* Package: sci-biology/ncbi-tools-2.2.26-r2  * Repository: gentoo  * Maintainer: weaver@gentoo.org sci-biology@gentoo.org  * USE: X amd64 doc elibc_glibc kernel_linux userland_GNU  * FEATURES: sandbox * Please note that the NCBI toolkit (and 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. >>> Unpacking source... >>> Unpacking ncbi-tools-2.2.26.tar.gz to /var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/work >>> Source unpacked in /var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/work >>> Preparing source in /var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/work/ncbi ... * Applying ncbi-tools-extra_vib.patch ...  [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/work/ncbi ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/work/ncbi ... LSB Version: n/a Distributor ID: Gentoo Description: NAME=Gentoo Release: n/a Codename: n/a libs version is: lrwxrwxrwx 1 root root 12 Nov 14 13:31 /lib/libc.so.6 -> libc-2.16.so the gcc version is: Using built-in specs. COLLECT_GCC=/usr/x86_64-pc-linux-gnu/gcc-bin/4.6.3/gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-pc-linux-gnu/4.6.3/lto-wrapper Target: x86_64-pc-linux-gnu Configured with: /var/tmp/portage/sys-devel/gcc-4.6.3/work/gcc-4.6.3/configure --prefix=/usr --bindir=/usr/x86_64-pc-linux-gnu/gcc-bin/4.6.3 --includedir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3/include --datadir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.6.3 --mandir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.6.3/man --infodir=/usr/share/gcc-data/x86_64-pc-linux-gnu/4.6.3/info --with-gxx-include-dir=/usr/lib/gcc/x86_64-pc-linux-gnu/4.6.3/include/g++-v4 --host=x86_64-pc-linux-gnu --build=x86_64-pc-linux-gnu --disable-altivec --disable-fixed-point --without-ppl --without-cloog --enable-lto --enable-nls --without-included-gettext --with-system-zlib --enable-obsolete --disable-werror --enable-secureplt --enable-multilib --enable-libmudflap --disable-libssp --enable-libgomp --with-python-dir=/share/gcc-data/x86_64-pc-linux-gnu/4.6.3/python --enable-checking=release --enable-java-awt=gtk --enable-libstdcxx-time --enable-languages=c,c++,java,objc,fortran --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu --enable-targets=all --with-bugurl=http://bugs.gentoo.org/ --with-pkgversion='Gentoo 4.6.3 p1.11, pie-0.5.2' Thread model: posix gcc version 4.6.3 (Gentoo 4.6.3 p1.11, pie-0.5.2) Motif found at /usr/include/Xm Warning: Motif version 1.2 is recommended OpenGL found at /usr/include/GL platform is linux Linux leopard 3.7.7-gentoo #1 SMP Wed Feb 13 12:15:41 CET 2013 x86_64 Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz GenuineIntel GNU/Linux Disabling assert(). BLAST version is 2.2.26 make CFLAGS1="-DNDEBUG asd -march=native -O2 -pipe -c " LDFLAGS1="asd -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed" OTHERLIBS="-lm" SHELL="/bin/sh" LCL="lnx" RAN="x86_64-pc-linux-gnu-ranlib" AR="x86_64-pc-linux-gnu-ar" CC="x86_64-pc-linux-gnu-gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_GNU_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 -Wl,-Bdynamic -lXft -lfontconfig -ljpeg -lpng -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 . rm -f ../include/asn.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_connssl.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_socketp.h . ./ln-if-absent ../connect/ncbi_dispd.h . ./ln-if-absent ../connect/ncbi_lbsmd.h . ./ln-if-absent ../connect/ncbi_local.h . ./ln-if-absent ../connect/ncbi_lb.h . ./ln-if-absent ../connect/ncbi_version.h . ./ln-if-absent ../connect/ncbi_base64.h . ./ln-if-absent ../connect/urlquery.h ../include mkdir ../include/connect chmod ug+rw,o+r ../include/connect 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 . ./ln-if-absent ../ctools/*.h . 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 ../api/*.inc . ./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 . ./ln-if-absent ../algo/blast/core/*.inl . cp -fp ../algo/blast/core/*.h ../include/algo/blast/core mkdir -p ../include/algo/blast/composition_adjustment ./ln-if-absent ../algo/blast/composition_adjustment/*.c . ./ln-if-absent ../algo/blast/composition_adjustment/*.h ../include cp -fp ../algo/blast/composition_adjustment/*.h \ ../include/algo/blast/composition_adjustment 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 x86_64-pc-linux-gnu-gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_GNU_SOURCE -DNDEBUG asd -march=native -O2 -pipe -c -I../include -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF ncbithr.c x86_64-pc-linux-gnu-gcc: error: asd: No such file or directory make: *** [ncbithr.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-2.2.26-r2 failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 93: Called src_compile * environment, line 2498: Called die * The specific snippet of code: * csh ncbi/make/makedis.csh || die; * * If you need support, post the output of `emerge --info '=sci-biology/ncbi-tools-2.2.26-r2'`, * the complete build log and the output of `emerge -pqv '=sci-biology/ncbi-tools-2.2.26-r2'`. * The complete build log is located at '/var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/work' * S: '/var/tmp/portage/sci-biology/ncbi-tools-2.2.26-r2/work/ncbi'