hi i get an error when trying to install R 2.9.1 from source on an intel mac os 10.5.7. i have used the gcc4.2 from xcode 3.1 and gfortran 4.2 from http://r.research.att.com/tools/. i also tried using gcc and gfortran 4.3 installed with macports. same error. im not an expert in this and im a bit lost as to the "source" of my problem? here follows some of the output from configure and make: ok-ulla:R-2.9.1 jr$ ./configure --with-blas='-framework vecLib' --with-aqua --enable-R- framework --enable-R-shlib checking build system type... i386-apple-darwin9.7.0 checking host system type... i386-apple-darwin9.7.0 loading site script './config.site' ... ... R is now configured for i386-apple-darwin9.7.0 Source directory: . Installation directory: /Library/Frameworks C compiler: gcc -std=gnu99 -g -O2 Fortran 77 compiler: gfortran -g -O2 C++ compiler: g++ -g -O2 Fortran 90/95 compiler: gfortran -g -O2 Obj-C compiler: gcc -g -O2 Interfaces supported: X11, aqua, tcltk External libraries: readline, BLAS(vecLib) Additional capabilities: PNG, JPEG, iconv, MBCS, NLS, cairo, ICU Options enabled: framework, R profiling, Java Recommended packages: yes R-2.9.1 jr$ sudo make make[1]: Nothing to be done for `R'. make[1]: Nothing to be done for `R'. make[2]: Nothing to be done for `R'. creating src/scripts/R.fe mkdir ../../bin mkdir ../../include mkdir ../../../include/R_ext making blocksort.d from blocksort.c making bzlib.d from bzlib.c making bzcompress.d from bzcompress.c ... ... gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c dynload.c -o dynload.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c edit.c -o edit.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c stubs.c -o stubs.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c system.c -o system.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c sys-unix.c -o sys-unix.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c sys-std.c -o sys-std.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c X11.c -o X11.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c aqua.c -o aqua.o gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c Rembedded.c -o Rembedded.o rm -rf libunix.a ar cr libunix.a dynload.o edit.o stubs.o system.o sys-unix.o sys-std.o X11.o aqua.o Rembedded.o ranlib libunix.a make[3]: *** No rule to make target `install/R-2.9.1'. Stop. make[2]: *** [R] Error 2 make[1]: *** [R] Error 1 make: *** [R] Error 1 any help highly appreciated:-) cheers, jesper Ryge karolinska Institutet

Jesper, I don't know if you have subscribed to the R-SIG-Mac mailing list (r-sig-mac at stat.math.ethz.ch). I think you'll find answers flow more readily on that board if you post R installation issues on the Mac. Patrick Jesper Ryge wrote: > hi > > i get an error when trying to install R 2.9.1 from source on an intel mac os 10.5.7. i have > used the gcc4.2 from xcode 3.1 and gfortran 4.2 from http://r.research.att.com/tools/. i > also tried using gcc and gfortran 4.3 installed with macports. same error. im not an expert in > this and im a bit lost as to the "source" of my problem? here follows some of the output > from configure and make: > > ok-ulla:R-2.9.1 jr$ ./configure --with-blas='-framework vecLib' --with-aqua --enable-R- > framework --enable-R-shlib > checking build system type... i386-apple-darwin9.7.0 > checking host system type... i386-apple-darwin9.7.0 > loading site script './config.site' > ... > ... > R is now configured for i386-apple-darwin9.7.0 > > Source directory: . > Installation directory: /Library/Frameworks > > C compiler: gcc -std=gnu99 -g -O2 > Fortran 77 compiler: gfortran -g -O2 > > C++ compiler: g++ -g -O2 > Fortran 90/95 compiler: gfortran -g -O2 > Obj-C compiler: gcc -g -O2 > > Interfaces supported: X11, aqua, tcltk > External libraries: readline, BLAS(vecLib) > Additional capabilities: PNG, JPEG, iconv, MBCS, NLS, cairo, ICU > Options enabled: framework, R profiling, Java > > Recommended packages: yes > > R-2.9.1 jr$ sudo make > make[1]: Nothing to be done for `R'. > make[1]: Nothing to be done for `R'. > make[2]: Nothing to be done for `R'. > creating src/scripts/R.fe > mkdir ../../bin > mkdir ../../include > mkdir ../../../include/R_ext > making blocksort.d from blocksort.c > making bzlib.d from bzlib.c > making bzcompress.d from bzcompress.c > ... > ... > gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c dynload.c -o dynload.o > gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c edit.c -o edit.o > gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c stubs.c -o stubs.o > gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c system.c -o system.o > gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c sys-unix.c -o sys-unix.o > gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c sys-std.c -o sys-std.o > gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c X11.c -o X11.o > gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c aqua.c -o aqua.o > gcc -std=gnu99 -I. -I../../src/include -I../../src/include -I/usr/X11/include - > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c Rembedded.c -o Rembedded.o > rm -rf libunix.a > ar cr libunix.a dynload.o edit.o stubs.o system.o sys-unix.o sys- std.o X11.o aqua.o > Rembedded.o > ranlib libunix.a > make[3]: *** No rule to make target `install/R-2.9.1'. Stop. > make[2]: *** [R] Error 2 > make[1]: *** [R] Error 1 > make: *** [R] Error 1 > > any help highly appreciated:-) > > cheers, > jesper Ryge > karolinska Institutet > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

thanx:-) solved it. was a stupid issue, part of the path to the R folder from which the installation was performed contained a space, like "user/install folder/R-2.9.0" which apparently it could not handle... now its running... jesper Ryge ----- Original Message ----- From: Patrick Aboyoun <paboyoun@fhcrc.org> Date: Friday, July 31, 2009 5:25 pm Subject: Re: [BioC] error installing R 2.9.1 from source on mac os 10.5? To: Jesper.Ryge at ki.se Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Jesper, > I don't know if you have subscribed to the R-SIG-Mac mailing list > (r-sig-mac at stat.math.ethz.ch). I think you'll find answers flow > more > readily on that board if you post R installation issues on the Mac. > > > Patrick > > > > Jesper Ryge wrote: > > hi > > > > i get an error when trying to install R 2.9.1 from source on an > intel mac os 10.5.7. i have > > used the gcc4.2 from xcode 3.1 and gfortran 4.2 from > http://r.research.att.com/tools/. i > > also tried using gcc and gfortran 4.3 installed with macports. > same error. im not an expert in > > this and im a bit lost as to the "source" of my problem? here > follows some of the output > > from configure and make: > > > > ok-ulla:R-2.9.1 jr$ ./configure --with-blas='-framework vecLib' -- > with-aqua --enable-R- > > framework --enable-R-shlib > > checking build system type... i386-apple-darwin9.7.0 > > checking host system type... i386-apple-darwin9.7.0 > > loading site script './config.site' > > ... > > ... > > R is now configured for i386-apple-darwin9.7.0 > > > > Source directory: . > > Installation directory: /Library/Frameworks > > > > C compiler: gcc -std=gnu99 -g -O2 > > Fortran 77 compiler: gfortran -g -O2 > > > > C++ compiler: g++ -g -O2 > > Fortran 90/95 compiler: gfortran -g -O2 > > Obj-C compiler: gcc -g -O2 > > > > Interfaces supported: X11, aqua, tcltk > > External libraries: readline, BLAS(vecLib) > > Additional capabilities: PNG, JPEG, iconv, MBCS, NLS, cairo, ICU > > Options enabled: framework, R profiling, Java > > > > Recommended packages: yes > > > > R-2.9.1 jr$ sudo make > > make[1]: Nothing to be done for `R'. > > make[1]: Nothing to be done for `R'. > > make[2]: Nothing to be done for `R'. > > creating src/scripts/R.fe > > mkdir ../../bin > > mkdir ../../include > > mkdir ../../../include/R_ext > > making blocksort.d from blocksort.c > > making bzlib.d from bzlib.c > > making bzcompress.d from bzcompress.c > > ... > > ... > > gcc -std=gnu99 -I. -I../../src/include -I../../src/include - > I/usr/X11/include - > > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c dynload.c - > o dynload.o > > gcc -std=gnu99 -I. -I../../src/include -I../../src/include - > I/usr/X11/include - > > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c edit.c -o > edit.o> gcc -std=gnu99 -I. -I../../src/include -I../../src/include - > I/usr/X11/include - > > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c stubs.c -o > stubs.o> gcc -std=gnu99 -I. -I../../src/include -I../../src/include > -I/usr/X11/include - > > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c system.c - > o system.o > > gcc -std=gnu99 -I. -I../../src/include -I../../src/include - > I/usr/X11/include - > > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c sys-unix.c > -o sys-unix.o > > gcc -std=gnu99 -I. -I../../src/include -I../../src/include - > I/usr/X11/include - > > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c sys-std.c - > o sys-std.o > > gcc -std=gnu99 -I. -I../../src/include -I../../src/include - > I/usr/X11/include - > > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c X11.c -o > X11.o> gcc -std=gnu99 -I. -I../../src/include -I../../src/include - > I/usr/X11/include - > > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c aqua.c -o > aqua.o> gcc -std=gnu99 -I. -I../../src/include -I../../src/include - > I/usr/X11/include - > > I/usr/local/include -DHAVE_CONFIG_H -fPIC -g -O2 -c > Rembedded.c -o Rembedded.o > > rm -rf libunix.a > > ar cr libunix.a dynload.o edit.o stubs.o system.o sys-unix.o sys- > std.o X11.o aqua.o > > Rembedded.o > > ranlib libunix.a > > make[3]: *** No rule to make target `install/R-2.9.1'. Stop. > > make[2]: *** [R] Error 2 > > make[1]: *** [R] Error 1 > > make: *** [R] Error 1 > > > > any help highly appreciated:-) > > > > cheers, > > jesper Ryge > > karolinska Institutet > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor> > > >