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Bug 122465 - dev-lang/R-2.2.1 fails
Summary: dev-lang/R-2.2.1 fails
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: x86 Linux
: High normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords: InVCS
Depends on:
Blocks:
 
Reported: 2006-02-11 08:22 UTC by Patrizio Bassi
Modified: 2006-05-22 12:36 UTC (History)
1 user (show)

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


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Description Patrizio Bassi 2006-02-11 08:22:07 UTC
urine                             text    html    latex
  var.linear                        text    html    latex   example
  wool                              text    html    latex
** 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
Comment 1 Marcus D. Hanwell (RETIRED) gentoo-dev 2006-04-09 18:31:06 UTC
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.
Comment 2 Patrizio Bassi 2006-04-10 03:27:12 UTC
with your suggested flags...same error.

plus...is that possibile to bypass all docs? it lasts more the docs section than the real compilation
Comment 3 Patrizio Bassi 2006-04-12 00:57:45 UTC
after deleting my LDFLAGS too it worked.

please unset LDFLAGS, this package seems too easy to break
Comment 4 Marcus D. Hanwell (RETIRED) gentoo-dev 2006-04-12 01:19:15 UTC
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.
Comment 5 Patrizio Bassi 2006-04-12 01:53:55 UTC
i suspect the problem is with -bdirect if that can help you.
Comment 6 Marcus D. Hanwell (RETIRED) gentoo-dev 2006-04-15 07:11:08 UTC
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...
Comment 7 Patrizio Bassi 2006-04-15 08:19:13 UTC
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.
Comment 8 Danny van Dyk (RETIRED) gentoo-dev 2006-05-10 14:53:09 UTC
R ebuilds now have

filter-ldflags -Wl,-Bdirect -Bdirect

to work around this bug. InCVS, FIXED.
Comment 9 Martin Mokrejš 2006-05-22 12:36:20 UTC
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 ...