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)

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).

I load the needed modules and run:

*./configure --prefix $install_dir --with-blas --with-lapack
--enable-R-shlib 2>&1 | tee config-R-$version.log*




The "configure" command seems to run ok:

*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 encountered an error running "make -n" with the libtre library not
generating libtre.a:

*rm -rf libnmath.a*
*ar -cr libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o
fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o
expm1.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o
gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o
bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o
rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o
dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o
pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o
rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o
dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o
pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o
pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o
pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o
dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o
qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o*
*ranlib libnmath.a*
*make[4]: Leaving directory `/data/mbp15ja/R-3.4.1/R-3.4.1/src/nmath'*
*make[3]: *** No rule to make target `../extra/tre/libtre.a', needed by
`libR.so'.  Stop.*
*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 read in here https://www-01.ibm.com/support/docview.wss?uid=swg1IV36656 that
the library isn't supposed to make libtre.a and that they assume the file
they are looking for is libtre.so
I therefore built the libtre and linked libtre.so from the library
to src/extra/tre/libtre.a and now the make




"make -n" now fails with:

*if test -f ./NAMESPACE;  then \*
*          /usr/bin/install -c -m 644 ./NAMESPACE
../../../library/compiler; \*
*        fi*
*rm -f ../../../library/compiler/Meta/nsInfo.rds*
*if test -f DESCRIPTION; then \*
*          if test "" != ""; then \*
*            echo "tools:::.install_package_description('.',
'../../../library/compiler', '')" | \*
*            R_DEFAULT_PACKAGES=NULL R_ENABLE_JIT=0 ../../../bin/R
--vanilla --slave > /dev/null ; \*
*          else \*
*          echo "tools:::.install_package_description('.',
'../../../library/compiler')" | \*
*          R_DEFAULT_PACKAGES=NULL R_ENABLE_JIT=0 ../../../bin/R --vanilla
--slave > /dev/null ; \*
*          fi; \*
*        fi*
*make[4]: Leaving directory
`/data/mbp15ja/R-3.4.1/R-3.4.1/src/library/compiler'*
*make mklazycomp*
*make[4]: Entering directory
`/data/mbp15ja/R-3.4.1/R-3.4.1/src/library/compiler'*
*make[4]: *** No rule to make target `all.R', needed by
`../../../library/compiler/R/compiler.rdb'.  Stop.*
*make[4]: Leaving directory
`/data/mbp15ja/R-3.4.1/R-3.4.1/src/library/compiler'*
*make[3]: *** [all] Error 2*
*make[3]: Leaving directory
`/data/mbp15ja/R-3.4.1/R-3.4.1/src/library/compiler'*
*make[2]: *** [R] Error 1*
*make[2]: Leaving directory `/data/mbp15ja/R-3.4.1/R-3.4.1/src/library'*
*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 haven't seen anything regarding *all.R and *
*../../../library/compiler/R/compiler.rdb*


Thanks in advance!

-- 

---------------------------------------------------------------------

Jaime ?lvarez Benayas

PhD. Student

Department of Molecular Biology and Biotechnology

University of Sheffield

	[[alternative HTML version deleted]]

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).
Before debugging this too far, is there a reason you're building from
source as opposed to using the R prebuilt packages in EPEL?

~tom

Hello,

I am installing R in an environment where I am not admin...

Thanks

-----Original Message-----
From: Tom Callaway [mailto:tcallawa at redhat.com] 
Sent: mi?rcoles, 23 de agosto de 2017 19:42
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).
Before debugging this too far, is there a reason you're building from source
as opposed to using the R prebuilt packages in EPEL?

~tom

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

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