[Rcpp-devel] strange new issue with installing Rcpp-0.10.5

Tim Triche, Jr. tim.triche at gmail.com
Mon Oct 14 19:32:56 CEST 2013

On Mon, Oct 14, 2013 at 10:18 AM, Dirk Eddelbuettel <edd at debian.org> wrote:

> I also run a little script 'update.r' every couple of days which updates
> /usr/local/lib/R/site-library/ based on what changed on CRAN (by calling
> update.packages(), more or less -- see the examples in the littler package)
> and those do not fail either.

That's basically what biocLite() does, so in this respect I do the same.

>  | etc. and have installed R-3.0.2 in order to maintain Bioconductor
> packages for
> | the upcoming release.  As of a few days ago, Rcpp stopped updating itself
> | either via biocLite() or via command line installation.  I
> forced /usr/lib64/
> Forcing is never good.

This was the key.  Second pair of eyeballs never hurt nobody, it seems!

> | export PKG_CPPFLAGS=`Rscript -e "Rcpp:::CxxFlags()"`
> | export PKG_CPPFLAGS=" -I. -lpthread "$PKG_CPPFLAGS
> | export PKG_LIBS=`Rscript -e "Rcpp:::LdFlags()"`
> Same. I never need any of these.

Well, if you don't, I probably don't either.  So...
I squashed these and it worked like a charm.


just a side note:

Let us start with the obvious. You tell the linker about
>     /usr/lib64/R/library/Rcpp/lib/libRcpp.*
> The linker tells you it is not there.  What does ls -l say?

tim at tim-ThinkPad-T420s:~$ ls -l /usr/lib64/R/library/Rcpp/lib/libRcpp.*
-rw-rw-r-- 1 tim tim 7523358 Oct 14 10:23
-rwxrwxr-x 1 tim tim 3122677 Oct 14 10:23

Previously the timestamp was June 24th, but otherwise no different.  That's
what threw me.  It turns out that I only needed the PKG_CPPFLAGS set for a
particular package (ExALT) that uses Rcpp in a fairly unusual fashion.  I
will keep those settings around but commented out so I remember this.

Anyways, it was the fault of PKG_CPPFLAGS, as you helped me deduce.

I am replying to the list just in case anyone has a similar problem in the

Thanks again!  I really appreciate your work on Rcpp and support for it.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/rcpp-devel/attachments/20131014/ea8edd9f/attachment-0001.html>

More information about the Rcpp-devel mailing list