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Bug 140716 - dev-lang/R-2.3.1 compilation fails on AMD64
Summary: dev-lang/R-2.3.1 compilation fails on AMD64
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: AMD64 Linux
: High normal (vote)
Assignee: Gentoo Linux bug wranglers
Depends on:
Reported: 2006-07-16 18:03 UTC by Nestor Arocha
Modified: 2006-07-17 02:34 UTC (History)
0 users

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


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Description Nestor Arocha 2006-07-16 18:03:03 UTC
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 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                           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:, line 1545:   Called dyn_compile, 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-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"
CFLAGS="-march=athlon64 -mtune=athlon64 -ffast-math -pipe -O3 -funroll-all-loops                                                                                            -fpeel-loops -ftracer -funswitch-loops -ftree-vectorize -mfpmath=sse"
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"
FEATURES="autoconfig ccache distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="                                                                                           distributions/gentoo"
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'"
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"
Comment 1 Nestor Arocha 2006-07-16 18:23:20 UTC
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 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

Comment 2 Ryan Hill (RETIRED) gentoo-dev 2006-07-16 18:33:24 UTC
(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.

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.
Comment 3 Jakub Moc (RETIRED) gentoo-dev 2006-07-16 23:48:41 UTC
Try w/ some more sane C[XX]FLAGS, as said above.
Comment 4 Nestor Arocha 2006-07-17 02:30:11 UTC
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 "

Comment 5 Jakub Moc (RETIRED) gentoo-dev 2006-07-17 02:34:21 UTC
Closing then. ;)