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Compilation error for R 4.0.2

4 messages · Kurt Hornik, Brian Ripley, Wim R. Cardoen

Original
Wim R. Cardoen
# 
Hello,

I experienced a compiler error when I tried to compile the latest version
of R i.e. R4.0.2
making iosupport.d from iosupport.c
making lapack.d from lapack.c
making list.d from list.c
making localecharset.d from localecharset.c
grep.c(74): catastrophic error: cannot open source file "pcre2.h"
  # include<pcre2.h>
(The pcre2.h header file is actually present!)


I used the following compiler flags:
# PCRE2:
# -----
setenv CC gcc
setenv CFLAGS " -O2 -fPIC "
./configure --prefix=/uufs/chpc.utah.edu/sys/installdir/pcre2/10.35 \
            --enable-pcre2-16 --enable-pcre2-32 --with-pic

module purge
module load intel/2019.5.281

# USe a modern version of curl & pcre2 (The current one on Centos 7 is TOO
old)
setenv CURLDIR "/uufs/chpc.utah.edu/sys/installdir/curl/7.65.3"
setenv PCRE2DIR "/uufs/chpc.utah.edu/sys/installdir/pcre2/10.35"

setenv PATH ${PCRE2DIR}/bin:$PATH

 Setting Compiler & linker flags:
setenv CC icc
setenv CXX icpc
setenv F77 ifort
setenv FC ifort
setenv CFLAGS   " -axCORE-AVX512,CORE-AVX2,AVX,SSE4.2 -O3 -qopenmp
-fp-model precise -fPIC -I${MKLROOT}/include -I${CURLDIR}/include
                  -I${PCRE2DIR}/include "
setenv CXXFLAGS " ${CFLAGS} "
setenv FFLAGS   " ${CFLAGS} "
setenv FCFLAGS  " ${CFLAGS} "
setenv LDFLAGS  " -Wl,-rpath=${MKLROOT}/lib/intel64_lin
-L${MKLROOT}/lib/intel64_lin -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
                  -Wl,-rpath=/uufs/
chpc.utah.edu/sys/installdir/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin
                           -L/uufs/
chpc.utah.edu/sys/installdir/intel/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin
                           -liomp5 -lpthread -ldl -Wl,-rpath=${CURLDIR}/lib
-L${CURLDIR}/lib -lcurl
                           -Wl,-rpath=${PCRE2DIR}/lib -L${PCRE2DIR}/lib
 -lpcre2-8 -lpcre2-posix "

./configure --prefix=/uufs/chpc.utah.edu/sys/installdir/R/4.0.2i
--enable-R-profiling --enable-R-shlib --enable-memory-profiling
--enable-java --enable-shared=yes --with-blas="$LDFLAGS" --with-readline
--with-cairo --with-tcltk --with-libpng --with-jpeglib --with-libtiff
--with-ICU --with-pic --with-x --with-lapack --with-pcre2

I also appended the corresponding config.log:

Thank you,

Wim
Kurt Hornik
# 
What I guess you should do is

 /path/to/configure CPPFLAGS="-I${PCRE2DIR}/include ......"
 make

Hth
-k
Brian Ripley
#
On 11/07/2020 11:47, Kurt Hornik wrote:
Or use a config.site file for all of these settings.

On some systems (including some Linux systems I have used and current 
macOS), setting too much in the environment (usually caused by long 
values) has caused software to malfunction, including to segfault so it 
is ingrained in me to avoid it.
It did not get through the filters.

  
    

      
      
    

  


  


      

    

    
7 days later

    

      
      

        


  

        

      Wim R. Cardoen
    

    

      
      #
    

  


  

      
Dear Kurt,

Your suggestion worked.

Thank you,
Wim

        
On Sat, Jul 11, 2020 at 4:47 AM Kurt Hornik <Kurt.Hornik at wu.ac.at> wrote: