pbdSLAP, pbdMAT, pbdBASE installs fail in R-3.2.2, with MKL and OpenMPI 1.8.8

[Bruce Foster]

I'm trying to install RBigData routines into R-3.2.2 on a Red Hat Linux 6 system, and the installations are all failing to find ./xintface.

Later on, the header files R.h and Rinternals.h are not found in BI_HypBS.c / Bdef.h. The bottom line is installation failure. I'm looking for some guidance to install RBigData.

In the following, you can see that I'm using OpenMPI 1.8.8 and the Intel MKL libraries.

* installing *source* package 'pbdSLAP' ...
** package 'pbdSLAP' successfully unpacked and MD5 sums checked
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
collect2: ld returned 1 exit status
./00_make.sh: line 11: ./xintface: No such file or directory
 
****************** Results of pbdSLAP package configure *****************
 
>> CC = gcc -std=gnu99
>> F77 =
>> FC = gfortran
>> EXT_LDFLAGS = $(LAPACK_LIBS) $(BLAS_LIBS)
>> EXT_OBJS = $(R_SLAP)
>> EXT_LIBS = userLibrary
>> CDEFS = -D
>> CDEFS_CHECK = TRUE
>> SPMD_CPPFLAGS = -I/opt/openmpi/GNU/1.8.8/include  -DMPI2 -DOPENMPI
>> SPMD_LDFLAGS = -L/opt/openmpi/GNU/1.8.8/lib -lmpi  -lutil -lpthread
 
*************************************************************************
 
configure: creating ./config.status
config.status: creating src/Makevars
** libs
echo "CC = gcc -std=gnu99" > Makeconf
echo "F77 = " >> Makeconf
echo "FC = gfortran" >> Makeconf
echo "SPMD_CPPFLAGS = -I/opt/openmpi/GNU/1.8.8/include  -DMPI2 -DOPENMPI" >> Makeconf
echo "SPMD_LDFLAGS = -L/opt/openmpi/GNU/1.8.8/lib -lmpi  -lutil -lpthread" >> Makeconf
echo "EXT_LDFLAGS =  -L/opt/intel/mkl/lib/intel64  -L/opt/intel/composerxe/lib/intel64     -Wl,--start-group     -lmkl_gf_lp64         -lmkl_intel_thread         -lmkl_core     -Wl,--end-group     -liomp5 -lpthread" >> Makeconf
echo "CDEFS = -D" >> Makeconf
echo "CDEFS_CHECK = TRUE" >> Makeconf
echo "PKG_CPPFLAGS = -I/opt/openmpi/GNU/1.8.8/include  -DMPI2 -DOPENMPI" >> Makeconf
echo "PKG_CFLAGS = -w" >> Makeconf
echo "PKG_FFLAGS = -g -O2 -ffloat-store -w" >> Makeconf
echo "PKG_LIBS =  -L/opt/intel/mkl/lib/intel64  -L/opt/intel/composerxe/lib/intel64     -Wl,--start-group     -lmkl_gf_lp64         -lmkl_intel_thread         -lmkl_core     -Wl,--end-group     -liomp5 -lpthread -lgfortran -lm -L/opt/openmpi/GNU/1.8.8/lib -lmpi  -lutil -lpthread" >> Makeconf
echo "R_SLAP = lib/libslap.a" >> Makeconf
gfortran  -g -O2 -ffloat-store -w -fpic  -g -O2  -c slap_blacs.f -o slap_blacs.o
echo "### Added by Makevars" > SLmake.inc
echo "include /sscc/opt/R-3.2.2/lib64/R/etc/Makeconf" >> SLmake.inc
echo "CC = gcc -std=gnu99" >> SLmake.inc        # overwrite MkInclude
echo "F77 = " >> SLmake.inc    # overwrite MkInclude
echo "FC = gfortran" >> SLmake.inc        # overwrite MkInclude
echo "CDEFS = -D" >> SLmake.inc
echo "PKG_CPPFLAGS = -I/opt/openmpi/GNU/1.8.8/include  -DMPI2 -DOPENMPI" >> SLmake.inc
echo "PKG_CFLAGS = -w" >> SLmake.inc
echo "PKG_FFLAGS = -g -O2 -ffloat-store -w" >> SLmake.inc
echo "R_SLAP = libslap.a" >> SLmake.inc
echo "" >> SLmake.inc
cat SLmake.inc.org >> SLmake.inc
( cd LAPACK; make )
make[1]: Entering directory `/tmp/root/RtmpkyVZrq/R.INSTALL561e674f7a00/pbdSLAP/src/LAPACK'
gfortran -o dlarra.fo -c -I/sscc/opt/R-3.2.2/lib64/R/include -DNDEBUG -I/opt/openmpi/GNU/1.8.8/include  -DMPI2 -DOPENMPI -I/usr/local/include   -g -O2 -ffloat-store -w -fpic  -g -O2  -O3 -w dlarra.f
gfortran -o dlarrc.fo -c -I/sscc/opt/R-3.2.2/lib64/R/include -DNDEBUG -I/opt/openmpi/GNU/1.8.8/include  -DMPI2 -DOPENMPI -I/usr/local/include   -g -O2 -ffloat-store -w -fpic  -g -O2  -O3 -w dlarrc.f
gfortran -o dlarrd.fo -c -I/sscc/opt/R-3.2.2/lib64/R/include -DNDEBUG -I/opt/openmpi/GNU/1.8.8/include  -DMPI2 -DOPENMPI -I/usr/local/include   -g -O2 -ffloat-store -w -fpic  -g -O2  -O3 -w dlarrd.f
gfortran -o dlarrk.fo -c -I/sscc/opt/R-3.2.2/lib64/R/include -DNDEBUG -I/opt/openmpi/GNU/1.8.8/include  -DMPI2 -DOPENMPI -I/usr/local/include   -g -O2 -ffloat-store -w -fpic  -g -O2  -O3 -w dlarrk.f
ar cr ../libslap.a    \
             dlarra.fo dlarrc.fo dlarrd.fo dlarrk.fo
ranlib ../libslap.a
make[1]: Leaving directory `/tmp/root/RtmpkyVZrq/R.INSTALL561e674f7a00/pbdSLAP/src/LAPACK'
( cd BLACS; make )
make[1]: Entering directory `/tmp/root/RtmpkyVZrq/R.INSTALL561e674f7a00/pbdSLAP/src/BLACS'
gcc -std=gnu99 -o BI_HypBS.fo -c -D -I/sscc/opt/R-3.2.2/lib64/R/include -DNDEBUG -I/opt/openmpi/GNU/1.8.8/include  -DMPI2 -DOPENMPI -I/usr/local/include   -w -fpic  -g -O2  -O3 -w BI_HypBS.c
<command-line>: error: macro names must be identifiers
In file included from BI_HypBS.c:1:
Bdef.h:2:15: error: R.h: No such file or directory
Bdef.h:3:24: error: Rinternals.h: No such file or directory
make[1]: *** [BI_HypBS.fo] Error 1
make[1]: Leaving directory `/tmp/root/RtmpkyVZrq/R.INSTALL561e674f7a00/pbdSLAP/src/BLACS'
make: *** [libslap.a] Error 2
ERROR: compilation failed for package 'pbdSLAP'
* removing '/sscc/opt/R-3.2.2/lib64/R/library/pbdSLAP'
ERROR: dependency 'pbdSLAP' is not available for package 'pbdBASE'
* removing '/sscc/opt/R-3.2.2/lib64/R/library/pbdBASE'
ERROR: dependencies 'pbdSLAP', 'pbdBASE' are not available for package 'pbdDMAT'
* removing '/sscc/opt/R-3.2.2/lib64/R/library/pbdDMAT'

[Wei-Chen Chen]

The ./inst/test_intface/00_make.sh does not check or return correctly.
Replace Makevars or Makevars.in by
  CDEFS=-DAdd_
  CDEFS_CHECK=FALSE
provided that Add_ is the right one for your gcc/gfortran.