[BioC] error installing R 2.9.1 from source on mac os 10.5?

[Jesper Ryge]

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 at 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
> >
> > _______________________________________________
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> 
> 
>