From andy.jacobson at noaa.gov  Tue Apr 21 19:46:40 2015
From: andy.jacobson at noaa.gov (Andy Jacobson (NOAA Affiliate))
Date: Tue, 21 Apr 2015 11:46:40 -0600
Subject: [Rd] shlib problems with Intel compiler
Message-ID: <9D2F27BD-240B-419F-8C0A-CCC3B1B4D680@noaa.gov>

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



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)




-- 
Andy Jacobson
andy.jacobson at noaa.gov

NOAA Earth System Research Lab
Global Monitoring Division
325 Broadway R/GMD1
Boulder, Colorado 80305

303/578-2237



[Rd] shlib problems with Intel compiler
Andy Jacobson (NOAA Affiliate