[Bioc-devel] FW: Package build error

Ioannis Vardaxis ioannis.vardaxis at ntnu.no
Fri Oct 27 03:44:21 CEST 2017


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.


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?

Ioannis Vardaxis
Stipendiat IMF
-------------- next part --------------
A non-text attachment was scrubbed...
Name: [History]Bioconductor Single Package Builder.pdf
Type: application/pdf
Size: 253195 bytes
Desc: [History]Bioconductor Single Package Builder.pdf
URL: <https://stat.ethz.ch/pipermail/bioc-devel/attachments/20171027/fbb84790/attachment.pdf>

More information about the Bioc-devel mailing list