On Tue, Jul 24, 2012 at 2:30 PM, luxInteg <lux-in...@btconnect.com> wrote: > Greetings, > > I am learning R > My machine has these; > CPU: 3cores amd64 > OS pure-64bit CBLFS liux compiled from sources (kernel 3.2.1, gcc-4.6.2 > R-2.15 > When I compiled R the compiler spewed out lines like these:- > > make[3]: Entering directory `/tmp/RtmpiHdDJy/R.INSTALL472339eeb23a/mgcv/src' > gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - > I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c > gcv.c -o gcv.o > gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - > I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c > gdi.c -o gdi.o > gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - > I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c > init.c -o init.o > gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - > I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c > magic.c -o magic.o > gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - > I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c > mat.c -o mat.o > gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - > I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c > matrix.c -o matrix.o > gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - > I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c > mgcv.c -o mgcv.o > gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - > I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c > misc.c -o misc.o > gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - > I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c > qp.c -o qp.o > gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - > I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c > sparse-smooth.c -o sparse-smooth.o > gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - > I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c > tprs.c -o tprs.o > gcc -m64 -std=gnu99 -shared -L/usr/local/atlas/lib -L/usr/local/numerics/lib - > L/usr/lib -o mgcv.so gcv.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o > qp.o sparse-smooth.o tprs.o -L/home/Rman/R-2.15.0/lib -lRlapack - > L/home/Rman/R-2.15.0/lib -lRblas -lgfortran -lm -L/home/Rman/R-2.15.0/lib -lR > make[3]: Leaving directory `/tmp/RtmpiHdDJy/R.INSTALL472339eeb23a/mgcv/src' > installing to /home/Rman/R-2.15.0/library/mgcv/libs > ** R > ** data > ** inst > ** byte-compile and prepare package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > > * DONE (mgcv) > make[2]: Leaving directory `/home/Rman/R-2.15.0/src/library/Recommended' > make[1]: Leaving directory `/home/Rman/R-2.15.0/src/library/Recommended' > > -----here is the source_tree for mgcv ---A > mgcv_SR_tree/mgcv/R > mgcv_SR_tree/mgcv/data > mgcv_SR_tree/mgcv/inst > mgcv_SR_tree/mgcv/man > mgcv_SR_tree/mgcv/po > mgcv_SR_tree/mgcv/src > mgcv_SR_tree/mgcv/DESCRIPTION > mgcv_SR_tree/mgcv/MD5 > mgcv_SR_tree/mgcv/NAMESPACE > mgcv_SR_tree/mgcv/changeLog > mgcv_SR_tree/mgcv/gnugpl2.txt > mgcv_SR_tree/mgcv/index > > #--and here is the build tree ---B > mgcv_postBuild_Tree/mgcv/Meta > mgcv_postBuild_Tree/mgcv/R > mgcv_postBuild_Tree/mgcv/data > mgcv_postBuild_Tree/mgcv/help > mgcv_postBuild_Tree/mgcv/html > mgcv_postBuild_Tree/mgcv/libs > mgcv_postBuild_Tree/mgcv/CITATION > mgcv_postBuild_Tree/mgcv/DESCRIPTION > mgcv_postBuild_Tree/mgcv/INDEX > mgcv_postBuild_Tree/mgcv/NAMESPACE > > I havent a clue what is happening in the lines prepended by **
Messages (to you) being given by the build script -- it looks like you got a good build. (The big "DONE" is a good sign) > > Also I used make VERBOSE=1 but the compiler gave no indication of how one > arives at B from A and > how the library created mgcv.so) is installed in mgcv_postBuild_Tree/mgcv/libs > > advise on hese would be much appreciated > > > Reading the manual I noticed the way of installing these recommendd packages > appears to be > R CMD -l path/to/libraries recommended_tarball.tar.gz I think you have a command missing after CMD. Usually the format is R CMD __what_to_do__ -flag options tarball.tar.gz. I.e., if I want to build xts, I get the source and run R CMD INSTALL xts_0.8-7.tar.gz and it all "just works." Linking uses -l as you noted, but only if you need libraries above and beyond the R headers (which are included automatically with R CMD install) that aren't in the package's */src directory. You'll see above the the appropriate flags were passed to gcc for you in specifing ATLAS and the gnu c99 extensions. Linking within R should be done properly for you. I'm not an expert on the package build process, so I'll wait for someone else to say more / correct me if needed. > > I would like to know if the following is possible and if so how so:- > a) obtaining more verbose output from make (is this makefile related ? ) > a) exercising control over the compiler settings for the creation of the > library module (mgcv.so in the above case) > b) manual setting of the source and destination directroies and keeping of > the source tree where the package is built. > Try R CMD INSTALL --help to see available flags. Best, Michael > thannks in advance > > sincerely > luxInteg > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
