195251 – [science overlay] sci-biology/ncbi-tools-20070826 fails to compile because of undefined reference to motif functions

Bug 195251 - [science overlay] sci-biology/ncbi-tools-20070826 fails to compile because of undefined reference to motif functions

Summary: [science overlay] sci-biology/ncbi-tools-20070826 fails to compile because of...

Status:	RESOLVED FIXED

Alias:	None

Product:	Gentoo Linux
Classification:	Unclassified
Component:	Current packages (show other bugs)
Hardware:	All Linux

Importance:	High normal (vote)
Assignee:	Jeffrey Gardner (RETIRED)

URL:
Whiteboard:
Keywords:

Depends on:
Blocks:

Reported:	2007-10-09 14:07 UTC by Juergen Rose
Modified:	2008-04-08 21:30 UTC (History)
CC List:	2 users (show)

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

Attachments
fixed ebuild including patches (ncbi-tools-20070826-r1.tar.gz,5.21 KB, patch) 2008-03-16 03:56 UTC, Till Korten	Details \| Diff
View All Add an attachment (proposed patch, testcase, etc.)

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Description Juergen Rose 2007-10-09 14:07:58 UTC

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 Jakub Moc (RETIRED) gentoo-dev

2007-10-09 17:18:59 UTC

There's no ncbi-tools-20070826 anywhere in the official tree.

Comment 2 Juergen Rose 2007-10-09 18:12:44 UTC

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 Jakub Moc (RETIRED) gentoo-dev

2007-10-09 18:15:21 UTC

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 Jeffrey Gardner (RETIRED) gentoo-dev

2007-10-14 04:12:05 UTC

Juergen,
Are you still having trouble with the version I've put in the official portage tree (ncbi-tools-20070826)?

Comment 5 Patrizio Bassi 2007-10-14 12:20:39 UTC

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 Patrizio Bassi 2007-10-14 12:21:25 UTC

...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 Jeffrey Gardner (RETIRED) gentoo-dev

2007-10-14 20:14:43 UTC

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 Patrizio Bassi 2007-10-14 20:30:36 UTC

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 Juergen Rose 2007-10-15 10:08:40 UTC

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 Patrizio Bassi 2007-10-15 11:18:10 UTC

can you try to switch to 2.3 on x86 too?

probably 2.3 introduced the issue

Comment 11 Jeffrey Gardner (RETIRED) gentoo-dev

2007-10-15 15:04:25 UTC

I think running revdep-rebuild will fix this for you guys.

Comment 12 Juergen Rose 2007-10-15 20:04:02 UTC

revdep-rebuild does not fix the problem for me.

Comment 13 Patrizio Bassi 2007-10-15 20:22:09 UTC

...neither for me...

Comment 14 Martin Mokrejš 2008-03-01 12:13:04 UTC

Recompile all versions of openmotif* and lesstif* or keep just one, freshly recompiled.

Comment 15 Patrizio Bassi 2008-03-01 13:24:54 UTC

tried...no way...

Comment 16 Till Korten 2008-03-15 19:15:35 UTC

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 Till Korten 2008-03-16 03:56:25 UTC

Created attachment 146266 [details, diff]
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 Donnie Berkholz (RETIRED) gentoo-dev

2008-04-08 21:30:28 UTC

I just hit this and fixed it in CVS, with a sed instead of patches.