For some reason I had to see my own post to realize my stupidity... Defining PG_HOME _before_ running the configure solved the problem. Sorry for wasting the bandwidth.
Andy From: Liaw, Andy > > Hi All, > > While attempting to build R-patched using the Portland Group > compiler suite on our dual Opteron 250 box running Scyld > 29cz5 (based on RH, kernel 2.4.29), I get: > > make[5]: Leaving directory > `/home/andy/Rbuild/R221-pgi/src/library/tools/src' > make[5]: Entering directory > `/home/andy/Rbuild/R221-pgi/src/library/tools/src' > pgcc -I../../../../include -I/include -I/include/CC -fpic > -O2 -Kieee -c > /home/andy/Rbuild/R-patched/src/library/tools/src/text.c -o text.o > pgcc -I../../../../include -I/include -I/include/CC -fpic > -O2 -Kieee -c > /home/andy/Rbuild/R-patched/src/library/tools/src/init.c -o init.o > pgcc -I../../../../include -I/include -I/include/CC -fpic > -O2 -Kieee -c > /home/andy/Rbuild/R-patched/src/library/tools/src/Rmd5.c -o Rmd5.o > pgcc -I../../../../include -I/include -I/include/CC -fpic > -O2 -Kieee -c > /home/andy/Rbuild/R-patched/src/library/tools/src/md5.c -o > md5.o pgcc -shared -L/libso -L/usr/lib64 -o tools.so text.o > init.o Rmd5.o md5.o > > mkdir -p -- ../../../../library/tools/libs > make[5]: Leaving directory > `/home/andy/Rbuild/R221-pgi/src/library/tools/src' > make[4]: Leaving directory > `/home/andy/Rbuild/R221-pgi/src/library/tools/src' > **ERROR: in routine alloca() there is a > stack overflow: thread 0, max 8180KB, used 0KB, request 16B > make[3]: *** [all] Error 1 > make[3]: Leaving directory > `/home/andy/Rbuild/R221-pgi/src/library/tools' > make[2]: *** [R] Error 1 > make[2]: Leaving directory `/home/andy/Rbuild/R221-pgi/src/library' > make[1]: *** [R] Error 1 > make[1]: Leaving directory `/home/andy/Rbuild/R221-pgi/src' > make: *** [R] Error 1 > > I configured it as follows: > > ~/Rbuild/R-patched/configure \ > PG_HOME=/usr/pgi/linux86-64/6.1 \ > CC=pgcc \ > CFLAGS="-O2 -Kieee" \ > CPPFLAGS="-I$PG_HOME/include -I$PG_HOME/include/CC" \ > CPICFLAGS=-fpic \ > F77=pgf77 \ > FFLAGS="-Kieee"\ > FPICFLAGS=-fpic \ > CXX=pgCC \ > CXXFLAGS="-Kieee"\ > CXXPICFLAGS=-fpic \ > SHLIB_CXXLDFLAGS=-shared \ > SHLIB_LDFLAGS=-shared \ > LDFLAGS="-L$PG_HOME/libso -L/usr/lib64" \ > --with-blas="-L/usr/pgi/linux86-64/6.1/libso -lacml" > > (Note that pgcc no longer recognize -mieee-fp, so I changed > to -Kieee instead, and had to manually remove -mieee-fp in > the resulting Makeconf and > config.status.) > > I'd very much appreciate any pointer as to how to proceed... > > Best, > Andy > > > Andy Liaw, PhD > Biometrics Research PO Box 2000 RY33-300 > Merck Research Labs Rahway, NJ 07065 > andy_liaw(a)merck.com 732-594-0820 > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > -------------------------------------------------------------- > ---------------- > Notice: This e-mail message, together with any attachments, > contains information of Merck & Co., Inc. (One Merck Drive, > Whitehouse Station, New Jersey, USA 08889), and/or its > affiliates (which may be known outside the United States as > Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as > Banyu) that may be confidential, proprietary copyrighted > and/or legally privileged. It is intended solely for the use > of the individual or entity named on this message. If you > are not the intended recipient, and have received this > message in error, please notify us immediately by reply > e-mail and then delete it from your system. > -------------------------------------------------------------- > ---------------- > ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html