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 content of ~/.R/Makevars
3) at package level by the content of src/Makevars
Problem I have is that src/Makevars is ignored
see following example:
R is compiled and use the following CC and CFLAGS definition
bigmess:epactsR/src > R CMD config CC
gcc -std=gnu99
bigmess:epactsR/src > R CMD config CFLAGS
-Wall -g
so building C sources lead to the following
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
normal, it uses defintion from RHOME/etc/Makeconf
when I set upp a ~/.R/Makevars that overwrite CC and CFLAGS definition.
bigmess:epactsR/src > cat ~/.R/Makevars
CC=gcc
CFLAGS=-O3
bigmess:epactsR/src > R CMD SHLIB index.c
gcc -I/local/gensoft2/adm/lib64/R/include -DNDEBUG -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 missed, misunderstood or is there something
wrong ?
PS I tested the ssame behaviour with various version of R from R/2.15 to
R/3.3
best regards
Eric
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 content of ~/.R/Makevars | 3) at package level by the content of src/Makevars | | Problem I have is that src/Makevars is ignored | | | see following example: | | R is compiled and use the following CC and CFLAGS definition | | bigmess:epactsR/src > R CMD config CC | gcc -std=gnu99 | bigmess:epactsR/src > R CMD config CFLAGS | -Wall -g | | so building C sources lead to the following | | 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 | | normal, it uses defintion from RHOME/etc/Makeconf | | | when I set upp a ~/.R/Makevars that overwrite CC and CFLAGS definition. | | bigmess:epactsR/src > cat ~/.R/Makevars | CC=gcc | CFLAGS=-O3 | bigmess:epactsR/src > R CMD SHLIB index.c | gcc -I/local/gensoft2/adm/lib64/R/include -DNDEBUG -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 missed, misunderstood or is there something | wrong ? You have not demonstrated that src/Makevars is ignored -- as it clearly isn't, given how thousands of CRAN packages use it. What you have done is demonstrate that you _cannot change CC and CXX_ in src/Makevars. And I think that was known, though maybe not as widely. Dirk | PS I tested the ssame behaviour with various version of R from R/2.15 to | R/3.3 | | best regards | | Eric | | ______________________________________________ | R-devel at r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-devel -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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/Makeconf > | 2) at user level by the content of ~/.R/Makevars > | 3) at package level by the content of src/Makevars > | > | Problem I have is that src/Makevars is ignored > | > | > | see following example: > | > | R is compiled and use the following CC and CFLAGS definition > | > | bigmess:epactsR/src > R CMD config CC > | gcc -std=gnu99 > | bigmess:epactsR/src > R CMD config CFLAGS > | -Wall -g > | > | so building C sources lead to the following > | > | 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 > | > | normal, it uses defintion from RHOME/etc/Makeconf > | > | > | when I set upp a ~/.R/Makevars that overwrite CC and CFLAGS definition. > | > | bigmess:epactsR/src > cat ~/.R/Makevars > | CC=gcc > | CFLAGS=-O3 > | bigmess:epactsR/src > R CMD SHLIB index.c > | gcc -I/local/gensoft2/adm/lib64/R/include -DNDEBUG -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 missed, misunderstood or is there something > | wrong ? > > You have not demonstrated that src/Makevars is ignored -- as it clearly > isn't, given how thousands of CRAN packages use it. > > What you have done is demonstrate that you _cannot change CC and CXX_ in > src/Makevars. And I think that was known, though maybe not as widely.Hello Dirk, so why ~/R/Makevars allows to change CC and not src/Makevars ? this is pretty confusing. in unix world mechanism of overwriting system default in user and package order is something standadr and consistent given the level priority is package specific stuff overwrite user configuration that overwrite system default mechanism of Makevars is NOT consistent furthermore diggng in $RHOME/bin/config one can see the following if test "${site}" = "yes"; then : ${R_MAKEVARS_SITE="${R_HOME}/etc${R_ARCH}/Makevars.site"} if test -f "${R_MAKEVARS_SITE}"; then makefiles="${makefiles} -f ${R_MAKEVARS_SITE}" fi fi if test "${personal}" = "yes"; then if test "${R_OSTYPE}" = "windows"; then if test -f "${R_MAKEVARS_USER}"; then makefiles="${makefiles} -f ${R_MAKEVARS_USER}" elif test ${R_ARCH} = "/x64" -a -f "${HOME}/.R/Makevars.win64"; then makefiles="${makefiles} -f ${HOME}/.R/Makevars.win64" elif test -f "${HOME}/.R/Makevars.win"; then makefiles="${makefiles} -f ${HOME}/.R/Makevars.win" elif test -f "${HOME}/.R/Makevars"; then makefiles="${makefiles} -f ${HOME}/.R/Makevars" fi else . ${R_HOME}/etc${R_ARCH}/Renviron if test -f "${R_MAKEVARS_USER}"; then makefiles="${makefiles} -f ${R_MAKEVARS_USER}" elif test -f "${HOME}/.R/Makevars-${R_PLATFORM}"; then makefiles="${makefiles} -f ${HOME}/.R/Makevars-${R_PLATFORM}" elif test -f "${HOME}/.R/Makevars"; then makefiles="${makefiles} -f ${HOME}/.R/Makevars" fi fi fi it checks and honours R_MAKEVARS_USER, ~/.R/Makevars, but not src/Makevars I'm not really familiar with the R policy about code comilation, but I consider this a bug but maybee I'm wrong as a side note I solved the problem of overwritting CC for this particular package using MAKEFLAGS="CC=gcc" R CMD INSTALL package best regards Eric