through all the notes in the file, just the first two highlighted ones.
> For the first one, I get a warning for : unknown macro \insertRef. I have a citation file in the package and I can't see any other way to add citation on some R functions. Can I change it to something else?
> Furthermore, I have only one c++ script, where I use Rcpp package. The header of the script is:
> #include <Rcpp.h>
> using namespace Rcpp;
> I wanted to include functions like std::round, std::log etc, but I got an error that round is not in std namespace (see highlight two). How can I tell Rcpp to recognise that? Because round Is at std for c++11 I think.
> However I don't specify any src/Makevars file, because I though that it is not needed anymore.
> Finally,
> When I make all the changes and fix the errors locally on my mac, I then commit and push to GitHub again. Will this automatically start the next build check for bioconuctor or do I have to do anything else?
> Best
> --
> Ioannis Vardaxis
> Stipendiat IMF
> _______________________________________________
> Bioc-devel at r-project.org mailing list
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
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