Hi Stephen, There is a new version of the NCBI C toolkit available. Just renaming the old ebuild worked for me. (The archive from the NCBI will have to be renamed and uploaded on the Gentoo mirrors, though.) Thanks,
I added it to Portage. I hope that is OK with you, Stephen.
# emerge -u world Calculating world dependencies ...done! >>> emerge (1 of 54) sci-biology/ncbi-tools-20041020-r1 to / >>> md5 src_uri ;-) ncbi-tools-20041020.tar.gz >>> md5 src_uri ;-) ncbi-tools-sdk-doc.tar.bz2 * It is important to note that the NCBI tools (especially the X * applications) are known to have compilation and run-time * problems when compiled with agressive compilation flags. The * "-O3" flag is filtered by the ebuild on the x86 architecture if * X support is enabled. If you experience difficulties with this * package and use agressive "CFLAGS", lower the "CFLAGS" and try * to install the NCBI tools again. >>> Unpacking source... >>> Unpacking ncbi-tools-20041020.tar.gz to /var/tmp/portage/ncbi-tools-20041020-r1/work >>> Unpacking ncbi-tools-sdk-doc.tar.bz2 to /var/tmp/portage/ncbi-tools-20041020-r1/work >>> Source unpacked. libs version is: lrwxrwxrwx 1 root root 13 Feb 17 11:17 /lib/libc.so.6 -> libc-2.3.4.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_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. Please be sure that you have X11 and Motif libraries installed. The NCBI toolkit FAQ at ftp://ftp.ncbi.nih.gov/toolbox/FAQ.html may be helpful. !!! ERROR: sci-biology/ncbi-tools-20041020-r1 failed. !!! Function src_compile, Line 99, Exitcode 1 !!! (no error message) !!! If you need support, post the topmost build error, NOT this status message.
Hi Martin, Sorry for taking so long to answer, but since you commented on the new version request rather than opening a new bug, and since you did not reopen this bug, it just does not show up when I check my bugs. (It also took me some time to find a machine where I could reproduce this.) The bug is not in the "ncbi-tools" package, but in "motif-config"; older versions did not properly link OpenMotif's "include" directory in "/usr/include/Xm". The solution is to unmerge OpenMotif and the config program, remove the directory, then reemerge them: # emerge --unmerge --ask openmotif motif-config # rm -r /usr/include/Xm # emerge --ask openmotif
