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)
No, not R's configure, PCRE's configure. The PCRE library that you've built is missing some functionality. ~tom On Aug 23, 2017 7:53 PM, "Jaime Alvarez Benayas" < jalvarezbenay...@sheffield.ac.uk> wrote: > 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:tcall...@redhat.com] > Sent: miércoles, 23 de agosto de 2017 21:48 > To: Jaime Alvarez Benayas ; > r-sig-fedora@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 > > > [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
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)
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:tcall...@redhat.com] Sent: miércoles, 23 de agosto de 2017 21:48 To: Jaime Alvarez Benayas ; r-sig-fedora@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 ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
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 ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
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)
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:tcall...@redhat.com] Sent: miércoles, 23 de agosto de 2017 20:01 To: Jaime Alvarez Benayas ; r-sig-fedora@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 ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
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 ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
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)
Hello, I am installing R in an environment where I am not admin... Thanks -Original Message- From: Tom Callaway [mailto:tcall...@redhat.com] Sent: miércoles, 23 de agosto de 2017 19:42 To: Jaime Alvarez Benayas ; r-sig-fedora@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 ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
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 ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
[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)
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 Álvarez Benayas
PhD. Student
Department of Molecular Biology and Biotechnology
University of Sheffield
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