From wc@rdoen @end|ng |rom gm@||@com  Fri Jul 10 20:59:37 2020
From: wc@rdoen @end|ng |rom gm@||@com (Wim R. Cardoen)
Date: Fri, 10 Jul 2020 12:59:37 -0600
Subject: [Rd] Compilation error for R 4.0.2
Message-ID: <CABNPx=zNLOiO=bHGhkW9nvP26OMMVjRp=rTiL0YgBf1=sm3tiA@mail.gmail.com>

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


[Rd] Compilation error for R 4.0.2
Wim R. Cardoen