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Bug 133387 - dev-lang/R-2.3.0 fails to emerge
Summary: dev-lang/R-2.3.0 fails to emerge
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Other
: High normal (vote)
Assignee: Gentoo Science Related Packages
Depends on:
Reported: 2006-05-15 08:42 UTC by Thomas Veith
Modified: 2006-05-23 11:08 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


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Description Thomas Veith 2006-05-15 08:42:09 UTC
emerging R-2.3.0 fails:

x86_64-pc-linux-gnu-gcc -I/var/tmp/portage/R-2.3.0/work/R-2.3.0/include -I/var/tmp/portage/R-2.3.0/work/R-2.3.0/include  -I/usr/local/include   -fpic  -march=athlon64 -O2 -ffast-math -ftracer -pipe -fomit-frame-pointer -c pam.c -o pam.o
x86_64-pc-linux-gnu-gcc -I/var/tmp/portage/R-2.3.0/work/R-2.3.0/include -I/var/tmp/portage/R-2.3.0/work/R-2.3.0/include  -I/usr/local/include   -fpic  -march=athlon64 -O2 -ffast-math -ftracer -pipe -fomit-frame-pointer -c sildist.c -o sildist.o
x86_64-pc-linux-gnu-gcc -I/var/tmp/portage/R-2.3.0/work/R-2.3.0/include -I/var/tmp/portage/R-2.3.0/work/R-2.3.0/include  -I/usr/local/include   -fpic  -march=athlon64 -O2 -ffast-math -ftracer -pipe -fomit-frame-pointer -c spannel.c -o spannel.o
gfortran   -fpic  -g -O2 -c twins.f -o twins.o
x86_64-pc-linux-gnu-gcc -shared -L/usr/local/lib64 -o clara.o daisy.o dysta.o fanny.o init.o meet.o mona.o pam.o sildist.o spannel.o twins.o  -lgfortran -lm -lgcc_s -L/var/tmp/portage/R-2.3.0/work/R-2.3.0/lib -lR
make[3]: Leaving directory `/var/tmp/portage/R-2.3.0/temp/R.INSTALL.bziu2z/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-2.3.0/work/R-2.3.0/library/cluster'
make[2]: *** [cluster.ts] Fehler 1
make[2]: Leaving directory `/var/tmp/portage/R-2.3.0/work/R-2.3.0/src/library/Recommended'
make[1]: *** [recommended-packages] Fehler 2
make[1]: Leaving directory `/var/tmp/portage/R-2.3.0/work/R-2.3.0/src/library/Recommended'
make: *** [stamp-recommended] Fehler 2

!!! ERROR: dev-lang/R-2.3.0 failed.
Call stack:, line 1527:   Called dyn_compile, line 931:   Called src_compile
  R-2.3.0.ebuild, line 71:   Called die

!!! emake failed
!!! If you need support, post the topmost build error, and the call stack if relevant.

emerge --info:

Portage 2.1_rc1-r2 (default-linux/amd64/2006.0, gcc-4.1.0, glibc-2.4-r3, 2.6.16-gentoo-r4 x86_64)
System uname: 2.6.16-gentoo-r4 x86_64 AMD Athlon(tm) 64 X2 Dual Core Processor 4200+
Gentoo Base System version 1.12.0_pre19
distcc 2.18.3 x86_64-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled]
dev-lang/python:     2.3.5-r2, 2.4.3-r1
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     [Not Present]
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.17
sys-devel/autoconf:  2.13, 2.59-r7
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:  2.16.1-r2
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.16
ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-march=athlon64 -O2 -ffast-math -ftracer -pipe -fomit-frame-pointer"
CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/kde/3/share/config /usr/lib64/mozilla/defaults/pref /usr/share/X11/xkb /usr/share/config /var/qmail/control"
CONFIG_PROTECT_MASK="/etc/eselect/compiler /etc/gconf /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/texmf/web2c /etc/env.d"
CXXFLAGS="-march=athlon64 -O2 -ffast-math -ftracer -pipe -fomit-frame-pointer"
FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict"
LINGUAS="de en ru"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'"
PORTDIR_OVERLAY="/usr/local/portage /usr/local/sci"
USE="amd64 X a52 aac acl acpi alsa apache2 arts artworkextra atlas audiofile avi bash-completion berkdb bitmap-fonts blas bzip2 cairo caps cddb cdr cg cli clisp crypt css cups curl dbus devil doc dri dts dv dvd dvdr dvdread eds emacs emboss encode esd examples exif expat fame fbcon ffmpeg fftw firefox flac flash font-server foomaticdb fortran fpx gcj gd gdbm gif ginac glitz glut gmp gnome gnomedb gnutls gphoto2 gpm graphviz gstreamer gtk gtk2 gtkhtml guile hal howl iconv icq idn ieee1394 imagemagick imap imlib irc isdnlog java javascript jbig jpeg jpeg2k kde lapack latex lcms libcaca lj lm_sensors logitech-mouse lua lzo lzw lzw-tiff mad mcal mikmod mjpeg mmap mng motif mozdevelop mozilla mozsvg mozxmlterm mp3 mpeg msn musepack mysql nas ncurses network nfs nls nntp nptl nptlonly nvidia objc odbc offensive ogg oggvorbis opengl pam pascal pcre pda pdflib perl plotutils png postgres pppd python qhull qt quicktime quotas rdesktop readline reflection rss samba sample sbcl sblive sdl session slang smp sndfile snmp speex spell spl sql sqlite ssl subversion svg tcltk tcpd tetex theora threads tidy tiff truetype truetype-fonts type1-fonts unicode usb vcd visualization vorbis winbind wmf xbase xcomposite xine xml xml2 xmms xorg xpm xprint xscreensaver xv xvid xvmc zeroconf zlib elibc_glibc input_devices_keyboard input_devices_mouse kernel_linux linguas_de linguas_en linguas_ru userland_GNU video_cards_nvidia"
Comment 1 Marcus D. Hanwell (RETIRED) gentoo-dev 2006-05-22 06:42:39 UTC
It compiles here on amd64 without issue. You are using a masked version of GCC along with -ffast-math -ftracer, and I know -ffast-math can cause issues with GCC 3.4. With 4.1 I am not certain. You could try toning down your CFLAGS. I am currently recompiling my main system with GCC 4.1, and so when it gets there I will see if I can reproduce your error. I have a feeling it has already done R successfully though. Can anyone else reproduce?

It looks to me like the -ffast-math has made it fail one of its own tests. I only apply flags like that to specific packages.
Comment 2 Thomas Veith 2006-05-23 07:42:59 UTC
(In reply to comment #1)
> It compiles here on amd64 without issue. You are using a masked version of GCC
> along with -ffast-math -ftracer, and I know -ffast-math can cause issues with
> GCC 3.4. With 4.1 I am not certain. You could try toning down your CFLAGS. 

emerging without -ffast-math worked, thanks. 

nevertheless the bug seems strange...
Comment 3 Marcus D. Hanwell (RETIRED) gentoo-dev 2006-05-23 11:08:34 UTC
Well GCC 4.1 is very new and so does require more testing, but -ffast-math is known to have issues such as this which is why it is not on by default and why I would not apply it globally. I don't think it failed here on GCC 3.4 - I may check if I get chance but I believe it is arch dependent too.