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Le 27/09/16 ? 13:31, Dirk Eddelbuettel a ?crit : > > On 27 September 2016 at 09:37, Eric Deveaud wrote: > | Hello, > | > | I'm tring to install a Rpackage that holds some C//C++ code > | > | as far as I understood the R library generic compilation mechanism, > | compilation of C//C++ sources is controled > | > | 1) at system level by the ocntentos RHOME/etc/Mak...

...ption is (in my opinion) if you need to decrease the level of optimization because you know or suspect the compiler to generate wrong code. What you should do, is use PKG_CFLAGS as documented in R-exts, 1.2.1 under "Using Makevars". Best, Kasper On Tue, Sep 27, 2016 at 9:23 AM, Eric Deveaud <edeveaud at pasteur.fr> wrote: > Le 27/09/16 ? 13:31, Dirk Eddelbuettel a ?crit : > > >> On 27 September 2016 at 09:37, Eric Deveaud wrote: >> | Hello, >> | >> | I'm tring to install a Rpackage that holds some C//C++ code >> | >> | as fa...

...G -I/usr/local/include -fpic -O3 -c index.c -o index.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o index.so index.o OK CC and CFLAGS are honored and set accordingly to ~/.R/Makevars but when I try to use src/Makevars, it is ignored bigmess:epactsR/src > cat ~/.R/Makevars cat: /home/edeveaud/.R/Makevars: No such file or directory bigmess:epactsR/src > cat ./Makevars CC = gcc CFLAGS=-O3 bigmess:epactsR/src > R CMD SHLIB index.c gcc -std=gnu99 -I/local/gensoft2/adm/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -Wall -g -c index.c -o index.o is there something I have m...

Le 27/09/16 ? 16:17, Kasper Daniel Hansen a ?crit : > As a package author, it is in my opinion irresponsible to override these > system settings (which is why it is also impossible). You have no idea > what system it is being deployed on, as the it guy dedicated to install and maintain softs on our cluster I have a reasonable knowledge of the systems I work on. I don't want to

On 27 September 2016 at 15:23, Eric Deveaud wrote: | so why ~/R/Makevars allows to change CC and not src/Makevars ? | | this is pretty confusing. It seems weird at first, but makes some sense when you think about it like this: -- src/Makevars is inside a package and cannot / should not alter "system" parameters like compi...

On 27 September 2016 at 09:37, Eric Deveaud wrote: | Hello, | | I'm tring to install a Rpackage that holds some C//C++ code | | as far as I understood the R library generic compilation mechanism, | compilation of C//C++ sources is controled | | 1) at system level by the ocntentos RHOME/etc/Makeconf | 2) at user level by the cont...

...could test your proposed fix. If the fix works, it seems to me like it should be included in the package source by the package maintainer, perhaps using a configure script, but that is ultimately something which is up to the package maintainer. Best, Kasper On Tue, Sep 27, 2016 at 10:52 AM, Eric Deveaud <edeveaud at pasteur.fr> wrote: > Le 27/09/16 ? 16:17, Kasper Daniel Hansen a ?crit : > >> As a package author, it is in my opinion irresponsible to override these >> system settings (which is why it is also impossible). You have no idea >> what system it is being de...