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
Re: [R-sig-Fedora] Error "translateCharUTF8' must be called on a CHARSXP Execution halted"
It is difficult to debug this without a reproducible example. Do you have, in the file system that you are trying to list, files with names that are not utf8-encoded? Martyn On Wed, 2017-08-23 at 13:12 +0200, Johannes Lips wrote: > On 23.08.2017 12:02, Braun, Stefan wrote: > > Dear list, > > > > I installed R 3.3.2 on a Red Hat Linux Enterprise 7.3 machine by > > adding the EPEL-repository and then installing it via yum. > > R starts up and seems to be doing fine at first sight. However, > > when I try to list the files in a directory with the command > > > > files <- list.files(path="/home/username/directory_name/", > > pattern="*.Rda",, full.names=T, recursive=FALSE) > > > > I get the error > > > > translateCharUTF8' must be called on a CHARSXP > > Execution halted > > > > On my local windows machine the command works fine. > > Googling this nothing really comes up except that the installation > > might be broken. (See http://r.789695.n4.nabble.com/list-files-erro > > r-message-translateCharUTF8-must-be-called-on-a-CHARSXP- > > td3250302.html) > > > > The strange thing is, that if I copy and paste the command into R > > and execute it, it does not work, but if I copy and paste it into R > > and change that command in a way that should not change its result > > but only add spaces or something like that it might run. E.g. > > changing it to > > > > files <- list.files(path = "/home/username/directory_name/", > > pattern = "*.Rda",, full.names = T, recursive = FALSE) > > > > might work, might not work and return the same error, or might > > execute but when I then type "files" that might return > > > > [1]Error: 'getCharCE' must be called on a CHARSXP > > > > The sessionInfo commmand gives me: > > sessionInfo() > > R version 3.3.2 (2016-10-31) > > Platform: x86_64-redhat-linux-gnu (64-bit) > > Running under: Red Hat Enterprise Linux Server 7.3 (Maipo) > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices > > utils datasets methods base > > > > uname -mrs gives me: > > Linux 3.10.0-514.el7.x86_64 x86_64 > > > > Any help would be greatly appreciated. > > > > Best regards, > > Stefan Braun > > Just for the record, there's the stackoverflow question > https://stackoverflow.com/questions/45835818/translatecharutf8-must-b > e-called-on-a-charsxp-execution-halted > Cheers > Johannes > > > > [[alternative HTML version deleted]] > > > > ___ > > R-SIG-Fedora mailing list > > R-SIG-Fedora@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora > > ___ > R-SIG-Fedora mailing list > R-SIG-Fedora@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-fedora ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
Re: [R-sig-Fedora] Error "translateCharUTF8' must be called on a CHARSXP Execution halted"
On 23.08.2017 12:02, Braun, Stefan wrote: Dear list, I installed R 3.3.2 on a Red Hat Linux Enterprise 7.3 machine by adding the EPEL-repository and then installing it via yum. R starts up and seems to be doing fine at first sight. However, when I try to list the files in a directory with the command files <- list.files(path="/home/username/directory_name/", pattern="*.Rda",, full.names=T, recursive=FALSE) I get the error translateCharUTF8' must be called on a CHARSXP Execution halted On my local windows machine the command works fine. Googling this nothing really comes up except that the installation might be broken. (See http://r.789695.n4.nabble.com/list-files-error-message-translateCharUTF8-must-be-called-on-a-CHARSXP-td3250302.html) The strange thing is, that if I copy and paste the command into R and execute it, it does not work, but if I copy and paste it into R and change that command in a way that should not change its result but only add spaces or something like that it might run. E.g. changing it to files <- list.files(path = "/home/username/directory_name/", pattern = "*.Rda",, full.names = T, recursive = FALSE) might work, might not work and return the same error, or might execute but when I then type "files" that might return [1]Error: 'getCharCE' must be called on a CHARSXP The sessionInfo commmand gives me: sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.3 (Maipo) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base uname -mrs gives me: Linux 3.10.0-514.el7.x86_64 x86_64 Any help would be greatly appreciated. Best regards, Stefan Braun Just for the record, there's the stackoverflow question https://stackoverflow.com/questions/45835818/translatecharutf8-must-be-called-on-a-charsxp-execution-halted Cheers Johannes [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
[R-sig-Fedora] Error "translateCharUTF8' must be called on a CHARSXP Execution halted"
Dear list, I installed R 3.3.2 on a Red Hat Linux Enterprise 7.3 machine by adding the EPEL-repository and then installing it via yum. R starts up and seems to be doing fine at first sight. However, when I try to list the files in a directory with the command files <- list.files(path="/home/username/directory_name/", pattern="*.Rda",, full.names=T, recursive=FALSE) I get the error translateCharUTF8' must be called on a CHARSXP Execution halted On my local windows machine the command works fine. Googling this nothing really comes up except that the installation might be broken. (See http://r.789695.n4.nabble.com/list-files-error-message-translateCharUTF8-must-be-called-on-a-CHARSXP-td3250302.html) The strange thing is, that if I copy and paste the command into R and execute it, it does not work, but if I copy and paste it into R and change that command in a way that should not change its result but only add spaces or something like that it might run. E.g. changing it to files <- list.files(path = "/home/username/directory_name/", pattern = "*.Rda",, full.names = T, recursive = FALSE) might work, might not work and return the same error, or might execute but when I then type "files" that might return [1]Error: 'getCharCE' must be called on a CHARSXP The sessionInfo commmand gives me: sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server 7.3 (Maipo) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base uname -mrs gives me: Linux 3.10.0-514.el7.x86_64 x86_64 Any help would be greatly appreciated. Best regards, Stefan Braun [[alternative HTML version deleted]] ___ R-SIG-Fedora mailing list R-SIG-Fedora@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
