[Rd] questions on R CMD INSTALL et al

From: luxInteg <lux-integ_at_btconnect.com>
Date: Tue, 24 Jul 2012 20:30:06 +0100


Greetings,

ink1">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

-----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 **

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 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.

582qlink4"><a name="1582qlink4">ame="1582qlink4">thannks in advance

sincerely
luxInteg



R-devel_at_r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel Received on Tue 24 Jul 2012 - 19:32:58 GMT

This quarter's messages: by month, or sorted: [ by date ] [ by thread ] [ by subject ] [ by author ]

All messages

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Tue 24 Jul 2012 - 21:00:32 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-devel. Please read the posting guide before posting to the list.

list of date sections of archive