R SIG Fedora - Aug 2017 - No rule to make target all.R, needed by compiler.rdb building R 3.4.1 from source, Scientific Linux release 6.9 (Carbon)

Thanks again, sorry I didn't specify this. I am loading new libraries to get
to this point. The script I run for "configure" is:

#Load the new curl module
module load libs/gcc/4.4.7/curl/7.47.1
#Load the new xzutils module
module load apps/gcc/4.4.7/xzutils/5.2.2
#Load the new zlib module
module load libs/gcc/4.4.7/zlib/1.2.8
#Load the new bzip2 module
module load libs/gcc/4.4.7/bzip2/1.0.6
export
LDFLAGS="-L/usr/local/packages6/libs/gcc/4.4.7/bzip2/1.0.6/lib/"
#load pcre module
module load libs/gcc/4.4.7/pcre/8.37


#Set up environment variables and create directories
version=3.4.1
install_dir=/fastdata/mbp15ja/R-$version
build_dir=/data/mbp15ja/R-$version
mkdir -p $build_dir
mkdir -p $install_dir

cd $build_dir

#Set up modules
module load libs/gcc/lapack
module load libs/gcc/blas

#Download, untar and enter build directory
wget https://cran.rstudio.com/src/base/R-3/R-$version.tar.gz
tar -xzf ./R-$version.tar.gz
cd R-$version

#Configure and build
# Original command
./configure --prefix $install_dir --with-blas --with-lapack --enable-R-shlib
2>&1 | tee config-R-$version.log






If I run the make command: 

make 2>&1 | tee make-R-$version.log


I get the following error:

make[4]: Entering directory `/data/mbp15ja/R-3.4.1/R-3.4.1/src/main'
mkdir -p -- /data/mbp15ja/R-3.4.1/R-3.4.1/bin/exec
make[4]: Leaving directory `/data/mbp15ja/R-3.4.1/R-3.4.1/src/main'
make[3]: Leaving directory `/data/mbp15ja/R-3.4.1/R-3.4.1/src/main'
make[3]: Entering directory `/data/mbp15ja/R-3.4.1/R-3.4.1/src/main'
gcc -I../../src/extra  -I. -I../../src/include -I../../src/include
-I/usr/local/packages6/libs/gcc/4.4.7/curl/7.47.1/include
-I/usr/local/packages6/compilers/gcc/5.4.0/include -I../../src/nmath
-DHAVE_CONFIG_H   -fopenmp -fpic 
-I/usr/local/packages6/compilers/gcc/5.4.0/include  -c Rmain.c -o Rmain.o
gcc -Wl,--export-dynamic -fopenmp  -L../../lib -L/usr/local/lib/gcc/blas/1
-L/usr/local/lib/gcc/lapack/3.3.0
-L/usr/local/packages6/libs/gcc/4.4.7/bzip2/1.0.6/lib/ -o R.bin Rmain.o  -lR
-lRblas
../../lib/libR.so: undefined reference to `pcre_assign_jit_stack'
../../lib/libR.so: undefined reference to `pcre_jit_stack_alloc'
../../lib/libR.so: undefined reference to `pcre_free_study'
collect2: error: ld returned 1 exit status
make[3]: *** [R.bin] Error 1
make[3]: Leaving directory `/data/mbp15ja/R-3.4.1/R-3.4.1/src/main'
make[2]: *** [R] Error 2
make[2]: Leaving directory `/data/mbp15ja/R-3.4.1/R-3.4.1/src/main'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/data/mbp15ja/R-3.4.1/R-3.4.1/src'
make: *** [R] Error 1


I was advised to do a dry-run trying to debug. That is why I was doing make -n

I have previously loaded the PCRE library:
echo $PATH
/usr/local/packages6/libs/gcc/4.4.7/pcre/8.37/bin:/usr/local/packages6/libs/gcc/4.4.7/bzip2/1.0.6/bin:/usr/local/packages6/apps/gcc/4.4.7/xzutils/5.2.2/bin:/usr/local/packages6/libs/gcc/4.4.7/curl/7.47.1//bin:/usr/local/packages6/R/3.2.1/bin



Thanks again for the help





-----Original Message-----
From: Tom Callaway [mailto:tcallawa at redhat.com] 
Sent: mi?rcoles, 23 de agosto de 2017 20:01
To: Jaime Alvarez Benayas <jalvarezbenayas1 at sheffield.ac.uk>;
r-sig-fedora at r-project.org
Subject: Re: [R-sig-Fedora] No rule to make target all.R, needed by compiler.rdb
building R 3.4.1 from source, Scientific Linux release 6.9 (Carbon)



On 08/18/2017 01:12 PM, Jaime Alvarez Benayas wrote:
> Hello,
> 
> I am trying to build R from source on Scientific Linux release 6.9 
> (Carbon), Linux version 2.6.32-696.3.2.el6.x86_64 (Red Hat 4.4.7-18).
Okay, so the versions of zlib, bzip2, xz, curl, and pcre are too old on
Scientific Linux 6.9 (unless they've updated all of them when I wasn't
looking). That said, I don't think your problem is there.

Why are you calling make -n instead of just make?

~tom

On 08/23/2017 03:58 PM, Jaime Alvarez Benayas wrote:
> ../../lib/libR.so: undefined reference to `pcre_assign_jit_stack'
> ../../lib/libR.so: undefined reference to `pcre_jit_stack_alloc'
> ../../lib/libR.so: undefined reference to `pcre_free_study'
This is the error. Your PCRE is being built with SUPPORT_JIT undefined.

You should see some warning during the configure phase for PCRE that
says "JIT support requires pthreads" or something like that. You
should
get that from glibc-devel.

~tom

Hello,

Thanks again. I have checked the configure step, the only messages I get
containing pcre are:

checking for pcre_fullinfo in -lpcre... yes
checking pcre.h usability... yes
checking pcre.h presence... yes
checking for pcre.h... yes
checking pcre/pcre.h usability... no
checking pcre/pcre.h presence... no
checking for pcre/pcre.h... no
checking if PCRE version >= 8.20, < 10.0 and has UTF-8 support... yes
checking if PCRE version >= 8.32... yes
checking whether PCRE support suffices... yes


The final status from the command:

R is now configured for x86_64-pc-linux-gnu

  Source directory:          .
  Installation directory:    /fastdata/mbp15ja/R-3.4.1

  C compiler:                gcc 
-I/usr/local/packages6/compilers/gcc/5.4.0/include
  Fortran 77 compiler:       gfortran  -g -O2

  Default C++ compiler:      g++   -g -O2
  C++98 compiler:            g++  -g -O2
  C++11 compiler:            g++ -std=gnu++11 -g -O2
  C++14 compiler:            g++ -std=gnu++14 -g -O2
  C++17 compiler:
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:

  Interfaces supported:      X11, tcltk
  External libraries:        readline, curl
  Additional capabilities:   PNG, JPEG, NLS, cairo
  Options enabled:           shared R library, shared BLAS, R profiling

  Capabilities skipped:      TIFF, ICU
  Options not enabled:       memory profiling

  Recommended packages:      yes



I haven't seen the JIT message but will give a try at the glibc-devel:


Here is the whole log from the configure command
https://www.dropbox.com/s/m4g2w1hrr2uqldr/configure%20result%20R.txt?dl=0



-----Original Message-----
From: Tom Callaway [mailto:tcallawa at redhat.com] 
Sent: mi?rcoles, 23 de agosto de 2017 21:48
To: Jaime Alvarez Benayas <jalvarezbenayas1 at sheffield.ac.uk>;
r-sig-fedora at r-project.org
Subject: Re: [R-sig-Fedora] No rule to make target all.R, needed by compiler.rdb
building R 3.4.1 from source, Scientific Linux release 6.9 (Carbon)



On 08/23/2017 03:58 PM, Jaime Alvarez Benayas wrote:
> ../../lib/libR.so: undefined reference to `pcre_assign_jit_stack'
> ../../lib/libR.so: undefined reference to `pcre_jit_stack_alloc'
> ../../lib/libR.so: undefined reference to `pcre_free_study'
This is the error. Your PCRE is being built with SUPPORT_JIT undefined.

You should see some warning during the configure phase for PCRE that says
"JIT support requires pthreads" or something like that. You should get
that from glibc-devel.

~tom