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

Dirk Eddelbuettel edd at debian.org
Mon Oct 14 19:18:22 CEST 2013


On 14 October 2013 at 09:56, Tim Triche, Jr. wrote:
| Hi all,
| This is new and perplexing to me.  I have an Ubuntu install of r-base, r-rcpp,

Same here, apart from the fact that I tend to build / install Rcpp locally
from the repo. 

And I never have issues. My Ubuntu box is otherwise very vanilla.

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.

| 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. Let's see what broke.

| R/library/Rcpp/lib into my library path, ran sudo ldconfig, set up environment
| variables that would seem to fix it e.g.
| export LD_LIBRARY_PATH=/usr/local/cuda/lib:/usr/local/cuda/lib64:/usr/lib64/R/library/Rcpp/lib/

I tend to add CUDA only when I use Cuda, ie rarely. Otherwise NO user set
LD_LIBRARY_PATH. System defaults work.

| 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.
| but, alas, no joy:
| # ...everything going fine up to this point...
| g++ -shared -L/usr/local/lib64 -o Rcpp.so Date.o Module.o Rcpp_init.o Timer.o
| api.o attributes.o barrier.o exceptions.o -L/usr/lib64/R/library/Rcpp/lib
| -lRcpp -Wl,-rpath,/usr/lib64/R/library/Rcpp/lib -L/usr/lib64/R/lib -lR
| /usr/local/bin/ld: cannot find -lRcpp
| collect2: ld returned 1 exit status
| make: *** [Rcpp.so] Error 1
| ERROR: compilation failed for package ‘Rcpp’
| * removing ‘/usr/lib64/R/library/Rcpp’
| * restoring previous ‘/usr/lib64/R/library/Rcpp’

Let us start with the obvious. You tell the linker about 

The linker tells you it is not there.  What does ls -l say?

| Searching Google did not reveal anything obvious, and this is a very new
| problem (it has only arisen in the past week or so).  Anyone have any
| suggestions?
| I was blowing this off but realized that dplyr now depends on Rcpp-0.10.5 so
| now I have to bite the bullet.  Again, I've never had any issues compiling
| Rcpp, and I haven't changed my R settings in a long, long time, so I wonder if
| something changed recently.  Normally I can figure out these things but this
| time I'm stumped.

We are generally trying to keep Rcpp installable / buildable at all times,
and I do not yet see why it would be different.


Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

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