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Bug#: 195251
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Status: RESOLVED
Resolution: FIXED
Assigned To: Jeffrey Gardner <je_fro@gentoo.org>
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Reporter: Juergen Rose <rose@rz.uni-potsdam.de>
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Filename Description Type Creator Created Size Actions
ncbi-tools-20070826-r1.tar.gz fixed ebuild including patches patch Till Korten 2008-03-16 03:56 0000 5.21 KB Details | Diff
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Bug 195251 depends on: Show dependency tree
Bug 195251 blocks:
Votes: 0    Show votes for this bug    Vote for this bug

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Description:   Opened: 2007-10-09 14:07 0000 
gcc -pipe -o Psequin -I. -O3 -I../include  -L../lib -I/usr/X11R6/include
-L/usr/X11R6/lib64 -L/usr/X11R6/lib -DW
IN_MOTIF -UINTERNAL_NCBI_SEQUIN sequin1.c sequin2.c sequin3.c sequin4.c
sequin5.c sequin6.c  sequin7.c sequin8.c
 sequin9.c sequin10.c sequinx.c  -lncbicn3d -lddvlib -lvibnet -lncbidesk
-lblastapi -lblast -lncbimmdb  -lncbitx
c2 -lncbiid1 -lnetblast -lncbitool -lblastcompadj -lncbimla  -lncbiNacc
-lnetentr -lnetcli -lncbicdr -lvibrant -
lncbiobj -lncbi -L/usr/X11R6/lib64 -L/usr/X11R6/lib -lXmu -Wl,-Bstatic -lXm
-Wl,-Bdynamic -lXt -lSM -lICE -lXext
 -lXp -lX11 -ldl -lm
sequin3.c: In function 'AddBlastTag':
sequin3.c:16648: warning: cast from pointer to integer of different size
sequin3.c: In function 'CommonAddBlastToSeqAnnot':
sequin3.c:16673: warning: cast to pointer from integer of different size
sequin6.c:260: warning: useless storage class specifier in empty declaration
sequin9.c: In function 'UpdatePairToUpdateTitlesDialog':
sequin9.c:13997: warning: large integer implicitly truncated to unsigned type
sequin9.c:14018: warning: large integer implicitly truncated to unsigned type
sequin9.c:14038: warning: large integer implicitly truncated to unsigned type
sequin9.c:14053: warning: large integer implicitly truncated to unsigned type
../lib/libncbi.a(ncbifile.o): In function `Nlm_TmpNam':
ncbifile.c:(.text+0x156): warning: the use of `tempnam' is dangerous, better
use `mkstemp'
/usr/X11R6/lib64/libXm.a(TextIn.o): In function `SelfInsert':
(.text+0x8604): undefined reference to `XftTextExtentsUtf8'
...
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x546): undefined reference to `png_destroy_read_struct'
collect2: ld returned 1 exit status


Reproducible: Always

------- Comment #1 From Jakub Moc (RETIRED) 2007-10-09 17:18:59 0000 ------- 
There's no ncbi-tools-20070826 anywhere in the official tree.

------- Comment #2 From Juergen Rose 2007-10-09 18:12:44 0000 ------- 
I have
/usr/portage/local/layman/science/sci-biology/ncbi-tools/ncbi-tools-20070826.ebuild

So I assume that ncbi-tools-20070826 is from the science overlay.

------- Comment #3 From Jakub Moc (RETIRED) 2007-10-09 18:15:21 0000 ------- 
Then note this in bug summary, I'm definitely not going to check out every
overlay out there to find out where did you take the ebuild.

------- Comment #4 From Jeffrey Gardner 2007-10-14 04:12:05 0000 ------- 
Juergen,
Are you still having trouble with the version I've put in the official portage
tree (ncbi-tools-20070826)?

------- Comment #5 From Patrizio Bassi 2007-10-14 12:20:39 0000 ------- 
i have this in official
gcc -pipe -o Psequin -I. -O3 -I../include  -L../lib -I/usr/X11R6/include
-L/usr/X11R6/lib64 -L/usr/X11R6/lib -DWIN_MOTIF -UINTERNAL_NCBI_SEQUIN
sequin1.c sequin2.c sequin3.c sequin4.c sequin5.c sequin6.c  sequin7.c
sequin8.c sequin9.c sequin10.c sequinx.c  -lncbicn3d -lddvlib -lvibnet
-lncbidesk -lblastapi -lblast -lncbimmdb  -lncbitxc2 -lncbiid1 -lnetblast
-lncbitool -lblastcompadj -lncbimla  -lncbiNacc -lnetentr -lnetcli -lncbicdr
-lvibrant -lncbiobj -lncbi -L/usr/X11R6/lib64 -L/usr/X11R6/lib -lXmu
-Wl,-Bstatic -lXm -Wl,-Bdynamic -lXt -lSM -lICE -lXext -lXp -lX11 -ldl -lm
sequin3.c: In function ‘AddBlastTag’:
sequin3.c:16648: warning: cast from pointer to integer of different size
sequin3.c: In function ‘CommonAddBlastToSeqAnnot’:
sequin3.c:16673: warning: cast to pointer from integer of different size
sequin6.c:260: warning: useless storage class specifier in empty declaration
sequin9.c: In function ‘UpdatePairToUpdateTitlesDialog’:
sequin9.c:13997: warning: large integer implicitly truncated to unsigned type
sequin9.c:14018: warning: large integer implicitly truncated to unsigned type
sequin9.c:14038: warning: large integer implicitly truncated to unsigned type
sequin9.c:14053: warning: large integer implicitly truncated to unsigned type
../lib/libncbi.a(ncbifile.o): In function `Nlm_TmpNam':
ncbifile.c:(.text+0x156): warning: the use of `tempnam' is dangerous, better
use `mkstemp'
/usr/X11R6/lib64/libXm.a(TextIn.o): In function `SelfInsert':
(.text+0x55f1): undefined reference to `XftTextExtentsUtf8'
/usr/X11R6/lib64/libXm.a(TextOut.o): In function `FindWidth':
(.text+0x356): undefined reference to `XftTextExtentsUtf8'
/usr/X11R6/lib64/libXm.a(TextOut.o): In function `FindWidth':
(.text+0x6d3): undefined reference to `XftTextExtentsUtf8'
/usr/X11R6/lib64/libXm.a(TextOut.o): In function `FindHeight':
(.text+0x22fe): undefined reference to `XftTextExtentsUtf8'
/usr/X11R6/lib64/libXm.a(TextOut.o): In function `FindHeight':
(.text+0x2567): undefined reference to `XftTextExtentsUtf8'
/usr/X11R6/lib64/libXm.a(XmString.o):(.text+0xb09): more undefined references
to `XftTextExtentsUtf8' follow
/usr/X11R6/lib64/libXm.a(XmString.o): In function `SubStringPosition':
(.text+0xf930): undefined reference to `XftTextExtents16'
/usr/X11R6/lib64/libXm.a(XmString.o): In function `SubStringPosition':
(.text+0xf954): undefined reference to `XftTextExtents16'
/usr/X11R6/lib64/libXm.a(TextF.o): In function `FindPixelLength':
(.text+0x3a5): undefined reference to `XftTextExtentsUtf8'
/usr/X11R6/lib64/libXm.a(TextF.o): In function `FindPixelLength':
(.text+0x41a): undefined reference to `XftTextExtentsUtf8'
/usr/X11R6/lib64/libXm.a(TextF.o): In function `FindPixelLength':
(.text+0x485): undefined reference to `XftTextExtentsUtf8'
/usr/X11R6/lib64/libXm.a(TextF.o): In function `PrintableString':
(.text+0x178b): undefined reference to `XftTextExtentsUtf8'
/usr/X11R6/lib64/libXm.a(TextF.o): In function `TextFieldResetIC':
(.text+0xac5e): undefined reference to `XftTextExtentsUtf8'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawCreate':
(.text+0x8fc): undefined reference to `XftDrawCreate'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawCreate':
(.text+0x99b): undefined reference to `XftDrawCreateBitmap'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawString':
(.text+0xad8): undefined reference to `XftDrawRect'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawString':
(.text+0xb58): undefined reference to `XftDrawString16'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawString':
(.text+0xb91): undefined reference to `XftDrawString32'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawString':
(.text+0xbcd): undefined reference to `XftDrawStringUtf8'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawString':
(.text+0xbf8): undefined reference to `XftTextExtents16'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawString':
(.text+0xc27): undefined reference to `XftTextExtentsUtf8'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawString':
(.text+0xcea): undefined reference to `XftTextExtents32'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawString2':
(.text+0xe9d): undefined reference to `XftDrawString16'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawString2':
(.text+0xece): undefined reference to `XftDrawString32'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawString2':
(.text+0xeff): undefined reference to `XftDrawStringUtf8'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `FreeRendition':
(.text+0x1a69): undefined reference to `XftFontClose'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `FreeRendition':
(.text+0x1a8e): undefined reference to `FcPatternDestroy'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `ValidateAndLoadFont':
(.text+0x237f): undefined reference to `FcPatternCreate'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `ValidateAndLoadFont':
(.text+0x23a4): undefined reference to `FcPatternAddString'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `ValidateAndLoadFont':
(.text+0x23c2): undefined reference to `FcPatternAddString'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `ValidateAndLoadFont':
(.text+0x23e0): undefined reference to `FcPatternAddString'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `ValidateAndLoadFont':
(.text+0x23fe): undefined reference to `FcPatternAddString'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `ValidateAndLoadFont':
(.text+0x2463): undefined reference to `XftFontMatch'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `ValidateAndLoadFont':
(.text+0x2474): undefined reference to `XftFontOpenPattern'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `ValidateAndLoadFont':
(.text+0x2500): undefined reference to `FcPatternAddInteger'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `ValidateAndLoadFont':
(.text+0x251a): undefined reference to `FcPatternAddInteger'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `ValidateAndLoadFont':
(.text+0x2534): undefined reference to `FcPatternAddInteger'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `ValidateAndLoadFont':
(.text+0x254e): undefined reference to `FcPatternAddInteger'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `ValidateAndLoadFont':
(.text+0x2568): undefined reference to `FcPatternAddInteger'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftDrawDestroy':
(.text+0x84a): undefined reference to `XftDrawDestroy'
/usr/X11R6/lib64/libXm.a(XmRenderT.o): In function `_XmXftSetClipRectangles':
(.text+0x9e5): undefined reference to `XftDrawSetClipRectangles'
/usr/X11R6/lib64/libXm.a(Jpeg.o): In function `load_jpeg':
(.text+0x87): undefined reference to `jpeg_std_error'
/usr/X11R6/lib64/libXm.a(Jpeg.o): In function `load_jpeg':
(.text+0xb5): undefined reference to `jpeg_destroy_decompress'
/usr/X11R6/lib64/libXm.a(Jpeg.o): In function `load_jpeg':
(.text+0xdb): undefined reference to `jpeg_CreateDecompress'
/usr/X11R6/lib64/libXm.a(Jpeg.o): In function `load_jpeg':
(.text+0xe8): undefined reference to `jpeg_stdio_src'
/usr/X11R6/lib64/libXm.a(Jpeg.o): In function `load_jpeg':
(.text+0xf5): undefined reference to `jpeg_read_header'
/usr/X11R6/lib64/libXm.a(Jpeg.o): In function `load_jpeg':
(.text+0xfd): undefined reference to `jpeg_calc_output_dimensions'
/usr/X11R6/lib64/libXm.a(Jpeg.o): In function `load_jpeg':
(.text+0x105): undefined reference to `jpeg_start_decompress'
/usr/X11R6/lib64/libXm.a(Jpeg.o): In function `load_jpeg':
(.text+0x16a): undefined reference to `jpeg_read_scanlines'
/usr/X11R6/lib64/libXm.a(Jpeg.o): In function `load_jpeg':
(.text+0x1a1): undefined reference to `jpeg_finish_decompress'
/usr/X11R6/lib64/libXm.a(Jpeg.o): In function `load_jpeg':
(.text+0x1a9): undefined reference to `jpeg_destroy_decompress'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x62): undefined reference to `png_check_sig'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x7a): undefined reference to `png_create_read_struct'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x8f): undefined reference to `png_create_info_struct'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0xad): undefined reference to `png_destroy_read_struct'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0xf0): undefined reference to `png_destroy_read_struct'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x115): undefined reference to `png_init_io'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x127): undefined reference to `png_set_sig_bytes'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x13c): undefined reference to `png_read_info'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x188): undefined reference to `png_get_IHDR'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x1e7): undefined reference to `png_get_valid'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x231): undefined reference to `png_get_valid'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x27a): undefined reference to `png_get_gAMA'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x298): undefined reference to `png_read_update_info'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x2ad): undefined reference to `png_get_rowbytes'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x2d0): undefined reference to `png_get_channels'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x316): undefined reference to `png_destroy_read_struct'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x32d): undefined reference to `png_set_gray_to_rgb'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':
(.text+0x33f): undefined reference to `png_set_expand'
/usr/X11R6/lib64/libXm.a(Png.o): In function `png_load_file':

------- Comment #6 From Patrizio Bassi 2007-10-14 12:21:25 0000 ------- 
...forgot...mine have --as-needed

Portage 2.1.3.13 (default-linux/amd64/2007.0, gcc-4.2.2, glibc-2.6.1-r0,
2.6.23.1 x86_64)
=================================================================
System uname: 2.6.23.1 x86_64 Intel(R) Core(TM)2 CPU 6300 @ 1.86GHz
Timestamp of tree: Sun, 14 Oct 2007 09:30:01 +0000
distcc 2.18.3 x86_64-pc-linux-gnu (protocols 1 and 2) (default port 3632)
[disabled]
ccache version 2.4 [disabled]
app-shells/bash:     3.2_p17-r1
dev-java/java-config: 1.3.7, 2.1.2-r1
dev-lang/python:     2.5.1-r2
dev-python/pycrypto: 2.0.1-r6
dev-util/ccache:     2.4-r7
sys-apps/baselayout: 1.12.10-r5
sys-apps/sandbox:    1.2.18.1
sys-devel/autoconf:  2.13, 2.61-r1
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/binutils:  2.18.50.0.1
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   1.5.24
virtual/os-headers:  2.6.23
ACCEPT_KEYWORDS="amd64 ~amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O3 -pipe -march=nocona -mtune=nocona -fomit-frame-pointer -mmmx -msse
-msse2 -msse3 -mfpmath=sse"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/mail/dspam /opt/openjms/config /usr/kde/3.5/env
/usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/lib/mozilla/defaults/pref
/usr/share/config /var/run/dspam"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/eselect/compiler
/etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/
/etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/splash /etc/terminfo
/etc/texmf/web2c /etc/udev/rules.d"
CXXFLAGS="-O3 -pipe -march=nocona -mtune=nocona -fomit-frame-pointer -mmmx
-msse -msse2 -msse3 -mfpmath=sse"
DISTDIR="/usr/portage/distfiles"
FEATURES="distlocks fixpackages metadata-transfer parallel-fetch sandbox
sfperms strict unmerge-orphans"
GENTOO_MIRRORS="http://distfiles.gentoo.org
http://distro.ibiblio.org/pub/linux/distributions/gentoo"
LANG="39"
LC_ALL="it_IT.utf8"
LDFLAGS="-Wl,-O1 -Wl,--sort-common -Wl,--enable-new-dtags -Wl,--as-needed
-Wl,--hash-style=both"
LINGUAS="it"
MAKEOPTS="-j4"
PKGDIR="/usr/portage/packages"
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
--filter=H_**/files/digest-*"
PORTAGE_TMPDIR="/mnt/Dati/Gentoo/tmp/"
PORTDIR="/mnt/Dati/Gentoo/portage/"
PORTDIR_OVERLAY="/usr/local/portage/myportage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="64bit 7zip X X509 Xaw3d a52 aac aalib accessibility ace acl acpi
activefilter adns aiglx aio alsa amd amd64 amr amrr amuled ao aoss apache2 arj
asf aspnet2 async atk audacious audiofile authfile automount bash-completion
berkdb bidi binary-drivers bitmap-fonts bittorrent blas bootsplash
browserplugin bzip2 cairo calendar caps cdda cddb cdio cdparanoia cdr cgi
charconv chardet chroot ciao clamav clearcase cli client codecs corba cracklib
crypt cscope css ctype cups curl cvs daemon dar64 dba dbus depth32 dga dhcp dio
directfb diskio divx djbfft dmi dri dvd dvdr dvdread edl encode ethereal exif
expat extraengine faac faad fam fastbuild fbcon ffmpeg fftw firefox flac flash
foreign-package fortran ftp gcj gd gdbm geometry ggi gif gimp gimpprint
glibc-omitfp glitz glut glx gnokii gnome gnutls gphoto2 gpm graphviz gs gtk
gtk2 gtkhtml guile h264 hal hddtemp iconv idea idn imagemagick imap innodb ipod
ipv6 irda irmc isdnlog jack java java5 javamail javascript jikes jit joystick
jpeg jpeg2k junit justify kde kdeenablefinal kdehiddenvisibility kerberos kqemu
lame lapack lcd lcms ldap libcaca libclamav libgda libusb lirc live lm_sensors
lua lzo mad mailwrapper matroska md5sum mdb mhash midi mikmod mime mmx mmx2
mmxext mng mono mozcalendar mozdevelop mozilla mozsvg mozxmlterm mp3 mp4
mp4live mpeg mpeg2 mpeg4 mplayer mpm-prefork msn msnextras mudflap musepack
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 nv nvidia oav odbc ogg openal opengl openmp openssl operanom2 pam pcre
pda pdf pdo pear perl php pmu png pnp postgres pppd pthreads pulseaudio python
qemu-fast qhull qt3 qt3support qt4 quicktime quotas readline reflection rrdtool
rtc ruby samba scanner sdl server session sftplogging sguil slang slp smp
snortsam soap sockets socks5 softmmu softquota spamassassin speex spell spl
sqlite3 sse sse2 sse3 ssl ssse3 subject-rewrite svg tao tcltk tcpd tetex tga
theora tiff tokenizer truetype truetype-fonts trusted type1-fonts unicode usb
userlocales vorbis wma wmf wmv wsconvert wxwindows x264 xanim xchatdccserver
xchattext xcomposite xine xinerama xml xml2 xmlrpc xorg xosd xpm xprint xsl xv
xvid xvm xvmc zlib" ALSA_CARDS="hda-intel" ALSA_PCM_PLUGINS="adpcm alaw asym
copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat
linear meter mulaw multi null plug rate route share shm softvol" ELIBC="glibc"
INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz
cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="it"
USERLAND="GNU" VIDEO_CARDS="fbdev vesa vga nv nvidia"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, PORTAGE_COMPRESS,
PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

------- Comment #7 From Jeffrey Gardner 2007-10-14 20:14:43 0000 ------- 
Yeah, you've got some aggressive CFLAGS and LDFLAGS. Perhaps that's the issue.
Anyway, try a revdep-rebuild and have a look at "motif-config -l". Mine is:

$ motif-config -l
[1] lesstif-2.1
[2] openmotif-2.2 *
[3] openmotif-2.3

------- Comment #8 From Patrizio Bassi 2007-10-14 20:30:36 0000 ------- 
mine:

motif-config -l
[1] openmotif-2.3 *

my flags are aggressive but safe, really. i have 4000 packets like this.
the problem is with this packet i suspect as-needed is adding the png problems,
but motif one are common to the author of this bug

------- Comment #9 From Juergen Rose 2007-10-15 10:08:40 0000 ------- 
I still have the same problems on all (two) x86_64 systems, the i686 systems
are fine.

At both x86_64 systems motif-config shows:
root@grizzly:/root(125)# motif-config -l
[1] openmotif-2.3 *

On the i686 motif-config shows:
root@cheetah:/root(40)# motif-config -l
[1] openmotif-2.2 *
[2] openmotif-2.3


   Juergen

------- Comment #10 From Patrizio Bassi 2007-10-15 11:18:10 0000 ------- 
can you try to switch to 2.3 on x86 too?

probably 2.3 introduced the issue

------- Comment #11 From Jeffrey Gardner 2007-10-15 15:04:25 0000 ------- 
I think running revdep-rebuild will fix this for you guys.

------- Comment #12 From Juergen Rose 2007-10-15 20:04:02 0000 ------- 
revdep-rebuild does not fix the problem for me.

------- Comment #13 From Patrizio Bassi 2007-10-15 20:22:09 0000 ------- 
...neither for me...

------- Comment #14 From Martin Mokrejš 2008-03-01 12:13:04 0000 ------- 
Recompile all versions of openmotif* and lesstif* or keep just one, freshly
recompiled.

------- Comment #15 From Patrizio Bassi 2008-03-01 13:24:54 0000 ------- 
tried...no way...

------- Comment #16 From Till Korten 2008-03-15 19:15:35 0000 ------- 
same here
openmotif was freshly pulled in by ncbi-tools...
emerge --info:
Portage 2.1.4.4 (default-linux/amd64/2007.0/desktop, gcc-4.1.2, glibc-2.6.1-r0,
2.6.23-gentoo-r3 x86_64)
=================================================================
System uname: 2.6.23-gentoo-r3 x86_64 AMD Athlon(tm) X2 Dual Core Processor
BE-2350
Timestamp of tree: Sat, 08 Mar 2008 21:47:01 +0000
app-shells/bash:     3.2_p17-r1
dev-java/java-config: 1.3.7, 2.1.4
dev-lang/python:     2.4.4-r9
dev-python/pycrypto: 2.0.1-r6
sys-apps/baselayout: 1.12.11.1
sys-apps/sandbox:    1.2.18.1-r2
sys-devel/autoconf:  2.13, 2.61-r1
sys-devel/automake:  1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10
sys-devel/binutils:  2.18-r1
sys-devel/gcc-config: 1.4.0-r4
sys-devel/libtool:   1.5.26
virtual/os-headers:  2.6.23-r3
ACCEPT_KEYWORDS="amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=k8 -O2 -pipe -msse3"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb"
CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf
/etc/gconf /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/udev/rules.d"
CXXFLAGS="-march=k8 -O2 -pipe -msse3"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS=""
FEATURES="ccache distlocks metadata-transfer sandbox sfperms strict
unmerge-orphans userfetch"
GENTOO_MIRRORS="ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo
http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/
http://distfiles.gentoo.org
http://www.ibiblio.org/pub/Linux/distributions/gentoo"
LANG="de_DE.UTF-8"
LC_ALL="de_DE.UTF-8"
LINGUAS="de en"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress
--force --whole-file --delete --stats --timeout=180 --exclude=/distfiles
--exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage"
USE="3dnow 3dnowext 7zip X a52 aac acl acpi alsa amd64 audiofile avahi berkdb
branding cairo ccache cddb cdr clamav cli cracklib crypt css cups dbus divx dri
dvd dvdnav dvdr dvdread eds emboss encode esd evo fam fame ffmpeg firefox flac
fortran gdbm gdm gif gmedia gnome gpm gstreamer gtk hal iconv isdnlog java jpeg
kerberos ladspa ldap mad midi mikmod mjpeg mmx mng mp2 mp3 mpeg mplayer mudflap
ncurses nls nptl nptlonly ogg opengl openmp oss pam pcre pdf perl png postproc
ppds pppd python qt3support quicktime readline realmedia reflection samba
scanner sdl session slp smp sndfile spell spl sse sse2 ssl subtitles subversion
svg tcpd theora thunderbird tiff truetype unicode vorbis vram wma wmf wmp x264
xine xml xorg xv xvid zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem
bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel
intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci"
ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file
hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route
share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias
authn_anon authn_dbm authn_default authn_file authz_dbm authz_default
authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs
dav_lock deflate dir disk_cache env expires ext_filter file_cache filter
headers include info log_config logio mem_cache mime mime_magic negotiation
rewrite setenvif speling status unique_id userdir usertrack vhost_alias"
ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux"
LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses
text" LINGUAS="de en" USERLAND="GNU" VIDEO_CARDS="radeon fglrx vesa fbdev"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LDFLAGS, PORTAGE_COMPRESS,
PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

------- Comment #17 From Till Korten 2008-03-16 03:56:25 0000 ------- 
Created an attachment (id=146266) [details]
fixed ebuild including patches

adds 2 patches for ncbi/platform/linux.ncbi.mk and
ncbi/platform/linux64.ncbi.mk
removing -W1,-Bstatic from the NCBI_DISTVIBLIBS variable

extract this tar into $PORTDIR_OVERLAY/sci-biology/
echo "sci-biology/ncbi-tools ~amd64" >> /etc/portage/package.keywords
emerge -1uDN ncbi-tools

------- Comment #18 From Donnie Berkholz 2008-04-08 21:30:28 0000 ------- 
I just hit this and fixed it in CVS, with a sed instead of patches.
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