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Bug 151908 - dev-lang/R-2.4.0 fails to emerge : lapack routines cannot be loaded
Summary: dev-lang/R-2.4.0 fails to emerge : lapack routines cannot be loaded
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Other
: High normal (vote)
Assignee: Gentoo Science Related Packages
: 151909 (view as bug list)
Depends on:
Blocks: as-needed
  Show dependency tree
Reported: 2006-10-18 22:58 UTC by Charlie Shepherd (RETIRED)
Modified: 2006-10-23 20:26 UTC (History)
0 users

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


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Description Charlie Shepherd (RETIRED) gentoo-dev 2006-10-18 22:58:02 UTC

make[5]: Leaving directory `/var/tmp/portage/dev-lang/R-2.4.0/work/R-2.4.0/src/library/grDevices/src'
make[5]: Entering directory `/var/tmp/portage/dev-lang/R-2.4.0/work/R-2.4.0/src/library/grDevices/src'
i686-pc-linux-gnu-gcc -I../../../../include -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -march=pentium4 -O2 -fomit-frame-pointer -pipe -Wall -c chull.c -o chull.o
i686-pc-linux-gnu-gcc -I../../../../include -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -march=pentium4 -O2 -fomit-frame-pointer -pipe -Wall -c devNull.c -o devNull.o
i686-pc-linux-gnu-gcc -I../../../../include -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -march=pentium4 -O2 -fomit-frame-pointer -pipe -Wall -c devPicTeX.c -o devPicTeX.o
i686-pc-linux-gnu-gcc -I../../../../include -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -march=pentium4 -O2 -fomit-frame-pointer -pipe -Wall -c devPS.c -o devPS.o
i686-pc-linux-gnu-gcc -I../../../../include -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -march=pentium4 -O2 -fomit-frame-pointer -pipe -Wall -c devQuartz.c -o devQuartz.o
i686-pc-linux-gnu-gcc -I../../../../include -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -march=pentium4 -O2 -fomit-frame-pointer -pipe -Wall -c init.c -o init.o
i686-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--sort-common -Wl,-z,now -o chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o   -L../../../../lib -lR
mkdir -p -- ../../../../library/grDevices/libs
make[5]: Leaving directory `/var/tmp/portage/dev-lang/R-2.4.0/work/R-2.4.0/src/library/grDevices/src'
make[4]: Leaving directory `/var/tmp/portage/dev-lang/R-2.4.0/work/R-2.4.0/src/library/grDevices/src'
Error in solve.default(rgb) : lapack routines cannot be loaded
In addition: Warning message:
unable to load shared library '/var/tmp/portage/dev-lang/R-2.4.0/work/R-2.4.0/modules//':
  /var/tmp/portage/dev-lang/R-2.4.0/work/R-2.4.0/lib/ undefined symbol: _gfortran_concat_string
Error: unable to load R code in package 'grDevices'
Execution halted
make[3]: *** [all] Error 1
make[3]: Leaving directory `/var/tmp/portage/dev-lang/R-2.4.0/work/R-2.4.0/src/library/grDevices'
make[2]: *** [R] Error 1
make[2]: Leaving directory `/var/tmp/portage/dev-lang/R-2.4.0/work/R-2.4.0/src/library'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/var/tmp/portage/dev-lang/R-2.4.0/work/R-2.4.0/src'
make: *** [R] Error 1

!!! ERROR: dev-lang/R-2.4.0 failed.
Call stack:, line 1568:   Called dyn_compile, line 937:   Called src_compile
  R-2.4.0.ebuild, line 76:   Called die

!!! emake failed
!!! If you need support, post the topmost build error, and the call stack if relevant.
Comment 1 Jakub Moc (RETIRED) gentoo-dev 2006-10-18 23:11:35 UTC
*** Bug 151909 has been marked as a duplicate of this bug. ***
Comment 2 Charlie Shepherd (RETIRED) gentoo-dev 2006-10-18 23:12:12 UTC
Portage 2.1.2_pre3-r4 (default-linux/x86/2006.1, gcc-4.1.1, glibc-2.5-r0, 2.6.19-rc1-mm1-badram i686)
System uname: 2.6.19-rc1-mm1-badram i686 Intel(R) Pentium(R) 4 CPU 2.80GHz
Gentoo Base System version 1.12.5
Last Sync: Wed, 18 Oct 2006 17:50:01 +0000
distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled]
ccache version 2.4 [enabled]
app-admin/eselect-compiler: [Not Present]
dev-java/java-config: 1.3.7, 2.0.30
dev-lang/python:     2.4.3-r4, 2.5-r1
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     2.4-r6
dev-util/confcache:  0.4.2-r1
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, 1.10
sys-devel/gcc-config: 1.3.13-r4
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.18
CFLAGS="-march=pentium4 -O2 -fomit-frame-pointer -pipe -Wall"
CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/texmf/web2c"
CXXFLAGS="-march=pentium4 -O2 -fomit-frame-pointer -pipe -Wall"
FEATURES="autoconfig candy ccache collision-protect confcache distlocks metadata-transfer nodoc noinfo parallel-fetch sandbox sfperms strict stricter userpriv usersandbox"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--sort-common -Wl,-z,now"
LINGUAS="en en_GB"
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 /home/chaza/devship/overlay /usr/portage/local/layman/liquidx /usr/portage/local/layman/vmware /usr/portage/local/layman/sunrise /usr/portage/local/layman/liquidx /usr/portage/local/layman/vmware /usr/portage/local/layman/sunrise /home/chaza/devship/overlay"
USE="x86 7zip X aac acl acpi alsa amd amuled ansi apache2 arts asf audacious bash-completion bzip2 cap ccache cdda cddb cdinstall cdparanoia cdr cdrom cgi chroot ck-plus cracklib crypt css cups curl curlwrappers dbus dhcp dillo dio directfb djbfft dnd dri dv dvdread edl elibc_glibc encode erandom exif ext-png ext-zlib extensions fastcgi fbcon fbsplash ffmpeg firefox flash fortify fortran fpx geoip gif gimp gimpprint glibc-omitfp glitz glut gnuplot gpm graphviz gs gsl gtk gtk2 hal hardenedphp hbci hdf iconv icq ide idl image imap imlib imlib2 infopipe ipv6 irda irmc j2ee jabber javacomm javamail javascript jbig jboss jce jms jmx joystick jpeg jpeg2k jta jython kakasi kde kdehiddenvisibility kdenewldflags kdexdeltas kerberos kernel_linux kqemu krb4 latex lcms leim libclamav libdsk libgd libgda libsamplerate libwww linguas_en linguas_en_GB live lua lzo lzw m17n-lib mad maildir matroska mbox migemo mime mixer mjpeg mmap mmx mmxext mono mozcalendar mozdevelop mozsvg mozxmlterm mp3 mpeg mpi mplayer msn mule multislot music mysql mysqli mythtv nagios-dns nagios-ntp nagios-ping nagios-ssh ncurses net netcdf network neural nis nls no-old-linux nomalloccheck nowin nptl nptlonly ntlm ntpl oav objc ocaml offensive ogg oggvorbis openal opengl oscar ospfapi pam parse-clocks pcap pcntl pcre pdf perl pertty pg-hier pg-intdatetime pg-vacuumdelay php physfs pic plotutils png portaudio povray ppds pri print procmail python qa qt3 qt4 quicktime quotas quotes readline real reiser4 reiserfs risky rogue rplay sdl seamonkey semanticfix session sftplogging shared sharedmem slp smime sndfile snortsam socks5 sox sse sse-filters sse2 ssl suspend2 svga symlink sysvipc szip tcltk tcpd tga theora tidy tk transcode truetype uim unicode usb userland_GNU v4l v4l2 vcd vda video_cards_i810 videos virus-scan vorbis wddx webdav wifi win32codecs winbind wma wmf wxwindows xanim xchatdccserver xchattext xcomposite xface xgetdefault xine xml xmlreader xmlrpc xmlwriter xmms xorg xosd xpm xprint xrandr xscreensaver xsettings xv xvid xvmc yahoo yaz yp yv12 zaptel zeo zlib zvbi"
Comment 3 Markus Dittrich (RETIRED) gentoo-dev 2006-10-19 07:17:27 UTC
(In reply to comment #2)
> LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--sort-common -Wl,-z,now"

Please try without the "-Wl,--as-needed".

Comment 4 Charlie Shepherd (RETIRED) gentoo-dev 2006-10-23 04:51:53 UTC
(In reply to comment #3)
> Please try without the "-Wl,--as-needed".

It works without --as-needed

Comment 5 Markus Dittrich (RETIRED) gentoo-dev 2006-10-23 20:26:52 UTC
(In reply to comment #4)
> (In reply to comment #3)
> > Please try without the "-Wl,--as-needed".
> It works without --as-needed

Thanks for testing! I just committed a patch to portage cvs
that should take care of this. Please re-open the bug should
you continue to have problems with this.