>>> Unpacking source... >>> Unpacking ncbi-tools-20050429.tar.gz to /var/tmp/portage/ncbi-tools-20050429/work >>> Unpacking ncbi-tools-sdk-doc.tar.bz2 to /var/tmp/portage/ncbi-tools-20050429/work >>> Source unpacked. lsb_release: Command not found. libs version is: lrwxrwxrwx 1 root root 13 May 31 16:37 /lib/libc.so.6 -> libc-2.3.5.so the gcc version is: Reading specs from /usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/specs Configured with: /var/tmp/portage/gcc-3.3.4-r1/work/gcc-3.3.4/configure --prefix=/usr --bindir=/usr/i686-pc-linux-gnu/gcc-bin/3.3 --includedir=/usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/include --datadir=/usr/share/gcc-data/i686-pc-linux-gnu/3.3 --mandir=/usr/share/gcc-data/i686-pc-linux-gnu/3.3/man --infodir=/usr/share/gcc-data/i686-pc-linux-gnu/3.3/info --enable-shared --host=i686-pc-linux-gnu --target=i686-pc-linux-gnu --with-system-zlib --enable-languages=c,c++,f77,java --enable-threads=posix --enable-long-long --disable-checking --disable-libunwind-exceptions --enable-cstdio=stdio --enable-version-specific-runtime-libs --with-gxx-include-dir=/usr/lib/gcc-lib/i686-pc-linux-gnu/3.3.4/include/g++-v3 --with-local-prefix=/usr/local --enable-shared --enable-nls --without-included-gettext --x-includes=/usr/X11R6/include --x-libraries=/usr/X11R6/lib --enable-interpreter --enable-java-awt=xlib --with-x --disable-multilib --enable-__cxa_atexit --enable-clocale=generic Thread model: posix gcc version 3.3.4 20040623 (Gentoo Linux 3.3.4-r1, ssp-3.3.2-2, pie-8.7.6) Motif found at /usr/X11R6/include/Xm Warning: Motif version 1.2 is recommended OpenGL found at /usr/X11R6/include/GL platform is linux-x86 Linux oxygen 2.4.30-pre2-bk3 #3 SMP Mon Mar 7 13:35:40 MET 2005 i686 Intel(R) Xeon(TM) CPU 3.06GHz GenuineIntel GNU/Linux BLAST version is 2.2.10 make CFLAGS1="-march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O2 -fomit-frame-pointer -funroll-loops -pipe -c -march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O2 -fomit-frame-pointer -funroll-loops -pipe " LDFLAGS1="-march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O2 -fomit-frame-pointer -funroll-loops -pipe" OTHERLIBS="-lm" SHELL="/bin/sh" LCL="lnx" RAN="ranlib" AR="ar" CC="i686-pc-linux-gnu-gcc -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE" LIB30=libncbicn3d.a LIB28=libvibgif.a LIB4=libvibrant.a LIB20=libncbidesk.a LIB45=libddvlib.a VIBFLAG="-I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF" VIBLIBS="-L/usr/X11R6/lib -lXmu -lXm -lXt -lSM -lICE -lXext -lXp -lX11 -ldl" all chmod -R ug+rw,o+r . ../include ./ln-if-absent ../corelib/tsprintf.h ../include ./ln-if-absent ../corelib/gifgen.h ../include ./ln-if-absent ../corelib/ncbi*.h ../include ./ln-if-absent ../corelib/tree*.h ../include ./ln-if-absent ../corelib/regex.h ../include ./ln-if-absent ../corelib/matrix.h ../include ./ln-if-absent ../corelib/binary.h ../include ./ln-if-absent ../corelib/morefile/*.h ../include ./ln-if-absent ../corelib/morefile/*.c . ./ln-if-absent ../link/macmet/MoreCarbonAccessors.h ../include ./ln-if-absent ../corelib/ncbilcl.lnx ../include/ncbilcl.h ./ln-if-absent ../corelib/*.c . ./ln-if-absent ../corelib/core*.h . ./ln-if-absent ../asnlib/*.h . mv asn.h ../include ./ln-if-absent ../asnlib/*.c . ./ln-if-absent ../connect/*.c . ./ln-if-absent ../connect/ncbi_ansi_ext.h . ./ln-if-absent ../connect/ncbi_assert.h . ./ln-if-absent ../connect/ncbi_priv.h . ./ln-if-absent ../connect/ncbi_comm.h . ./ln-if-absent ../connect/ncbi_config.h . ./ln-if-absent ../connect/ncbi_lbsm.h . make: [copy] Error 1 (ignored) ./ln-if-absent ../connect/ncbi_lbsm_ipc.h . make: [copy] Error 1 (ignored) ./ln-if-absent ../connect/ncbi_host_infop.h . ./ln-if-absent ../connect/ncbi_server_infop.h . ./ln-if-absent ../connect/ncbi_servicep.h . ./ln-if-absent ../connect/ncbi_dispd.h . ./ln-if-absent ../connect/ncbi_lbsmd.h . ./ln-if-absent ../connect/*.h ../include mkdir ../include/connect chmod ug+rw,o+r ../include/connect rm ../include/ncbi_*.h ../include/connect_export.h cp -fp ../connect/ncbi_*.h ../connect/connect_export.h ../include/connect ./ln-if-absent ../util/tables/*.c . mkdir -p ../include/util/tables cp -fp ../util/tables/*.h ../include/util/tables ./ln-if-absent ../util/creaders/*.c . mkdir -p ../include/util/creaders cp -fp ../util/creaders/*.h ../include/util/creaders ./ln-if-absent ../ctools/*.c . mkdir ../include/ctools chmod ug+rw,o+r ../include/ctools cp -fp ../ctools/*.h ../include/ctools ./ln-if-absent ../object/*.c . ./ln-if-absent ../object/*.h ../include ./ln-if-absent ../access/*.c . ./ln-if-absent ../access/*.h ../include ./ln-if-absent ../asnstat/*.h ../include ./ln-if-absent ../api/*.h ../include ./ln-if-absent ../api/*.c . ./ln-if-absent ../cdromlib/*.h ../include ./ln-if-absent ../cdromlib/*.c . ./ln-if-absent ../vibrant/*.h ../include ./ln-if-absent ../vibrant/*.c . ./ln-if-absent ../desktop/*.h ../include ./ln-if-absent ../desktop/*.c . ./ln-if-absent ../biostruc/*.h ../include ./ln-if-absent ../biostruc/*.c . ./ln-if-absent ../biostruc/cdd/*.h ../include ./ln-if-absent ../biostruc/cdd/*.c . ./ln-if-absent ../biostruc/cn3d/*.h ../include ./ln-if-absent ../biostruc/cn3d/*.c . ./ln-if-absent ../tools/*.h ../include ./ln-if-absent ../tools/*.c . ./ln-if-absent ../cn3d/*.h ../include ./ln-if-absent ../cn3d/*.c . ./ln-if-absent ../gif/*.c . ./ln-if-absent ../gif/*.h ../include ./ln-if-absent ../ddv/*.h ../include ./ln-if-absent ../ddv/*.c . ./ln-if-absent ../regexp/*.c . ./ln-if-absent ../regexp/*.h ../include ./ln-if-absent ../internal/compr/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/compr/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/libindx/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/libindx/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/libpars/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/libpars/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/*.dat . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/ideochr*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ideogram/ideoorgs.h . make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ccap/*.c . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ccap/*.dat . set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ../internal/ccap/*.h ../include set: No match. make: [copy] Error 1 (ignored) ./ln-if-absent ncbidraw.c ncbidrwg.c ./ln-if-absent ncbithr.c ncbithrs.c ./ln-if-absent ../network/nsclilib/*.h ../include ./ln-if-absent ../network/blast3/client/*.h ../include ./ln-if-absent ../network/id1arch/*.h ../include ./ln-if-absent ../network/id2arch/*.h ../include mkdir -p ../include/algo/blast/core ./ln-if-absent ../algo/blast/core/*.c . ./ln-if-absent ../algo/blast/core/*.h . cp -fp ../algo/blast/core/*.h ../include/algo/blast/core mkdir -p ../include/algo/blast/api ./ln-if-absent ../algo/blast/api/*.c . cp -fp ../algo/blast/api/*.h ../include/algo/blast/api chmod -R ug+rw,o+r . echo Waiting...go Waiting...go i686-pc-linux-gnu-gcc -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O2 -fomit-frame-pointer -funroll-loops -pipe -c -march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O2 -fomit-frame-pointer -funroll-loops -pipe -I../include -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF ncbithr.c cp -p ncbithr.o ../lib i686-pc-linux-gnu-gcc -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O2 -fomit-frame-pointer -funroll-loops -pipe -c -march=pentium4 -mcpu=pentium4 -mmmx -msse -msse2 -msse3 -O2 -fomit-frame-pointer -funroll-loops -pipe -I../include -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF ncbibs.c In file included from ncbibs.c:108: ../include/ncbiwin.h:237:19: Xm/Xm.h: No such file or directory ../include/ncbiwin.h:238:24: Xm/AtomMgr.h: No such file or directory ../include/ncbiwin.h:239:26: Xm/BulletinB.h: No such file or directory ../include/ncbiwin.h:240:25: Xm/CascadeB.h: No such file or directory ../include/ncbiwin.h:241:25: Xm/DrawingA.h: No such file or directory ../include/ncbiwin.h:242:21: Xm/Form.h: No such file or directory ../include/ncbiwin.h:243:22: Xm/Label.h: No such file or directory ../include/ncbiwin.h:244:21: Xm/List.h: No such file or directory ../include/ncbiwin.h:245:22: Xm/MainW.h: No such file or directory ../include/ncbiwin.h:246:26: Xm/MenuShell.h: No such file or directory ../include/ncbiwin.h:247:23: Xm/PanedW.h: No such file or directory ../include/ncbiwin.h:248:26: Xm/Protocols.h: No such file or directory ../include/ncbiwin.h:249:22: Xm/PushB.h: No such file or directory ../include/ncbiwin.h:250:26: Xm/RowColumn.h: No such file or directory ../include/ncbiwin.h:251:26: Xm/ScrollBar.h: No such file or directory ../include/ncbiwin.h:252:26: Xm/ScrolledW.h: No such file or directory ../include/ncbiwin.h:253:26: Xm/Separator.h: No such file or directory ../include/ncbiwin.h:254:21: Xm/Text.h: No such file or directory ../include/ncbiwin.h:255:22: Xm/TextF.h: No such file or directory ../include/ncbiwin.h:256:24: Xm/ToggleB.h: No such file or directory make: *** [ncbibs.o] Error 1 Fatal error building NCBI core libraries.
The "ncbi-tools" package *does* depend on motif libraries. This looks rather like yet another motif bug. I suggest you uninstall all motif implementations from your system (and also the "motif-config" package if applicable), manually check that the directory "/usr/include/Xm" and its content was removed (and, if not, remove it yourself), then reinstall OpenMotif.
