On Tue, 2015-04-21 at 11:46 -0600, Andy Jacobson (NOAA Affiliate) wrote: > Hi, > > I'm encountering trouble compiling caTools_1.17.1.tar.gz and > e1071_1.6-4.tar.gz on a Linux system using the Intel compiler suite. > 14 other packages I generally use installed without any trouble. I > notice both of these trouble packages have a C++ component, so I > wonder if that might be the issue. Below, there's information on my > platform, compiler, and some diagnostic output showing the errors. > > Advice appreciated! > > Thanks, > > Andy
There are two things missing when R tries to create the shared object file on this line: icpc -L/usr/local/lib64 -o e1071.so Rsvm.o cmeans.o cshell.o floyd.o svm.o Firstly, the compiler flag "-shared" is missing. It tells the compiler to build a shared object instead of an executable. Secondly the linker flag "-lR" is missing, along with the "-L" flag that tells the linker where to find the shared R library. To find out what went wrong, you should share the configuration you used when building R. Martyn > > > Intel compiler suite: icc (ICC) 14.0.2 20140120 > > sessionInfo() reports: > > R version 3.1.3 (2015-03-09) > Platform: x86_64-unknown-linux-gnu (64-bit) > Running under: Red Hat Enterprise Linux Server release 6.5 (Santiago) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_3.1.3 > > > Abbreviated versions of the output from R CMD INSTALL: > > For caTools: > > * installing to library ‘/scratch3/BMC/co2/lib/R-3.1/x86_64-unknown-linux-gnu’ > * installing *source* package ‘caTools’ ... > ** package ‘caTools’ successfully unpacked and MD5 sums checked > ** libs > icpc -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG -I/usr/local/include > -fpic -g -O3 -fp-model precise -c Gif2R.cpp -o Gif2R.o > icpc -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG -I/usr/local/include > -fpic -g -O3 -fp-model precise -c GifTools.cpp -o GifTools.o > icc -std=gnu99 -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG > -I/usr/local/include -fpic -g -O3 -wd188 -ip -fp-model precise -c > runfunc.c -o runfunc.o > icpc -L/usr/local/lib64 -o caTools.so Gif2R.o GifTools.o runfunc.o > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function > `_start': > (.text+0x20): undefined reference to `main' > Gif2R.o: In function `imwritegif': > /tmp/RtmpEfnBsm/R.INSTALL17c3a7327d4fb/caTools/src/Gif2R.cpp:19: undefined > reference to `R_chk_calloc' > /tmp/RtmpEfnBsm/R.INSTALL17c3a7327d4fb/caTools/src/Gif2R.cpp:23: undefined > reference to `R_chk_free' > ... (many more R_* undefined references) > > For e1071: > > * installing to library ‘/scratch3/BMC/co2/lib/R-3.1/x86_64-unknown-linux-gnu’ > * installing *source* package ‘e1071’ ... > ** package ‘e1071’ successfully unpacked and MD5 sums checked > checking for C++ compiler default output file name... a.out > checking whether the C++ compiler works... yes > checking whether we are cross compiling... no > checking for suffix of executables... > checking for suffix of object files... o > checking whether we are using the GNU C++ compiler... yes > checking whether icpc accepts -g... yes > ** libs > icc -std=gnu99 -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG > -I/usr/local/include -fpic -g -O3 -wd188 -ip -fp-model precise -c Rsvm.c > -o Rsvm.o > icc -std=gnu99 -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG > -I/usr/local/include -fpic -g -O3 -wd188 -ip -fp-model precise -c > cmeans.c -o cmeans.o > icc -std=gnu99 -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG > -I/usr/local/include -fpic -g -O3 -wd188 -ip -fp-model precise -c > cshell.c -o cshell.o > icc -std=gnu99 -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG > -I/usr/local/include -fpic -g -O3 -wd188 -ip -fp-model precise -c > floyd.c -o floyd.o > icpc -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG -I/usr/local/include > -fpic -g -O3 -fp-model precise -c svm.cpp -o svm.o > icpc -L/usr/local/lib64 -o e1071.so Rsvm.o cmeans.o cshell.o floyd.o svm.o > /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function > `_start': > (.text+0x20): undefined reference to `main' > Rsvm.o: In function `do_cross_validation': > /tmp/Rtmp9h7iYE/R.INSTALL1d9615a42180e/e1071/src/Rsvm.c:91: undefined > reference to `GetRNGstate' > /tmp/Rtmp9h7iYE/R.INSTALL1d9615a42180e/e1071/src/Rsvm.c:94: undefined > reference to `unif_rand' > /tmp/Rtmp9h7iYE/R.INSTALL1d9615a42180e/e1071/src/Rsvm.c:106: undefined > reference to `PutRNGstate' > ... (many more undefined references) > > > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
