shlib problems with Intel compiler

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shlib problems with Intel compiler

Andy Jacobson
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
[hidden email]

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

303/578-2237

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Re: shlib problems with Intel compiler

Martyn Plummer-3
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)
>
>
>
>

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Re: shlib problems with Intel compiler

Andy Jacobson
Hi Martyn,

Thanks for your insight, that seems pretty direct.  Unfortunately, I did not compile this version of R (it's on a large supercomputer system and this version of R was installed by the admins).  Using "R CMD config", I see the following relevant settings:

DYLIB_LD = icc -std=gnu99
DYLIB_LDFLAGS = -shared -openmp
LDFLAGS = -L/opt/compilers/intel/cce/9.1.039/lib -L/opt/compilers/intel/fce/9.1.033/lib -L/usr/local/lib64
SHLIB_CXXLD = icpc
SHLIB_CXXLDFLAGS =
SHLIB_LD = icc -std=gnu99
SHLIB_LDFLAGS = -shared

It looks like the SHLIB_CXXLDFLAGS is missing the "-shared -lR -L<loc-of-libR>".  It's a mystery to me how R was built and configured such that it has incomplete/incorrect flags.

By trial and error I figured out how to use a .R/Makevars setting to add the required flags to SHLIB_CXXLDFLAGS.  (It sure would have been useful to have a reference about the syntax and variable names that the Makevars file can contain...is that documented somewhere?)

I wonder if the recommendation for "-lR" is correct.  None of the other packages are compiled with that flag, and everything seems to compile and load OK in R without using that.

Best Regards,

Andy

> On Apr 22, 2015, at 9:30 AM, Martyn Plummer <[hidden email]> wrote:
>
> 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)
>>
>>
>>
>>
>

--
Andy Jacobson
[hidden email]

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

303/578-2237

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Re: shlib problems with Intel compiler

Martyn Plummer-3
I was assuming that R was configured with --enable-R-shlib but if that's not the case then you don't need it.

Martyn


> On 22 Apr 2015, at 18:40, Andy Jacobson (NOAA Affiliate) <[hidden email]> wrote:
>
> Hi Martyn,
>
> Thanks for your insight, that seems pretty direct.  Unfortunately, I did not compile this version of R (it's on a large supercomputer system and this version of R was installed by the admins).  Using "R CMD config", I see the following relevant settings:
>
> DYLIB_LD = icc -std=gnu99
> DYLIB_LDFLAGS = -shared -openmp
> LDFLAGS = -L/opt/compilers/intel/cce/9.1.039/lib -L/opt/compilers/intel/fce/9.1.033/lib -L/usr/local/lib64
> SHLIB_CXXLD = icpc
> SHLIB_CXXLDFLAGS =
> SHLIB_LD = icc -std=gnu99
> SHLIB_LDFLAGS = -shared
>
> It looks like the SHLIB_CXXLDFLAGS is missing the "-shared -lR -L<loc-of-libR>".  It's a mystery to me how R was built and configured such that it has incomplete/incorrect flags.
>
> By trial and error I figured out how to use a .R/Makevars setting to add the required flags to SHLIB_CXXLDFLAGS.  (It sure would have been useful to have a reference about the syntax and variable names that the Makevars file can contain...is that documented somewhere?)
>
> I wonder if the recommendation for "-lR" is correct.  None of the other packages are compiled with that flag, and everything seems to compile and load OK in R without using that.
>
> Best Regards,
>
> Andy
>
>> On Apr 22, 2015, at 9:30 AM, Martyn Plummer <[hidden email]> wrote:
>>
>> 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)
>
> --
> Andy Jacobson
> [hidden email]
>
> NOAA Earth System Research Lab
> Global Monitoring Division
> 325 Broadway R/GMD1
> Boulder, Colorado 80305
>
> 303/578-2237
>
>
>
>
>
>
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