On Mon, Oct 14, 2013 at 10:18 AM, Dirk Eddelbuettel <[email protected]> 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 "$PKG_CPPFLAGS > | export PKG_LIBS=`Rscript -e "Rcpp:::LdFlags()"` > > Same. I never need any of these. > Well, if you don't, I probably don't either. So... I squashed these and it worked like a charm. THANK YOU! just a side note: Let us start with the obvious. You tell the linker about > > /usr/lib64/R/library/Rcpp/lib/libRcpp.* > > The linker tells you it is not there. What does ls -l say? tim@tim-ThinkPad-T420s:~$ ls -l /usr/lib64/R/library/Rcpp/lib/libRcpp.* -rw-rw-r-- 1 tim tim 7523358 Oct 14 10:23 /usr/lib64/R/library/Rcpp/lib/libRcpp.a -rwxrwxr-x 1 tim tim 3122677 Oct 14 10:23 /usr/lib64/R/library/Rcpp/lib/libRcpp.so 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 future. Thanks again! I really appreciate your work on Rcpp and support for it. Best, --t
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