* Package: sci-biology/vienna-rna-1.8.5  * Repository: gentoo  * Maintainer: sci-biology@gentoo.org  * USE: elibc_glibc kernel_linux ppc test userland_GNU  * FEATURES: sandbox test >>> Unpacking source... >>> Unpacking ViennaRNA-1.8.5.tar.gz to /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work >>> Source unpacked in /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work >>> Preparing source in /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5 ... * Applying vienna-rna-1.6.5-c-fixes.patch ...  [ ok ] * Applying vienna-rna-1.7.2-LDFLAGS.patch ...  [ ok ] * Applying vienna-rna-1.8.3-gcc4.3.patch ...  [ ok ] * Applying vienna-rna-1.8.3-disable-gd.patch ...  [ ok ] * Applying vienna-rna-1.8.4-jobserver-fix.patch ...  [ ok ] * Applying vienna-rna-1.8.4-bindir.patch ...  [ ok ] * Applying vienna-rna-1.8.4-overflows.patch ...  [ ok ] * Applying vienna-rna-1.8.4-implicits.patch ...  [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70' ... * Running aclocal ...  [ ok ] * Running autoconf ...  [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester' ... * Running aclocal ...  [ ok ] * Running autoconf ...  [ ok ] * Running autoheader ...  [ ok ] * Running automake --add-missing --copy ...  [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold' ... * Running aclocal ...  [ ok ] * Running autoconf ...  [ ok ] * Running autoheader ...  [ ok ] * Running automake --add-missing --copy ...  [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5' ... * Running aclocal ...  [ ok ] * Running autoconf ...  [ ok ] * Running autoheader ...  [ ok ] * Running automake --add-missing --copy ...  [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70' ... * Running aclocal ...  [ ok ] * Running autoconf ...  [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester' ... * Running aclocal ...  [ ok ] * Running autoconf ...  [ ok ] * Running autoheader ...  [ ok ] * Running automake --add-missing --copy ...  [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5 ... * econf: updating ViennaRNA-1.8.5/RNAforester/g2-0.70/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-1.8.5/RNAforester/g2-0.70/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-1.8.5/RNAforester/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-1.8.5/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-1.8.5/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=powerpc-unknown-linux-gnu --host=powerpc-unknown-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib --with-cluster checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking if malloc debugging is wanted... no checking build system type... powerpc-unknown-linux-gnu checking host system type... powerpc-unknown-linux-gnu checking for powerpc-unknown-linux-gnu-gcc... powerpc-unknown-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether powerpc-unknown-linux-gnu-gcc accepts -g... yes checking for powerpc-unknown-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of powerpc-unknown-linux-gnu-gcc... gcc3 checking whether powerpc-unknown-linux-gnu-gcc accepts -fpic... yes checking for powerpc-unknown-linux-gnu-ranlib... powerpc-unknown-linux-gnu-ranlib checking whether powerpc-unknown-linux-gnu-gcc and cc understand -c and -o together... yes checking for perl... /usr/bin/perl checking how to run the C preprocessor... powerpc-unknown-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for strdup... yes checking for strstr... yes checking for strchr... yes checking for erand48... yes configure: creating ./config.status config.status: creating Makefile config.status: creating ViennaRNA.spec config.status: creating Utils/Makefile config.status: creating Progs/Makefile config.status: creating lib/Makefile config.status: creating man/Makefile config.status: creating Cluster/Makefile config.status: creating H/Makefile config.status: creating Perl/Makefile config.status: creating man/RNAheat.1 config.status: creating man/RNAsubopt.1 config.status: creating man/RNAdistance.1 config.status: creating man/RNAinverse.1 config.status: creating man/RNAeval.1 config.status: creating man/RNAfold.1 config.status: creating man/RNApdist.1 config.status: creating man/RNAplot.1 config.status: creating man/RNALfold.1 config.status: creating man/RNAalifold.1 config.status: creating man/RNAduplex.1 config.status: creating man/RNAcofold.1 config.status: creating man/RNAplfold.1 config.status: creating man/RNAup.1 config.status: creating man/RNApaln.1 config.status: creating man/RNAaliduplex.1 config.status: creating config.h config.status: executing depfiles commands === configuring in RNAforester (/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=powerpc-unknown-linux-gnu' '--host=powerpc-unknown-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib' '--with-cluster' 'build_alias=powerpc-unknown-linux-gnu' 'host_alias=powerpc-unknown-linux-gnu' 'CFLAGS=-O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for powerpc-unknown-linux-gnu-g++... powerpc-unknown-linux-gnu-g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether powerpc-unknown-linux-gnu-g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of powerpc-unknown-linux-gnu-g++... gcc3 checking for powerpc-unknown-linux-gnu-gcc... powerpc-unknown-linux-gnu-gcc checking whether we are using the GNU C compiler... yes checking whether powerpc-unknown-linux-gnu-gcc accepts -g... yes checking for powerpc-unknown-linux-gnu-gcc option to accept ISO C89... none needed checking dependency style of powerpc-unknown-linux-gnu-gcc... gcc3 using (to be built) libRNA.a in ../lib checking how to run the C++ preprocessor... powerpc-unknown-linux-gnu-g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking g2.h usability... yes checking g2.h presence... yes checking for g2.h... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in g2-0.70 (/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=powerpc-unknown-linux-gnu' '--host=powerpc-unknown-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib' '--with-cluster' 'build_alias=powerpc-unknown-linux-gnu' 'host_alias=powerpc-unknown-linux-gnu' 'CFLAGS=-O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CXXFLAGS=-O2 -pipe' --cache-file=/dev/null --srcdir=. checking build system type... powerpc-unknown-linux-gnu checking host system type... powerpc-unknown-linux-gnu checking for powerpc-unknown-linux-gnu-gcc... powerpc-unknown-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether powerpc-unknown-linux-gnu-gcc accepts -g... yes checking for powerpc-unknown-linux-gnu-gcc option to accept ISO C89... none needed checking how to run the C preprocessor... powerpc-unknown-linux-gnu-gcc -E checking for powerpc-unknown-linux-gnu-g++... powerpc-unknown-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether powerpc-unknown-linux-gnu-g++ accepts -g... yes checking for powerpc-unknown-linux-gnu-ranlib... powerpc-unknown-linux-gnu-ranlib checking for a BSD-compatible install... /usr/bin/install -c checking for find... find checking for makedepend... makedepend checking for dlopen in -ldl... yes checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for main in -lm... yes checking for main in -lX11... yes checking for main in -lgd... yes checking for gdImagePng... no checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes configure: creating ./config.status config.status: creating Makefile config.status: creating demo/Makefile config.status: creating g2_perl/Makefile.PL Supported devices: PostScript FIG X11 Unsupported devices: Win32 GD Run 'make depend' to create dependencies. === configuring in Kinfold (/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=powerpc-unknown-linux-gnu' '--host=powerpc-unknown-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib' '--with-cluster' 'build_alias=powerpc-unknown-linux-gnu' 'host_alias=powerpc-unknown-linux-gnu' 'CFLAGS=-O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking if malloc debugging is wanted... no checking for powerpc-unknown-linux-gnu-gcc... powerpc-unknown-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether powerpc-unknown-linux-gnu-gcc accepts -g... yes checking for powerpc-unknown-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of powerpc-unknown-linux-gnu-gcc... gcc3 checking build system type... powerpc-unknown-linux-gnu checking host system type... powerpc-unknown-linux-gnu checking for strdup... yes checking for memset... yes checking for strchr... yes checking for ViennaRNA package... headers in "../H" and library... "../lib" checking how to run the C preprocessor... powerpc-unknown-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking fold.h usability... yes checking fold.h presence... yes checking for fold.h... yes checking for exp in -lm... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for an ANSI C-conforming const... yes configure: creating ./config.status config.status: creating Example/Makefile config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands configure: Configure successful with the following options: Perl Extension: yes Analyse{Dists,Seqs}: yes Kinfold: yes RNAforester: yes Files will be installed in the following directories: Executables: /usr/bin Libraries: /usr/lib Header files: /usr/include Extra Data: /usr/share Man pages: /usr/share/man >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5 ... make -j20 clean Making clean in Kinfold make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold' Making clean in Example make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold/Example' make[2]: Nothing to be done for `clean'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold/Example' Making clean in . make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold' test -z "Kinfold" || rm -f Kinfold rm -f *.o make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold' Making clean in RNAforester make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester' Making clean in man make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/man' make[2]: Nothing to be done for `clean'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/man' Making clean in src make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/src' test -z "RNAforester" || rm -f RNAforester rm -f *.o make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/src' Making clean in g2-0.70 make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70' (cd ./demo ; make clean) make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70/demo' rm g2_test g2_arc g2_splines_demo demo_cpp simple_PS simple_FIG simple_X11 pointer handles g2testf g2testf.f demo_f *~ core *.ps *.fig *.eps *.png *.jpg *.fig.bak rm: cannot remove `g2_test': No such file or directory rm: cannot remove `g2_arc': No such file or directory rm: cannot remove `g2_splines_demo': No such file or directory rm: cannot remove `demo_cpp': No such file or directory rm: cannot remove `simple_PS': No such file or directory rm: cannot remove `simple_FIG': No such file or directory rm: cannot remove `simple_X11': No such file or directory rm: cannot remove `pointer': No such file or directory rm: cannot remove `handles': No such file or directory rm: cannot remove `g2testf': No such file or directory rm: cannot remove `g2testf.f': No such file or directory rm: cannot remove `demo_f': No such file or directory rm: cannot remove `*~': No such file or directory rm: cannot remove `core': No such file or directory rm: cannot remove `*.ps': No such file or directory rm: cannot remove `*.fig': No such file or directory rm: cannot remove `*.eps': No such file or directory rm: cannot remove `*.png': No such file or directory rm: cannot remove `*.jpg': No such file or directory rm: cannot remove `*.fig.bak': No such file or directory make[3]: [clean] Error 1 (ignored) make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70/demo' rm -f ./src/g2_device.o ./src/g2_ui_control.o ./src/g2_util.o ./src/g2_fif.o ./src/g2_virtual_device.o ./src/g2_physical_device.o ./src/g2_graphic_pd.o ./src/g2_control_pd.o ./src/g2_ui_graphic.o ./src/g2_ui_virtual_device.o ./src/g2_ui_device.o ./src/g2_splines.o ./src/PS/g2_PS.o ./src/FIG/g2_FIG.o ./src/X11/g2_X11.o rm -f libg2.a config.cache config.log Makefile.bak config.status rm -f ./include/*.h find . -name "*~" -exec rm -f {} \; (cd ./g2_perl ; make clean) make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70/g2_perl' make[3]: *** No rule to make target `clean'. Stop. make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70/g2_perl' make[2]: [clean] Error 2 (ignored) rm -f ./g2_perl/test.ps rm -f ./g2_perl/test.png rm -f ./g2_perl/test.jpg rm -f ./g2_perl/test.fig rm -f ./g2_perl/Makefile.old rm -f ./libg2.so.0.0.70 rm -f libg2.0.70.a rm -f a.out rm -fr doc/html/ doc/latex/ doc/g2_refman.ps doc/g2_refman.pdf make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70' Making clean in . make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester' make[2]: Nothing to be done for `clean-am'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester' Making clean in Cluster make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Cluster' test -z "AnalyseDists AnalyseSeqs" || rm -f AnalyseDists AnalyseSeqs rm -f *.o make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Cluster' Making clean in Perl make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl' /usr/bin/perl Makefile.PL INSTALLDIRS=vendor LDDLFLAGS="-Wl,-O1 -Wl,--as-needed -shared" Writing Makefile.perl for RNA make -f Makefile.perl clean make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl' rm -f \ *.a core \ core.[0-9] blib/arch/auto/RNA/extralibs.all \ core.[0-9][0-9] RNA.bso \ pm_to_blib.ts core.[0-9][0-9][0-9][0-9] \ RNA.x RNA.bs \ perl tmon.out \ *.o pm_to_blib \ blib/arch/auto/RNA/extralibs.ld blibdirs.ts \ core.[0-9][0-9][0-9][0-9][0-9] *perl.core \ core.*perl.*.? Makefile.perl.aperl \ perl RNA.def \ core.[0-9][0-9][0-9] mon.out \ libRNA.def perlmain.c \ perl.exe so_locations \ RNA.exp rm -rf \ blib mv Makefile.perl Makefile.perl.old > /dev/null 2>&1 make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl' Making clean in H make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H' make[1]: Nothing to be done for `clean'. make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H' Making clean in Utils make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils' test -z "b2ct popt" || rm -f b2ct popt rm -f *.o make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils' Making clean in man make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man' test -z "RNAlib.dvi RNAlib.pdf RNAlib.ps RNAlib.html" \ || rm -rf RNAlib.dvi RNAlib.pdf RNAlib.ps RNAlib.html rm -rf RNAlib.aux RNAlib.cp RNAlib.cps RNAlib.fn RNAlib.fns RNAlib.ky \ RNAlib.kys RNAlib.log RNAlib.pg RNAlib.pgs RNAlib.tmp \ RNAlib.toc RNAlib.tp RNAlib.tps RNAlib.vr RNAlib.vrs make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man' Making clean in Progs make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs' test -z "RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex" || rm -f RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex rm -f *.o make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs' Making clean in lib make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib' test -z "libRNA.a" || rm -f libRNA.a rm -f *.o make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib' Making clean in . make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5' make[1]: Nothing to be done for `clean-am'. make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5' make -j20 make all-recursive make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5' Making all in lib make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib' powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-dist_vars.o -MD -MP -MF .deps/libRNA_a-dist_vars.Tpo -c -o libRNA_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-fold_vars.o -MD -MP -MF .deps/libRNA_a-fold_vars.Tpo -c -o libRNA_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-part_func.o -MD -MP -MF .deps/libRNA_a-part_func.Tpo -c -o libRNA_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-read_epars.o -MD -MP -MF .deps/libRNA_a-read_epars.Tpo -c -o libRNA_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-treedist.o -MD -MP -MF .deps/libRNA_a-treedist.Tpo -c -o libRNA_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-energy_par.o -MD -MP -MF .deps/libRNA_a-energy_par.Tpo -c -o libRNA_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-inverse.o -MD -MP -MF .deps/libRNA_a-inverse.Tpo -c -o libRNA_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-ProfileDist.o -MD -MP -MF .deps/libRNA_a-ProfileDist.Tpo -c -o libRNA_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-RNAstruct.o -MD -MP -MF .deps/libRNA_a-RNAstruct.Tpo -c -o libRNA_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-utils.o -MD -MP -MF .deps/libRNA_a-utils.Tpo -c -o libRNA_a-utils.o `test -f 'utils.c' || echo './'`utils.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-fold.o -MD -MP -MF .deps/libRNA_a-fold.Tpo -c -o libRNA_a-fold.o `test -f 'fold.c' || echo './'`fold.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-naview.o -MD -MP -MF .deps/libRNA_a-naview.Tpo -c -o libRNA_a-naview.o `test -f 'naview.c' || echo './'`naview.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-PS_dot.o -MD -MP -MF .deps/libRNA_a-PS_dot.Tpo -c -o libRNA_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-stringdist.o -MD -MP -MF .deps/libRNA_a-stringdist.Tpo -c -o libRNA_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-params.o -MD -MP -MF .deps/libRNA_a-params.Tpo -c -o libRNA_a-params.o `test -f 'params.c' || echo './'`params.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-subopt.o -MD -MP -MF .deps/libRNA_a-subopt.Tpo -c -o libRNA_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-list.o -MD -MP -MF .deps/libRNA_a-list.Tpo -c -o libRNA_a-list.o `test -f 'list.c' || echo './'`list.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-Lfold.o -MD -MP -MF .deps/libRNA_a-Lfold.Tpo -c -o libRNA_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-cofold.o -MD -MP -MF .deps/libRNA_a-cofold.Tpo -c -o libRNA_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-part_func_co.o -MD -MP -MF .deps/libRNA_a-part_func_co.Tpo -c -o libRNA_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c mv -f .deps/libRNA_a-dist_vars.Tpo .deps/libRNA_a-dist_vars.Po powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-ProfileAln.o -MD -MP -MF .deps/libRNA_a-ProfileAln.Tpo -c -o libRNA_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c mv -f .deps/libRNA_a-fold_vars.Tpo .deps/libRNA_a-fold_vars.Po powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-duplex.o -MD -MP -MF .deps/libRNA_a-duplex.Tpo -c -o libRNA_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c stringdist.c:24:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:40, from stringdist.c:12: /usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition inverse.c: In function 'pf_cost': inverse.c:488: warning: passing argument 1 of 'pf_fold' discards qualifiers from pointer target type ./../H/part_func.h:6: note: expected 'char *' but argument is of type 'const char *' duplex.c: In function 'aliduplexfold': duplex.c:385: warning: passing argument 3 of 'alibacktrack' from incompatible pointer type duplex.c:37: note: expected 'const short int **' but argument is of type 'short int **' duplex.c:385: warning: passing argument 4 of 'alibacktrack' from incompatible pointer type duplex.c:37: note: expected 'const short int **' but argument is of type 'short int **' duplex.c: In function 'aliduplex_subopt': duplex.c:462: warning: passing argument 3 of 'alibacktrack' from incompatible pointer type duplex.c:37: note: expected 'const short int **' but argument is of type 'short int **' duplex.c:462: warning: passing argument 4 of 'alibacktrack' from incompatible pointer type duplex.c:37: note: expected 'const short int **' but argument is of type 'short int **' mv -f .deps/libRNA_a-list.Tpo .deps/libRNA_a-list.Po powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-alifold.o -MD -MP -MF .deps/libRNA_a-alifold.Tpo -c -o libRNA_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c mv -f .deps/libRNA_a-utils.Tpo .deps/libRNA_a-utils.Po powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-alipfold.o -MD -MP -MF .deps/libRNA_a-alipfold.Tpo -c -o libRNA_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c alifold.c: In function 'make_pscores': alifold.c:722: warning: passing argument 1 of 'get_ribosum' from incompatible pointer type ./../H/ribo.h:1: note: expected 'char **' but argument is of type 'const char * const*' mv -f .deps/libRNA_a-ProfileAln.Tpo .deps/libRNA_a-ProfileAln.Po powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-aln_util.o -MD -MP -MF .deps/libRNA_a-aln_util.Tpo -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c mv -f .deps/libRNA_a-ProfileDist.Tpo .deps/libRNA_a-ProfileDist.Po powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-LPfold.o -MD -MP -MF .deps/libRNA_a-LPfold.Tpo -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c mv -f .deps/libRNA_a-stringdist.Tpo .deps/libRNA_a-stringdist.Po powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-part_func_up.o -MD -MP -MF .deps/libRNA_a-part_func_up.Tpo -c -o libRNA_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.c alipfold.c: In function 'make_pscores': alipfold.c:1154: warning: passing argument 1 of 'get_ribosum' from incompatible pointer type ./../H/ribo.h:1: note: expected 'char **' but argument is of type 'const char * const*' mv -f .deps/libRNA_a-energy_par.Tpo .deps/libRNA_a-energy_par.Po powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-ribo.o -MD -MP -MF .deps/libRNA_a-ribo.Tpo -c -o libRNA_a-ribo.o `test -f 'ribo.c' || echo './'`ribo.c mv -f .deps/libRNA_a-params.Tpo .deps/libRNA_a-params.Po powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-findpath.o -MD -MP -MF .deps/libRNA_a-findpath.Tpo -c -o libRNA_a-findpath.o `test -f 'findpath.c' || echo './'`findpath.c mv -f .deps/libRNA_a-aln_util.Tpo .deps/libRNA_a-aln_util.Po powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -MT libRNA_a-MEA.o -MD -MP -MF .deps/libRNA_a-MEA.Tpo -c -o libRNA_a-MEA.o `test -f 'MEA.c' || echo './'`MEA.c mv -f .deps/libRNA_a-treedist.Tpo .deps/libRNA_a-treedist.Po mv -f .deps/libRNA_a-inverse.Tpo .deps/libRNA_a-inverse.Po mv -f .deps/libRNA_a-RNAstruct.Tpo .deps/libRNA_a-RNAstruct.Po mv -f .deps/libRNA_a-naview.Tpo .deps/libRNA_a-naview.Po mv -f .deps/libRNA_a-read_epars.Tpo .deps/libRNA_a-read_epars.Po mv -f .deps/libRNA_a-MEA.Tpo .deps/libRNA_a-MEA.Po mv -f .deps/libRNA_a-PS_dot.Tpo .deps/libRNA_a-PS_dot.Po mv -f .deps/libRNA_a-findpath.Tpo .deps/libRNA_a-findpath.Po mv -f .deps/libRNA_a-Lfold.Tpo .deps/libRNA_a-Lfold.Po mv -f .deps/libRNA_a-subopt.Tpo .deps/libRNA_a-subopt.Po mv -f .deps/libRNA_a-duplex.Tpo .deps/libRNA_a-duplex.Po mv -f .deps/libRNA_a-ribo.Tpo .deps/libRNA_a-ribo.Po mv -f .deps/libRNA_a-part_func_co.Tpo .deps/libRNA_a-part_func_co.Po mv -f .deps/libRNA_a-part_func.Tpo .deps/libRNA_a-part_func.Po mv -f .deps/libRNA_a-part_func_up.Tpo .deps/libRNA_a-part_func_up.Po mv -f .deps/libRNA_a-alifold.Tpo .deps/libRNA_a-alifold.Po mv -f .deps/libRNA_a-LPfold.Tpo .deps/libRNA_a-LPfold.Po mv -f .deps/libRNA_a-cofold.Tpo .deps/libRNA_a-cofold.Po mv -f .deps/libRNA_a-alipfold.Tpo .deps/libRNA_a-alipfold.Po mv -f .deps/libRNA_a-fold.Tpo .deps/libRNA_a-fold.Po rm -f libRNA.a ar cru libRNA.a libRNA_a-dist_vars.o libRNA_a-fold_vars.o libRNA_a-part_func.o libRNA_a-read_epars.o libRNA_a-treedist.o libRNA_a-energy_par.o libRNA_a-inverse.o libRNA_a-ProfileDist.o libRNA_a-RNAstruct.o libRNA_a-utils.o libRNA_a-fold.o libRNA_a-naview.o libRNA_a-PS_dot.o libRNA_a-stringdist.o libRNA_a-params.o libRNA_a-subopt.o libRNA_a-list.o libRNA_a-Lfold.o libRNA_a-cofold.o libRNA_a-part_func_co.o libRNA_a-ProfileAln.o libRNA_a-duplex.o libRNA_a-alifold.o libRNA_a-alipfold.o libRNA_a-aln_util.o libRNA_a-LPfold.o libRNA_a-part_func_up.o libRNA_a-ribo.o libRNA_a-findpath.o libRNA_a-MEA.o powerpc-unknown-linux-gnu-ranlib libRNA.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib' Making all in Progs make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs' powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAfold.o -MD -MP -MF .deps/RNAfold.Tpo -c -o RNAfold.o RNAfold.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAeval.o -MD -MP -MF .deps/RNAeval.Tpo -c -o RNAeval.o RNAeval.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAheat.o -MD -MP -MF .deps/RNAheat.Tpo -c -o RNAheat.o RNAheat.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNApdist.o -MD -MP -MF .deps/RNApdist.Tpo -c -o RNApdist.o RNApdist.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAdistance.o -MD -MP -MF .deps/RNAdistance.Tpo -c -o RNAdistance.o RNAdistance.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAinverse.o -MD -MP -MF .deps/RNAinverse.Tpo -c -o RNAinverse.o RNAinverse.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAplot.o -MD -MP -MF .deps/RNAplot.Tpo -c -o RNAplot.o RNAplot.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAsubopt.o -MD -MP -MF .deps/RNAsubopt.Tpo -c -o RNAsubopt.o RNAsubopt.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNALfold.o -MD -MP -MF .deps/RNALfold.Tpo -c -o RNALfold.o RNALfold.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAcofold.o -MD -MP -MF .deps/RNAcofold.Tpo -c -o RNAcofold.o RNAcofold.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNApaln.o -MD -MP -MF .deps/RNApaln.Tpo -c -o RNApaln.o RNApaln.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAduplex.o -MD -MP -MF .deps/RNAduplex.Tpo -c -o RNAduplex.o RNAduplex.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAalifold.o -MD -MP -MF .deps/RNAalifold.Tpo -c -o RNAalifold.o RNAalifold.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAplfold.o -MD -MP -MF .deps/RNAplfold.Tpo -c -o RNAplfold.o RNAplfold.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAup.o -MD -MP -MF .deps/RNAup.Tpo -c -o RNAup.o RNAup.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT RNAaliduplex.o -MD -MP -MF .deps/RNAaliduplex.Tpo -c -o RNAaliduplex.o RNAaliduplex.c RNAinverse.c:31:1: warning: "INFINITY" redefined In file included from /usr/include/math.h:40, from RNAinverse.c:9: /usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition RNAup.c: In function 'main': RNAup.c:110: warning: format '%100s' expects type 'char *', but argument 3 has type 'char (*)[201]' RNAaliduplex.c: In function 'main': RNAaliduplex.c:128: warning: passing argument 1 of 'aliduplex_subopt' from incompatible pointer type ./../H/duplex.h:14: note: expected 'const char **' but argument is of type 'char **' RNAaliduplex.c:128: warning: passing argument 2 of 'aliduplex_subopt' from incompatible pointer type ./../H/duplex.h:14: note: expected 'const char **' but argument is of type 'char **' RNAaliduplex.c:135: warning: passing argument 1 of 'aliduplexfold' from incompatible pointer type RNAaliduplex.c:22: note: expected 'const char **' but argument is of type 'char **' RNAaliduplex.c:135: warning: passing argument 2 of 'aliduplexfold' from incompatible pointer type RNAaliduplex.c:22: note: expected 'const char **' but argument is of type 'char **' mv -f .deps/RNAplot.Tpo .deps/RNAplot.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAplot RNAplot.o ../lib/libRNA.a -lm mv -f .deps/RNAeval.Tpo .deps/RNAeval.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAeval RNAeval.o ../lib/libRNA.a -lm mv -f .deps/RNAduplex.Tpo .deps/RNAduplex.Po mv -f .deps/RNAaliduplex.Tpo .deps/RNAaliduplex.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAduplex RNAduplex.o ../lib/libRNA.a -lm powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAaliduplex RNAaliduplex.o ../lib/libRNA.a -lm mv -f .deps/RNAheat.Tpo .deps/RNAheat.Po mv -f .deps/RNALfold.Tpo .deps/RNALfold.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAheat RNAheat.o ../lib/libRNA.a -lm powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNALfold RNALfold.o ../lib/libRNA.a -lm mv -f .deps/RNAinverse.Tpo .deps/RNAinverse.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAinverse RNAinverse.o ../lib/libRNA.a -lm mv -f .deps/RNApdist.Tpo .deps/RNApdist.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNApdist RNApdist.o ../lib/libRNA.a -lm mv -f .deps/RNAfold.Tpo .deps/RNAfold.Po mv -f .deps/RNApaln.Tpo .deps/RNApaln.Po mv -f .deps/RNAsubopt.Tpo .deps/RNAsubopt.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAfold RNAfold.o ../lib/libRNA.a -lm powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNApaln RNApaln.o ../lib/libRNA.a -lm mv -f .deps/RNAplfold.Tpo .deps/RNAplfold.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAsubopt RNAsubopt.o ../lib/libRNA.a -lm powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAplfold RNAplfold.o ../lib/libRNA.a -lm mv -f .deps/RNAcofold.Tpo .deps/RNAcofold.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAcofold RNAcofold.o ../lib/libRNA.a -lm mv -f .deps/RNAdistance.Tpo .deps/RNAdistance.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAdistance RNAdistance.o ../lib/libRNA.a -lm mv -f .deps/RNAalifold.Tpo .deps/RNAalifold.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAalifold RNAalifold.o ../lib/libRNA.a -lm mv -f .deps/RNAup.Tpo .deps/RNAup.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAup RNAup.o ../lib/libRNA.a -lm make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs' Making all in man make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man' Making all in Utils make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils' powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT b2ct.o -MD -MP -MF .deps/b2ct.Tpo -c -o b2ct.o b2ct.c powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -MT popt.o -MD -MP -MF .deps/popt.Tpo -c -o popt.o popt.c if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' b2mt.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' ct2b.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' dpzoom.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' mountain.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' relplot.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' rotate_ss.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' cmount.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' colorrna.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' coloraln.pl ; \ fi if test -n "/usr/bin/perl"; then \ /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' refold.pl ; \ fi mv -f .deps/popt.Tpo .deps/popt.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o popt popt.o -L../lib -lRNA -lm mv -f .deps/b2ct.Tpo .deps/b2ct.Po powerpc-unknown-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -o b2ct b2ct.o -L../lib -lRNA -lm make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils' Making all in H make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H' Making all in Perl make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl' /usr/bin/perl Makefile.PL INSTALLDIRS=vendor LDDLFLAGS="-Wl,-O1 -Wl,--as-needed -shared" Writing Makefile.perl for RNA make -f Makefile.perl make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl' powerpc-unknown-linux-gnu-gcc -c -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O1 -pipe -DVERSION=\"0.2\" -DXS_VERSION=\"0.2\" -fPIC "-I/usr/lib/perl5/5.12.4/powerpc-linux/CORE" RNA_wrap.c Running Mkbootstrap for RNA () cp RNA.pm blib/lib/RNA.pm chmod 644 RNA.bs cp RNA.bs blib/arch/auto/RNA/RNA.bs chmod 644 blib/arch/auto/RNA/RNA.bs In file included from RNA_wrap.c:1547: ../H/part_func_co.h:28: warning: 'struct plist' declared inside parameter list ../H/part_func_co.h:33: error: expected identifier or '(' before numeric constant ../H/part_func_co.h:34: error: expected ';' before 'double' RNA_wrap.c:2169: error: expected ';', ',' or ')' before numeric constant make[3]: *** [RNA_wrap.o] Error 1 make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl' make[2]: *** [all-local] Error 2 make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5' make: *** [all] Error 2 emake failed * ERROR: sci-biology/vienna-rna-1.8.5 failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 85: Called src_compile * environment, line 5889: Called die * The specific snippet of code: * emake || die; * * If you need support, post the output of 'emerge --info =sci-biology/vienna-rna-1.8.5', * the complete build log and the output of 'emerge -pqv =sci-biology/vienna-rna-1.8.5'. * The complete build log is located at '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/temp/environment'. * S: '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'