When I do "emerge --update R" or "emerge -e R" and after some time, I get this error: ... x86_64-pc-linux-gnu-gcc -I/var/tmp/portage/R-2.3.1/work/R-2.3.1/include -I/var/tmp/portage/R-2.3.1/work/R-2.3.1/include -I/usr/local/include -fPIC -march=athlon64 -mtune=athlon64 -ffast-math -pipe -O3 -funroll-all-loops -fpeel-loops -ftracer -funswitch-loops -ftree-vectorize -mfpmath=sse -c pps.c -o pps.o x86_64-pc-linux-gnu-gcc -shared -o spatial.so init.o krc.o pps.o -L/var/tmp/portage/R-2.3.1/work/R-2.3.1/lib -lR make[3]: se sale del directorio `/var/tmp/portage/R-2.3.1/temp/R.INSTALL.qi9Djf/VR/spatial/src' ** R ** inst ** help >>> Building/Updating help pages for package 'spatial' Formats: text html latex example Kaver text html latex example Kenvl text html latex example Kfn text html latex example Psim text html latex example SSI text html latex example Strauss text html latex example anova.trls text html latex example correlogram text html latex example expcov text html latex example ppgetregion text html latex ppinit text html latex example pplik text html latex example ppregion text html latex predict.trls text html latex example prmat text html latex example semat text html latex example surf.gls text html latex example surf.ls text html latex example trls.influence text html latex example trmat text html latex example variogram text html latex example ** building package indices ... * DONE (spatial) make[2]: se sale del directorio `/var/tmp/portage/R-2.3.1/work/R-2.3.1/src/library/Recommended' make[1]: *** [recommended-packages] Error 2 make[1]: se sale del directorio `/var/tmp/portage/R-2.3.1/work/R-2.3.1/src/library/Recommended' make: *** [stamp-recommended] Error 2 !!! ERROR: dev-lang/R-2.3.1 failed. Call stack: ebuild.sh, line 1545: Called dyn_compile ebuild.sh, line 940: Called src_compile R-2.3.1.ebuild, line 76: Called die !!! emake failed !!! If you need support, post the topmost build error, and the call stack if relevant. I can't see any errors at R compilation, so I believe there is a problem in the ebuild file. -------------------------------------------------- emerge info Portage 2.1.1_pre3 (default-linux/amd64/2005.0/no-multilib, gcc-4.1.1/vanilla, g libc-2.4-r3, 2.6.17-gentoo x86_64) ================================================================= System uname: 2.6.17-gentoo x86_64 AMD Athlon(tm) 64 Processor 3000+ Gentoo Base System version 1.12.1 ccache version 2.4 [enabled] app-admin/eselect-compiler: 2.0.0_rc2-r1 dev-lang/python: 2.3.5-r2, 2.4.3-r1 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: 2.4-r1 dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.18.1 sys-devel/autoconf: 2.13, 2.60 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.17 sys-devel/gcc-config: 2.0.0_rc1 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.16 ACCEPT_KEYWORDS="amd64 ~amd64" AUTOCLEAN="yes" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=athlon64 -mtune=athlon64 -ffast-math -pipe -O3 -funroll-all-loops -fpeel-loops -ftracer -funswitch-loops -ftree-vectorize -mfpmath=sse" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shu tdown /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/eselect/compiler /etc/gconf /etc/revdep-reb uild /etc/terminfo /etc/texmf/web2c" CXXFLAGS="-march=athlon64 -mtune=athlon64 -ffast-math -pipe -O3 -funroll-all-loo ps -fpeel-loops -ftracer -funswitch-loops -ftree-vectorize -mfpmath=sse" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig ccache distlocks metadata-transfer sandbox sfperms strict" GENTOO_MIRRORS="http://distfiles.gentoo.org http://distro.ibiblio.org/pub/linux/ distributions/gentoo" LC_ALL="es_ES" LINGUAS="es" MAKEOPTS="-j2" PKGDIR="/tmp" PORTAGE_RSYNC_EXTRA_OPTS="--exclude='/etc/portage/sync.exclude'" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/d istfiles' --exclude='/local' --exclude='/packages'" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="amd64 X alsa bitmap-fonts cid cli crypt dlloader dri dvd fortran gif ipv6 j peg mp3 mpeg ncurses nls nptl nptlonly opengl pam pcre pdflib perl png python qt qt4 readline reflection sdl session spell spl ssl truetype-fonts type1-fonts un icode usb xcomposite xorg xv zlib elibc_glibc input_devices_keyboard input_devic es_mouse kernel_linux linguas_es userland_GNU video_cards_radeon" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LDFLAGS
Oops. I'm sorry about the original post formatting. In addition, I didn't sent it properly because I didn't see the compilation error message: ... begin installing recommended package cluster * Installing *source* package 'cluster' ... ** libs make[3]: se ingresa al directorio `/var/tmp/portage/R-2.3.1/temp/R.INSTALL.57PM7 h/cluster/src' x86_64-pc-linux-gnu-gcc -I/var/tmp/portage/R-2.3.1/work/R-2.3.1/include -I/var/t mp/portage/R-2.3.1/work/R-2.3.1/include -I/usr/local/include -fPIC -march=at hlon64 -mtune=athlon64 -ffast-math -pipe -O3 -funroll-all-loops -fpeel-loops -ft racer -funswitch-loops -ftree-vectorize -mfpmath=sse -c clara.c -o clara.o gfortran -fPIC -g -O2 -c daisy.f -o daisy.o ... x86_64-pc-linux-gnu-gcc -shared -o cluster.so clara.o daisy.o dysta.o fanny.o i nit.o meet.o mona.o pam.o sildist.o spannel.o twins.o -lgfortran -lm -lgcc_s -L /var/tmp/portage/R-2.3.1/work/R-2.3.1/lib -lR make[3]: se sale del directorio `/var/tmp/portage/R-2.3.1/temp/R.INSTALL.57PM7h/ cluster/src' ** R ** data ** moving datasets to lazyload DB Error in factor(c(1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1), : invalid labels; length 2 should be 1 or 1 Execution halted ERROR: lazydata failed for package 'cluster' ** Removing '/var/tmp/portage/R-2.3.1/work/R-2.3.1/library/cluster' ----------------------------------------------------- Anyway, I have no idea about the origin of the problem
(In reply to comment #0) > CFLAGS="-march=athlon64 -mtune=athlon64 -ffast-math -pipe -O3 > -funroll-all-loops -fpeel-loops -ftracer -funswitch-loops > -ftree-vectorize -mfpmath=sse" > CXXFLAGS="-march=athlon64 -mtune=athlon64 -ffast-math -pipe -O3 > -funroll-all-loops -fpeel-loops -ftracer -funswitch-loops > -ftree-vectorize -mfpmath=sse" You know the drill. http://gentoo-wiki.com/Safe_Cflags In particular, -ftree-vectorize is still broken in 4.1.1. -mfpmath=sse is already the default for x86_64. -ffast-math should only be used with programs that don't need double-precision floating point math, which i'd think a statistical graphing language might just need.
Try w/ some more sane C[XX]FLAGS, as said above.
Compilation finished successfully without -ffast-math and -ftree-vectorize. Current CXXFLAGS="-march=athlon64 -mtune=athlon64 -pipe -O3 -funroll-all-loops -fpeel-loops -ftracer -funswitch-loops " Thanks
Closing then. ;)
