I am not too worried about the Aqua GUI: basically, one needs access to the development version of R when working with the development version of Bioconductor. The entire exercise is an attempt to make a devel version of R while retaining an installation of stable R with R.app and all that jazz.
I want this to be relatively easy because several others need to do this as well, so that was why I refrained from installing tcltk. I am not really using these gui packages myself (but I sometimes need to install them to satisfy dependencies), perhaps I need to rethink this approach. Kasper On Aug 25, 2005, at 11:28 AM, Jan de Leeuw wrote: > Of course now you have R with AquaTcl, your Tcl/Tk based packages > will not work from the Aqua GUI, and packages such as tkrplot will not > work at all. > > On Aug 25, 2005, at 11:17 , Kasper Daniel Hansen wrote: > > >> >> On Aug 24, 2005, at 4:43 PM, Simon Urbanek wrote: >> >> >>> On Aug 24, 2005, at 4:58 PM, Kasper Daniel Hansen wrote: >>> >>> >>> >>>> On Aug 24, 2005, at 11:09 AM, Simon Urbanek wrote: >>>> >>>> >>>>> I just repeat what I've said here already: unless you desperately >>>>> need 64-bit R there is no real benefit from using gcc4, because >>>>> it's >>>>> still very instable (gfortran segfaults even on simple examples) >>>>> and >>>>> unreliable (gfortran is even slower than g77). There is a good >>>>> reason >>>>> why the CRAN build uses gcc3 and g77. >>>>> >>>>> >>>> >>>> That was a nice clear statement. So given that I want to compile R >>>> from source (because I need the devel version), without too much >>>> hassle I should use gcc 3.3 supplied by Xcode 2.1. But what do I do >>>> with respect to the Fortran compiler? >>>> >>>> >>> >>> CRAN installer package of R comes with g77 3.4 which is recommended. >>> You can install it even separately from the R binary (preferably >>> using sudo installer ... because there is a bug in the package that >>> doesn't allow non-admins to install it - c.f. the list). That >>> version >>> is tested to work with the gcc3 that cones with Xcode 2.x. If you >>> plan to compile R from sources you may also want to run >>> sudo gcc_select 3.3 >>> to prevent having problems with cc_dynamic. >>> >>> >>> >>>> How close should the versions match? Should I get >>>> - gcc 3.3.6 (latest version of the 3.3 branch) from Gnu's website >>>> - gcc 3.4.4 from Gnu's website >>>> - gcc 3.4 from the hpc.sourceforge website >>>> >>>> >>> >>> It doesn't really matter as long as it is >=3.3 and <=3.9 except >>> that >>> it should use static Fortran libraries if possible (unfortunately >>> the >>> more recent ones don't). >>> >> >> It works! >> >> So here is what I did: >> 1) Downloaded the most recent (binary) version of R from cran and >> mounted the disk image. >> 2) installed the g77 compiler from the package by >> sudo installer -pkg /Volumes/R-2.1.1/Packages/g77.pkg -target / >> (if you just want to check the package information, do >> installer -pkg /Volumes/R-2.1.1/Packages/g77.pkg -pkginfo >> ) >> 3) compiled R using the flags >> ./configure --with-aqua \ >> --with-blas='-framework vecLib' --with-lapack \ >> --with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh \ >> --with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh \ >> R_PAPERSIZE=letter \ >> F77=g77 \ >> TCLTK_LIBS='-framework Tcl -framework Tk' \ >> TCLTK_CPPFLAGS='-I/Library/Frameworks/Tcl.framework/Headers >> -I/Library/Frameworks/Tk.frameworks/Headers' >> (bad linebreak because of the mail program in the two last lines) >> >> Thanks a lot! >> >> Kasper >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-SIG-Mac mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> > > ========================================================== > Jan de Leeuw, 11667 Steinhoff Rd, Frazier Park, CA 93225, 661-245-1725 > http://www.cuddyvalley.org/ > dunklen.mov > ========================================================== > Und die Einen sind im Dunkeln > Und die Andern sind im Licht > Doch man sieht nur die im Lichte > Die im Dunkeln sieht man > nicht (Brecht) > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
