Bugzilla Bug 122465

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** building package indices ...
* DONE (boot)
cat: /var/tmp/portage/R-2.2.1/work/R-2.2.1/library/*/CONTENTS: No such file or
directory
begin installing recommended package cluster
* Installing *source* package 'cluster' ...
** libs
make[3]: Entering directory
`/var/tmp/portage/R-2.2.1/temp/R.INSTALL.CgyC7X/cluster/src'
i686-pc-linux-gnu-gcc -I/var/tmp/portage/R-2.2.1/work/R-2.2.1/include 
-I/usr/local/include   -fPIC  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
-D_LARGEFILE_SOURCE -O3 -mtune=pentium3 -march=pentium3 -pipe
-fomit-frame-pointer -mmmx -msse -ffast-math -c clara.c -o clara.o
gfortran   -fPIC  -g -O2 -c daisy.f -o daisy.o
gfortran   -fPIC  -g -O2 -c dysta.f -o dysta.o
gfortran   -fPIC  -g -O2 -c fanny.f -o fanny.o
gfortran   -fPIC  -g -O2 -c meet.f -o meet.o
gfortran   -fPIC  -g -O2 -c mona.f -o mona.o
i686-pc-linux-gnu-gcc -I/var/tmp/portage/R-2.2.1/work/R-2.2.1/include 
-I/usr/local/include   -fPIC  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
-D_LARGEFILE_SOURCE -O3 -mtune=pentium3 -march=pentium3 -pipe
-fomit-frame-pointer -mmmx -msse -ffast-math -c pam.c -o pam.o
i686-pc-linux-gnu-gcc -I/var/tmp/portage/R-2.2.1/work/R-2.2.1/include 
-I/usr/local/include   -fPIC  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
-D_LARGEFILE_SOURCE -O3 -mtune=pentium3 -march=pentium3 -pipe
-fomit-frame-pointer -mmmx -msse -ffast-math -c spannel.c -o spannel.o
gfortran   -fPIC  -g -O2 -c twins.f -o twins.o
i686-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--sort-common -Wl,--enable-new-dtags
-Wl,-Bdirect -Wl,--as-needed -Wl,-hashvals -Wl,-zdynsort -o cluster.so clara.o
daisy.o dysta.o fanny.o meet.o mona.o pam.o spannel.o twins.o  -lgfortran -lm
-lgcc_s -L/var/tmp/portage/R-2.2.1/work/R-2.2.1/lib -lR
make[3]: Leaving directory
`/var/tmp/portage/R-2.2.1/temp/R.INSTALL.CgyC7X/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-2.2.1/work/R-2.2.1/library/cluster'
make[2]: *** [cluster.ts] Error 1
make[2]: Leaving directory
`/var/tmp/portage/R-2.2.1/work/R-2.2.1/src/library/Recommended'
make[1]: *** [recommended-packages] Error 2
make[1]: Leaving directory
`/var/tmp/portage/R-2.2.1/work/R-2.2.1/src/library/Recommended'
make: *** [stamp-recommended] Error 2

!!! ERROR: dev-lang/R-2.2.1 failed.
Call stack:
  ebuild.sh, line 1894:   Called dyn_compile
  ebuild.sh, line 941:   Called src_compile

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

emerge info
Portage 2.1_pre4-r1 (default-linux/x86/2005.1, gcc-4.0.2, glibc-2.3.6-r5,
2.6.16-rc2-git1 i686)
=================================================================
System uname: 2.6.16-rc2-git1 i686 Pentium III (Katmai)
Gentoo Base System version 1.12.0_pre15
distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632)
[disabled]
ccache version 2.4 [disabled]
dev-lang/python:     2.4.2
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-r1
sys-devel/binutils:  2.16.91.0.5-r2
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.11-r3
ACCEPT_KEYWORDS="x86 ~x86"
AUTOCLEAN="yes"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O3 -mtune=pentium3 -march=pentium3 -pipe -fomit-frame-pointer -mmmx
-msse -ffast-math"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/mail/dspam /opt/openjms/config
/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/lib/X11/xkb
/usr/lib/mozilla/defaults/pref /usr/share/config /var/bind /var/qmail/control
/var/run/dspam"
CONFIG_PROTECT_MASK="/etc/gconf /etc/splash /etc/terminfo /etc/texmf/web2c
/etc/env.d"
CXXFLAGS="-O3 -mtune=pentium3 -march=pentium3 -pipe -fomit-frame-pointer -mmmx
-msse -ffast-math"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks fixpackages sandbox sfperms strict"
GENTOO_MIRRORS="http://gentoo.ngi.it
http://www.die.unipd.it/pub/Linux/distributions/gentoo-sources/"
LANG="it_IT.utf8"
LC_ALL="it_IT.utf8"
LDFLAGS="-Wl,-O1 -Wl,--sort-common -Wl,--enable-new-dtags -Wl,-Bdirect
-Wl,--as-needed -Wl,-hashvals -Wl,-zdynsort"
LINGUAS="it"
PKGDIR="/usr/portage/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="x86 X X509 Xaw3d a52 aac aalib accessibility acl acpi activefilter adns
alsa apache2 apm arts asf audiofile avi bash-completion berkdb bidi
bitmap-fonts bootsplash browserplugin bzip2 cairo caps cdda cddb cdio
cdparanoia cdr cgi chroot clamav cli client codecs crypt css cups curl dba dbus
dga dhcp directfb djbfft dri edl eds emboss encode ethereal exif expat
extraengine faac faad fam fbcon ffmpeg fftw firefox flac flash foomaticdb
foreign-package fortran gcj gd gdbm geometry ggi gif gimp gimpprint glut glx
gnokii gnome gphoto2 gpm graphviz gs gstreamer gtk gtk2 gtkhtml guile h264 hal
iconv idea idn imagemagick imap imlib innodb ipod irda irmc jack java
javascript jikes jit joystick jpeg jpeg2k junit justify kde kdeenablefinal
kerberos kqemu lame lcd lcms ldap libcaca libclamav libg++ libgda libusb libwww
lirc live lm_sensors lua lzo mad mailwrapper matroska md5sum mdb mikmod mime
mmx mmx2 mmxext mng mono motif mozcalendar mozdevelop mozilla mozsvg mozxmlterm
mp3 mp4live mpeg mpeg2 mpeg4 mplayer mysql mysqli mythtv nagios-dns nagios-ntp
nagios-ping nagios-ssh ncurses neXt network ngui nls nntp no_wxgtk1 nobsh nopie
nossp noxalan nptl nptlonly nsplugin oav odbc ogg oggvorbis openal opengl
operanom2 oss pam pcre pda pdf pdflib pdo pear perl php png pnp postgres ppds
pthreads python qemu-fast qhull qt quicktime quotas readline real rrdtool rtc
ruby samba scanner sdl server session sftplogging sguil slang slp snortsam soap
sockets socks5 softmmu softquota spamassassin speex spell sqlite3 sse ssl
subject-rewrite svg svga tcltk tcpd tetex tga theora tiff tokenizer truetype
truetype-fonts trusted type1-fonts unicode usb userlocales vidix vorbis
win32codecs wmf wsconvert wxwindows x264 xanim xchatdccserver xchattext xine
xinerama xml xml2 xmlrpc xmms xosd xpm xprint xsl xv xvid xvm xvmc zlib
elibc_glibc kernel_linux linguas_it userland_GNU"
Unset:  ASFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, MAKEOPTS

Have you tried it with more conservative CFLAGS? -march=pentium3 -pipe -O2
would be a good start. I am unable to reproduce the error you have seen even on
my experimental system using GCC 4.1. As it is GCC 4 is still masked and some
of the CFLAGS you are using are aggressive.

with your suggested flags...same error.

plus...is that possibile to bypass all docs? it lasts more the docs section
than the real compilation

after deleting my LDFLAGS too it worked.

please unset LDFLAGS, this package seems too easy to break

Again with less aggressive LDFLAGS it will probably be fine, but most do not
play with these. I will try to find a little time to experiment this weekend. I
would rather not simply unset them and need to check the ramifications for
archs which might need to set things here.

i suspect the problem is with -bdirect if that can help you.

I don't have the time to take care of this right now and am off on holiday for
a couple of weeks. We cannot simply unset LDFLAGS AFAIK. The flags you are
using are fairly experimental and very few users have this type of stuff set. I
would like opinions on how best to deal with this - are we going to have to
start restricting LDFLAGS and various other bits now too??? We cannot protect
people from every flag they might choose to apply globally to their systems...

you're right, but i add this:

generally those flags are safe. with generally i mean that my world is about
3700 packages and i have a really stable system.

when i notice a problem with a certain package i use to fill a bug.
you can't protect from all bad flag, this is true, but you can protect from
known-not-working-ones.

R ebuilds now have

filter-ldflags -Wl,-Bdirect -Bdirect

to work around this bug. InCVS, FIXED.

Please re-open, I get at the moment:

>>> checking ebuild checksums ;-)
>>> checking auxfile checksums ;-)
>>> checking miscfile checksums ;-)
>>> checking R-2.3.0.tar.gz ;-)
 * You need one of these Fortran Compilers: gfortran g77 f2c
 * Installed are:  g77
/usr/portage/dev-lang/R/R-2.3.0.ebuild: line 48: filter-ldflags: command not
found
>>> Unpacking source...
>>> Unpacking R-2.3.0.tar.gz to /var/tmp/portage/R-2.3.0/work
revdep-rebuild
 * Applying patches for selected FORTRAN compiler: g77
>>> Source unpacked.
>>> Compiling source in /var/tmp/portage/R-2.3.0/work/R-2.3.0 ...