* Package: sci-biology/vienna-rna-1.8.4-r1 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: elibc_glibc kernel_linux test userland_GNU x86 >>> Unpacking source... >>> Unpacking ViennaRNA-1.8.4.tar.gz to /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work >>> Preparing source in /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4 ... * 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 ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70' ... * Running aclocal ... [ ok ] * Running autoconf ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/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-1.8.4-r1/work/ViennaRNA-1.8.4/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-1.8.4-r1/work/ViennaRNA-1.8.4' ... * 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-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70' ... * Running aclocal ... [ ok ] * Running autoconf ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/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-1.8.4-r1/work/ViennaRNA-1.8.4 ... * econf: updating ViennaRNA-1.8.4/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-1.8.4/Kinfold/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-1.8.4/Kinfold/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-1.8.4/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-1.8.4/RNAforester/g2-0.70/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-1.8.4/RNAforester/g2-0.70/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-1.8.4/RNAforester/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=i686-pc-linux-gnu --host=i686-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --with-cluster configure: loading site script /usr/share/config.site configure: loading site script /usr/share/crossdev/include/site/linux 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... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for i686-pc-linux-gnu-gcc... i686-pc-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 i686-pc-linux-gnu-gcc accepts -g... yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of i686-pc-linux-gnu-gcc... gcc3 checking whether i686-pc-linux-gnu-gcc accepts -fpic... yes checking for i686-pc-linux-gnu-ranlib... i686-pc-linux-gnu-ranlib checking whether i686-pc-linux-gnu-gcc and cc understand -c and -o together... yes checking for perl... /usr/bin/perl checking how to run the C preprocessor... i686-pc-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-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=i686-pc-linux-gnu' '--host=i686-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--with-cluster' 'build_alias=i686-pc-linux-gnu' 'host_alias=i686-pc-linux-gnu' 'CFLAGS=-O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu' --cache-file=/dev/null --srcdir=. configure: loading site script /usr/share/config.site configure: loading site script /usr/share/crossdev/include/site/linux 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 i686-pc-linux-gnu-g++... i686-pc-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 i686-pc-linux-gnu-g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of i686-pc-linux-gnu-g++... gcc3 checking for i686-pc-linux-gnu-gcc... i686-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... yes checking whether i686-pc-linux-gnu-gcc accepts -g... yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed checking dependency style of i686-pc-linux-gnu-gcc... gcc3 using (to be built) libRNA.a in ../lib checking how to run the C++ preprocessor... i686-pc-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... 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 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-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=i686-pc-linux-gnu' '--host=i686-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--with-cluster' 'build_alias=i686-pc-linux-gnu' 'host_alias=i686-pc-linux-gnu' 'CFLAGS=-O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu' 'CXXFLAGS=-O2 -pipe' --cache-file=/dev/null --srcdir=. configure: loading site script /usr/share/config.site configure: loading site script /usr/share/crossdev/include/site/linux checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for i686-pc-linux-gnu-gcc... i686-pc-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 i686-pc-linux-gnu-gcc accepts -g... yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed checking how to run the C preprocessor... i686-pc-linux-gnu-gcc -E checking for i686-pc-linux-gnu-g++... i686-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether i686-pc-linux-gnu-g++ accepts -g... yes checking for i686-pc-linux-gnu-ranlib... i686-pc-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-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=i686-pc-linux-gnu' '--host=i686-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--with-cluster' 'build_alias=i686-pc-linux-gnu' 'host_alias=i686-pc-linux-gnu' 'CFLAGS=-O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu' --cache-file=/dev/null --srcdir=. configure: loading site script /usr/share/config.site configure: loading site script /usr/share/crossdev/include/site/linux 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 i686-pc-linux-gnu-gcc... i686-pc-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 i686-pc-linux-gnu-gcc accepts -g... yes checking for i686-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of i686-pc-linux-gnu-gcc... gcc3 checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-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... i686-pc-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-1.8.4-r1/work/ViennaRNA-1.8.4 ... make -j14 clean Making clean in Kinfold make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' Making clean in Example make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example' make[2]: Nothing to be done for `clean'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example' Making clean in . make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' test -z "Kinfold" || rm -f Kinfold rm -f *.o make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' Making clean in RNAforester make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' Making clean in man make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man' make[2]: Nothing to be done for `clean'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man' Making clean in src make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src' test -z "RNAforester" || rm -f RNAforester rm -f *.o make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src' Making clean in g2-0.70 make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70' (cd ./demo ; make clean) make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/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-1.8.4-r1/work/ViennaRNA-1.8.4/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-1.8.4-r1/work/ViennaRNA-1.8.4/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-1.8.4-r1/work/ViennaRNA-1.8.4/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-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70' Making clean in . make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' make[2]: Nothing to be done for `clean-am'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' Making clean in Cluster make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster' test -z "AnalyseDists AnalyseSeqs" || rm -f AnalyseDists AnalyseSeqs rm -f *.o make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster' Making clean in Perl make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' /usr/bin/perl Makefile.PL LDDLFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -shared" Writing Makefile.perl for RNA make -f Makefile.perl clean make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/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-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' Making clean in H make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H' make[1]: Nothing to be done for `clean'. make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H' Making clean in Utils make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils' test -z "b2ct popt" || rm -f b2ct popt rm -f *.o make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils' Making clean in man make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/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-1.8.4-r1/work/ViennaRNA-1.8.4/man' Making clean in Progs make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/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-1.8.4-r1/work/ViennaRNA-1.8.4/Progs' Making clean in lib make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib' test -z "libRNA.a" || rm -f libRNA.a rm -f *.o make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib' Making clean in . make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4' make[1]: Nothing to be done for `clean-am'. make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4' make -j14 make all-recursive make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4' Making all in lib make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib' i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 mv -f .deps/libRNA_a-dist_vars.Tpo .deps/libRNA_a-dist_vars.Po i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 mv -f .deps/libRNA_a-fold_vars.Tpo .deps/libRNA_a-fold_vars.Po i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 inverse.c: In function ‘pf_cost’: inverse.c:488:4: warning: passing argument 1 of ‘pf_fold’ discards qualifiers from pointer target type ./../H/part_func.h:6:15: note: expected ‘char *’ but argument is of type ‘const char *’ stringdist.c:24:0: warning: "INFINITY" redefined /usr/include/bits/inf.h:27:0: note: this is the location of the previous definition mv -f .deps/libRNA_a-ProfileDist.Tpo .deps/libRNA_a-ProfileDist.Po i686-pc-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 mv -f .deps/libRNA_a-utils.Tpo .deps/libRNA_a-utils.Po i686-pc-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 mv -f .deps/libRNA_a-energy_par.Tpo .deps/libRNA_a-energy_par.Po i686-pc-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 mv -f .deps/libRNA_a-list.Tpo .deps/libRNA_a-list.Po i686-pc-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-params.Tpo .deps/libRNA_a-params.Po i686-pc-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-RNAstruct.Tpo .deps/libRNA_a-RNAstruct.Po mv -f .deps/libRNA_a-PS_dot.Tpo .deps/libRNA_a-PS_dot.Po i686-pc-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 i686-pc-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-stringdist.Tpo .deps/libRNA_a-stringdist.Po mv -f .deps/libRNA_a-treedist.Tpo .deps/libRNA_a-treedist.Po i686-pc-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 i686-pc-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-inverse.Tpo .deps/libRNA_a-inverse.Po i686-pc-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 duplex.c: In function ‘aliduplexfold’: duplex.c:385:3: warning: passing argument 3 of ‘alibacktrack’ from incompatible pointer type duplex.c:37:16: note: expected ‘const short int **’ but argument is of type ‘short int **’ duplex.c:385:3: warning: passing argument 4 of ‘alibacktrack’ from incompatible pointer type duplex.c:37:16: note: expected ‘const short int **’ but argument is of type ‘short int **’ duplex.c: In function ‘aliduplex_subopt’: duplex.c:462:7: warning: passing argument 3 of ‘alibacktrack’ from incompatible pointer type duplex.c:37:16: note: expected ‘const short int **’ but argument is of type ‘short int **’ duplex.c:462:7: warning: passing argument 4 of ‘alibacktrack’ from incompatible pointer type duplex.c:37:16: note: expected ‘const short int **’ but argument is of type ‘short int **’ alifold.c: In function ‘make_pscores’: alifold.c:722:5: warning: passing argument 1 of ‘get_ribosum’ from incompatible pointer type ./../H/ribo.h:1:16: note: expected ‘char **’ but argument is of type ‘const char * const*’ mv -f .deps/libRNA_a-ProfileAln.Tpo .deps/libRNA_a-ProfileAln.Po mv -f .deps/libRNA_a-read_epars.Tpo .deps/libRNA_a-read_epars.Po i686-pc-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:1154:5: warning: passing argument 1 of ‘get_ribosum’ from incompatible pointer type ./../H/ribo.h:1:16: note: expected ‘char **’ but argument is of type ‘const char * const*’ i686-pc-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-aln_util.Tpo .deps/libRNA_a-aln_util.Po i686-pc-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-part_func.Tpo .deps/libRNA_a-part_func.Po i686-pc-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-naview.Tpo .deps/libRNA_a-naview.Po mv -f .deps/libRNA_a-subopt.Tpo .deps/libRNA_a-subopt.Po mv -f .deps/libRNA_a-MEA.Tpo .deps/libRNA_a-MEA.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 In file included from /usr/include/stdio.h:930:0, from part_func_up.c:56: In function ‘sprintf’, inlined from ‘plot_free_pu_out’ at part_func_up.c:1449:10: /usr/include/bits/stdio2.h:34:3: warning: call to __builtin___sprintf_chk will always overflow destination buffer mv -f .deps/libRNA_a-ribo.Tpo .deps/libRNA_a-ribo.Po mv -f .deps/libRNA_a-duplex.Tpo .deps/libRNA_a-duplex.Po mv -f .deps/libRNA_a-part_func_co.Tpo .deps/libRNA_a-part_func_co.Po mv -f .deps/libRNA_a-LPfold.Tpo .deps/libRNA_a-LPfold.Po mv -f .deps/libRNA_a-alifold.Tpo .deps/libRNA_a-alifold.Po mv -f .deps/libRNA_a-part_func_up.Tpo .deps/libRNA_a-part_func_up.Po mv -f .deps/libRNA_a-cofold.Tpo .deps/libRNA_a-cofold.Po mv -f .deps/libRNA_a-fold.Tpo .deps/libRNA_a-fold.Po mv -f .deps/libRNA_a-alipfold.Tpo .deps/libRNA_a-alipfold.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 i686-pc-linux-gnu-ranlib libRNA.a make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib' Making all in Progs make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs' i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 i686-pc-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 mv -f .deps/RNAplot.Tpo .deps/RNAplot.Po RNAinverse.c:31:0: warning: "INFINITY" redefined /usr/include/bits/inf.h:27:0: note: this is the location of the previous definition i686-pc-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 mv -f .deps/RNApdist.Tpo .deps/RNApdist.Po mv -f .deps/RNAeval.Tpo .deps/RNAeval.Po RNAup.c: In function ‘main’: RNAup.c:110:5: warning: format ‘%100s’ expects type ‘char *’, but argument 3 has type ‘char (*)[201]’ mv -f .deps/RNAheat.Tpo .deps/RNAheat.Po mv -f .deps/RNAduplex.Tpo .deps/RNAduplex.Po i686-pc-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 mv -f .deps/RNALfold.Tpo .deps/RNALfold.Po mv -f .deps/RNAinverse.Tpo .deps/RNAinverse.Po mv -f .deps/RNAfold.Tpo .deps/RNAfold.Po mv -f .deps/RNAsubopt.Tpo .deps/RNAsubopt.Po i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAeval RNAeval.o ../lib/libRNA.a -lm RNAaliduplex.c: In function ‘main’: RNAaliduplex.c:128:5: warning: passing argument 1 of ‘aliduplex_subopt’ from incompatible pointer type ./../H/duplex.h:14:17: note: expected ‘const char **’ but argument is of type ‘char **’ RNAaliduplex.c:128:5: warning: passing argument 2 of ‘aliduplex_subopt’ from incompatible pointer type ./../H/duplex.h:14:17: note: expected ‘const char **’ but argument is of type ‘char **’ RNAaliduplex.c:135:5: warning: passing argument 1 of ‘aliduplexfold’ from incompatible pointer type RNAaliduplex.c:22:16: note: expected ‘const char **’ but argument is of type ‘char **’ RNAaliduplex.c:135:5: warning: passing argument 2 of ‘aliduplexfold’ from incompatible pointer type RNAaliduplex.c:22:16: note: expected ‘const char **’ but argument is of type ‘char **’ i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAheat RNAheat.o ../lib/libRNA.a -lm i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNApdist RNApdist.o ../lib/libRNA.a -lm mv -f .deps/RNAplfold.Tpo .deps/RNAplfold.Po i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAinverse RNAinverse.o ../lib/libRNA.a -lm mv -f .deps/RNApaln.Tpo .deps/RNApaln.Po mv -f .deps/RNAaliduplex.Tpo .deps/RNAaliduplex.Po i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAplot RNAplot.o ../lib/libRNA.a -lm i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAsubopt RNAsubopt.o ../lib/libRNA.a -lm mv -f .deps/RNAdistance.Tpo .deps/RNAdistance.Po i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNALfold RNALfold.o ../lib/libRNA.a -lm i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNApaln RNApaln.o ../lib/libRNA.a -lm i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAduplex RNAduplex.o ../lib/libRNA.a -lm mv -f .deps/RNAcofold.Tpo .deps/RNAcofold.Po i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAplfold RNAplfold.o ../lib/libRNA.a -lm i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAaliduplex RNAaliduplex.o ../lib/libRNA.a -lm i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAfold RNAfold.o ../lib/libRNA.a -lm i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAdistance RNAdistance.o ../lib/libRNA.a -lm i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAcofold RNAcofold.o ../lib/libRNA.a -lm mv -f .deps/RNAalifold.Tpo .deps/RNAalifold.Po i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAalifold RNAalifold.o ../lib/libRNA.a -lm mv -f .deps/RNAup.Tpo .deps/RNAup.Po i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAup RNAup.o ../lib/libRNA.a -lm make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs' Making all in man make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man' Making all in Utils make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils' i686-pc-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 i686-pc-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 i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o popt popt.o -L../lib -lRNA -lm mv -f .deps/b2ct.Tpo .deps/b2ct.Po i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o b2ct b2ct.o -L../lib -lRNA -lm make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils' Making all in H make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H' Making all in Perl make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' /usr/bin/perl Makefile.PL LDDLFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -shared" Writing Makefile.perl for RNA make -f Makefile.perl make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' cp RNA.pm blib/lib/RNA.pm i686-pc-linux-gnu-gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -DVERSION=\"0.2\" -DXS_VERSION=\"0.2\" -fPIC "-I/usr/lib/perl5/5.12.2/i686-linux-thread-multi/CORE" RNA_wrap.c Running Mkbootstrap for RNA () 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:1501:0: ../H/part_func_co.h:28:9: warning: ‘struct plist’ declared inside parameter list ../H/part_func_co.h:28:9: warning: its scope is only this definition or declaration, which is probably not what you want rm -f blib/arch/auto/RNA/RNA.so i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -shared RNA_wrap.o -o blib/arch/auto/RNA/RNA.so ../lib/libRNA.a \ -lm \ chmod 755 blib/arch/auto/RNA/RNA.so Manifying blib/man3/RNA.3pm make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' Making all in Cluster make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster' i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -MT split.o -MD -MP -MF .deps/split.Tpo -c -o split.o split.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -MT distance_matrix.o -MD -MP -MF .deps/distance_matrix.Tpo -c -o distance_matrix.o distance_matrix.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -MT cluster.o -MD -MP -MF .deps/cluster.Tpo -c -o cluster.o cluster.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -MT treeplot.o -MD -MP -MF .deps/treeplot.Tpo -c -o treeplot.o treeplot.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -MT AD_main.o -MD -MP -MF .deps/AD_main.Tpo -c -o AD_main.o AD_main.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -c ./../lib/utils.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -MT statgeom.o -MD -MP -MF .deps/statgeom.Tpo -c -o statgeom.o statgeom.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -MT AS_main.o -MD -MP -MF .deps/AS_main.Tpo -c -o AS_main.o AS_main.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -MT PS3D.o -MD -MP -MF .deps/PS3D.Tpo -c -o PS3D.o PS3D.c mv -f .deps/AD_main.Tpo .deps/AD_main.Po AS_main.c: In function ‘main’: AS_main.c:229:7: warning: attempt to free a non-heap object ‘ss’ mv -f .deps/PS3D.Tpo .deps/PS3D.Po mv -f .deps/split.Tpo .deps/split.Po mv -f .deps/treeplot.Tpo .deps/treeplot.Po mv -f .deps/AS_main.Tpo .deps/AS_main.Po mv -f .deps/cluster.Tpo .deps/cluster.Po mv -f .deps/statgeom.Tpo .deps/statgeom.Po mv -f .deps/distance_matrix.Tpo .deps/distance_matrix.Po i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o utils.o -lm i686-pc-linux-gnu-gcc -O2 -pipe -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o utils.o -lm make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster' Making all in RNAforester make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' make all-recursive make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' Making all in g2-0.70 make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70' i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_device.c -o src/g2_device.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_control.c -o src/g2_ui_control.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_util.c -o src/g2_util.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_fif.c -o src/g2_fif.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_virtual_device.c -o src/g2_virtual_device.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_physical_device.c -o src/g2_physical_device.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_graphic_pd.c -o src/g2_graphic_pd.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_control_pd.c -o src/g2_control_pd.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_graphic.c -o src/g2_ui_graphic.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_virtual_device.c -o src/g2_ui_virtual_device.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_device.c -o src/g2_ui_device.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_splines.c -o src/g2_splines.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/PS/g2_PS.c -o src/PS/g2_PS.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/FIG/g2_FIG.c -o src/FIG/g2_FIG.o i686-pc-linux-gnu-gcc -I./src -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/X11/g2_X11.c -o src/X11/g2_X11.o ar -cr libg2.a ./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 test ! -n "i686-pc-linux-gnu-ranlib" || i686-pc-linux-gnu-ranlib libg2.a test -d ./include || mkdir ./include cp ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ./include/ make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70' Making all in src make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src' i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT Arguments.o -MD -MP -MF .deps/Arguments.Tpo -c -o Arguments.o Arguments.cpp i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT glib.o -MD -MP -MF .deps/glib.Tpo -c -o glib.o glib.c i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT ppforestbase.o -MD -MP -MF .deps/ppforestbase.Tpo -c -o ppforestbase.o ppforestbase.cpp i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT progressive_align.o -MD -MP -MF .deps/progressive_align.Tpo -c -o progressive_align.o progressive_align.cpp i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT rna_profile_alignment.o -MD -MP -MF .deps/rna_profile_alignment.Tpo -c -o rna_profile_alignment.o rna_profile_alignment.cpp i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT rna_alignment.o -MD -MP -MF .deps/rna_alignment.Tpo -c -o rna_alignment.o rna_alignment.cpp i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT rna_algebra.o -MD -MP -MF .deps/rna_algebra.Tpo -c -o rna_algebra.o rna_algebra.cpp i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT rna_alphabet.o -MD -MP -MF .deps/rna_alphabet.Tpo -c -o rna_alphabet.o rna_alphabet.cpp i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT rnaforest.o -MD -MP -MF .deps/rnaforest.Tpo -c -o rnaforest.o rnaforest.cpp glib.c: In function ‘ReadMatrix’: glib.c:272:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result glib.c:282:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result glib.c: In function ‘ReadEuclid’: glib.c:225:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result glib.c:234:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result glib.c: In function ‘ReadGraph’: glib.c:161:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result glib.c:170:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result glib.c:176:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT rnaforestsz.o -MD -MP -MF .deps/rnaforestsz.Tpo -c -o rnaforestsz.o rnaforestsz.cpp i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT rnafuncs.o -MD -MP -MF .deps/rnafuncs.Tpo -c -o rnafuncs.o rnafuncs.cpp i686-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT rnaforester_options.o -MD -MP -MF .deps/rnaforester_options.Tpo -c -o rnaforester_options.o rnaforester_options.cpp i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -MT wmatch.o -MD -MP -MF .deps/wmatch.Tpo -c -o wmatch.o wmatch.c mv -f .deps/glib.Tpo .deps/glib.Po mv -f .deps/rna_alphabet.Tpo .deps/rna_alphabet.Po In file included from rnaforest.h:22:0, from rna_alignment.h:24, from main.cpp:52: rnafuncs.h:42:3: warning: ‘typedef’ was ignored in this declaration In file included from rna_profile_alignment.cpp:37:0: rnafuncs.h:42:3: warning: ‘typedef’ was ignored in this declaration In file included from rnaforest.h:22:0, from rnaforest.cpp:24: rnafuncs.h:42:3: warning: ‘typedef’ was ignored in this declaration In file included from rnafuncs.cpp:23:0: rnafuncs.h:42:3: warning: ‘typedef’ was ignored in this declaration In file included from rnaforestsz.cpp:15:0: rnafuncs.h:42:3: warning: ‘typedef’ was ignored in this declaration mv -f .deps/ppforestbase.Tpo .deps/ppforestbase.Po mv -f .deps/rnaforest.Tpo .deps/rnaforest.Po In file included from rnaforest.h:22:0, from rna_alignment.h:24, from rna_alignment.cpp:22: rnafuncs.h:42:3: warning: ‘typedef’ was ignored in this declaration progressive_align.cpp: In function ‘node_entry* makePairsGraph(const RNAProfileAliMapType&, const DoubleScoreProfileAlgebraType*, const Matrix*, double)’: progressive_align.cpp:341:30: warning: deprecated conversion from string constant to ‘char*’ mv -f .deps/rnaforestsz.Tpo .deps/rnaforestsz.Po mv -f .deps/rna_algebra.Tpo .deps/rna_algebra.Po mv -f .deps/wmatch.Tpo .deps/wmatch.Po mv -f .deps/rna_alignment.Tpo .deps/rna_alignment.Po mv -f .deps/Arguments.Tpo .deps/Arguments.Po mv -f .deps/rnafuncs.Tpo .deps/rnafuncs.Po mv -f .deps/rnaforester_options.Tpo .deps/rnaforester_options.Po mv -f .deps/rna_profile_alignment.Tpo .deps/rna_profile_alignment.Po mv -f .deps/progressive_align.Tpo .deps/progressive_align.Po mv -f .deps/main.Tpo .deps/main.Po i686-pc-linux-gnu-g++ -O2 -pipe -L../g2-0.70 -L../../lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o RNAforester Arguments.o glib.o main.o ppforestbase.o progressive_align.o rna_profile_alignment.o rna_alignment.o rna_algebra.o rna_alphabet.o rnaforest.o rnaforestsz.o rnafuncs.o rnaforester_options.o wmatch.o -lg2 -lRNA make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src' Making all in man make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man' make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' Making all in Kinfold make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' make all-recursive make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' Making all in Example make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example' make[4]: Nothing to be done for `all'. make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example' make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -MT baum.o -MD -MP -MF .deps/baum.Tpo -c -o baum.o baum.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -MT cache.o -MD -MP -MF .deps/cache.Tpo -c -o cache.o cache.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -MT globals.o -MD -MP -MF .deps/globals.Tpo -c -o globals.o globals.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -MT nachbar.o -MD -MP -MF .deps/nachbar.Tpo -c -o nachbar.o nachbar.c i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -MT cmdline.o -MD -MP -MF .deps/cmdline.Tpo -c -o cmdline.o cmdline.c globals.c: In function ‘process_options_gg’: globals.c:320:9: warning: format ‘%g’ expects type ‘float *’, but argument 3 has type ‘double *’ globals.c:320:9: warning: format ‘%g’ expects type ‘float *’, but argument 4 has type ‘double *’ globals.c:320:9: warning: format ‘%g’ expects type ‘float *’, but argument 5 has type ‘double *’ globals.c: In function ‘process_options’: globals.c:406:8: warning: format ‘%g’ expects type ‘float *’, but argument 3 has type ‘double *’ globals.c:406:8: warning: format ‘%g’ expects type ‘float *’, but argument 4 has type ‘double *’ globals.c:406:8: warning: format ‘%g’ expects type ‘float *’, but argument 5 has type ‘double *’ mv -f .deps/cache.Tpo .deps/cache.Po mv -f .deps/main.Tpo .deps/main.Po mv -f .deps/globals.Tpo .deps/globals.Po mv -f .deps/nachbar.Tpo .deps/nachbar.Po mv -f .deps/baum.Tpo .deps/baum.Po mv -f .deps/cmdline.Tpo .deps/cmdline.Po i686-pc-linux-gnu-gcc -O2 -pipe -L../lib -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o -lRNA -lm make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4' make -j14 -C Readseq make: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Readseq' Compiling readseq... i686-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -O2 -pipe -o readseq readseq.c ureadseq.c readseq.c: In function ‘formatstr’: readseq.c:261:27: warning: return discards qualifiers from pointer target type readseq.c:263:31: warning: return discards qualifiers from pointer target type readseq.c:267:8: warning: return discards qualifiers from pointer target type readseq.c: In function ‘usage’: readseq.c:332:3: warning: format not a string literal and no format arguments readseq.c: In function ‘main’: readseq.c:772:3: warning: format not a string literal and no format arguments readseq.c:914:13: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:916:13: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ readseq.c:959:17: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ readseq.c:959:17: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:959:17: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ readseq.c:969:15: warning: format not a string literal and no format arguments readseq.c:976:19: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ readseq.c:976:19: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:977:19: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ readseq.c:977:19: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:1080:19: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:1080:19: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘long unsigned int’ readseq.c:1091:5: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:1092:5: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:1116:9: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:761:11: warning: ignoring return value of ‘tmpnam’, declared with attribute warn_unused_result readseq.c:779:9: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result readseq.c:843:11: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result readseq.c:889:13: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result readseq.c:915:20: warning: ignoring return value of ‘freopen’, declared with attribute warn_unused_result readseq.c: In function ‘chooseFormat’: readseq.c:423:11: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result ureadseq.c: In function ‘seqFileFormatFp’: ureadseq.c:1346:5: warning: format ‘%d’ expects type ‘int *’, but argument 3 has type ‘long int *’ ureadseq.c:1346:5: warning: format ‘%d’ expects type ‘int *’, but argument 4 has type ‘long int *’ ureadseq.c: In function ‘writeSeq’: ureadseq.c:1595:3: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ ureadseq.c:1624:7: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1625:7: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1625:7: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1639:7: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1639:7: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1649:7: warning: format ‘%10d’ expects type ‘int’, but argument 3 has type ‘long int’ ureadseq.c:1659:7: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1659:7: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1668:7: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1668:7: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1669:7: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ ureadseq.c:1680:7: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1680:7: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1689:7: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1689:7: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1695:7: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1695:7: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1726:7: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1748:7: warning: format ‘%6d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1748:7: warning: format ‘%8X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1765:9: warning: format ‘%6d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1765:9: warning: format ‘%8X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1772:21: warning: format ‘%6d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1772:21: warning: format ‘%5d’ expects type ‘int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1783:7: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1783:7: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1791:7: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1791:7: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1797:7: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1797:7: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1838:9: warning: format ‘%-9d’ expects type ‘int’, but argument 3 has type ‘long int’ In file included from /usr/include/string.h:642:0, from ureadseq.c:22: In function ‘strcpy’, inlined from ‘writeSeq’ at ureadseq.c:1736:13: /usr/include/bits/string3.h:107:3: warning: call to __builtin___strcpy_chk will always overflow destination buffer /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/temp/ccwgtVj7.o: In function `main': readseq.c:(.text+0x1d6b): warning: the use of `tmpnam' is dangerous, better use `mkstemp' /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/temp/ccwgtVj7.o: In function `chooseFormat': readseq.c:(.text+0x8e2): warning: the `gets' function is dangerous and should not be used. make: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Readseq' >>> Source compiled. make -j14 check make -f Makefile.perl make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make check-local make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make -f Makefile.perl make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make -f Makefile.perl test make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' PERL_DL_NONLAZY=1 /usr/bin/perl5.12.2 "-Iblib/lib" "-Iblib/arch" test.pl 1..24 # Running under perl version 5.012002 for linux # Current time local: Fri Oct 15 04:14:35 2010 # Current time GMT: Fri Oct 15 02:14:35 2010 # Using Test.pm version 1.25 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 please check the two postscript files test_ss.ps and test_dp.ps ok 20 14 suboptimals (((.((....)).))) -5.50 (((.(((...)))))) -5.30 .((.((....)).)). -5.10 (((.((.....))))) -5.00 .((.(((...))))). -4.90 .((.((.....)))). -4.60 ....(((...)))... -2.80 ....((.....))... -2.50 (((..((....))))) -2.20 .((..((....)))). -1.80 ....((....)).... -1.10 .....((....))... -0.90 (((..........))) -0.80 ((..((....))..)) -0.50 ok 21 ok 22 ok 23 ok 24 make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make -j14 test Test for general read/write of all chars: ./readseq -p alphabet.std -otest.alpha diff -w test.alpha alphabet.std 1c1 < >alphabet['!'..'~'], 83 bases, E14ECBE2 checksum. --- > >alphabet['!'..'~'], 83 bases, 9429 checksum. make: [test] Error 1 (ignored) Test for valid format conversions: ./readseq -p -f=ig nucleic.std -otest.ig ./readseq -p -f=gb test.ig -otest.gb ./readseq -p -f=nbrf test.gb -otest.nbrf ./readseq -p -f=embl test.nbrf -otest.embl ./readseq -p -f=gcg test.embl -otest.gcg ./readseq -p -f=strider test.gcg -otest.strider ./readseq -p -f=fitch test.strider -otest.fitch ./readseq -p -f=fasta test.fitch -otest.fasta ./readseq -p -f=pir test.fasta -otest.pir ./readseq -p -f=ig test.pir -otest.ig-b diff -w test.ig test.ig-b 1,2c1,2 < ;nucleic/amino test, 228 bases, 1B5655D0 checksum. < nucleic/amino --- > ;nucleic/amino, , 228 bases, 1B5655D0 checksum. > nucleic/amino, make: [test] Error 1 (ignored) Test for multiple-sequence format conversions: ./readseq -p -f=ig multi.std -otest.m-ig ./readseq -p -f=gb test.m-ig -otest.m-gb ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf ./readseq -p -f=embl test.m-nbrf -otest.m-embl ./readseq -p -f=fasta test.m-embl -otest.m-fasta ./readseq -p -f=pir test.m-fasta -otest.m-pir ./readseq -p -f=msf test.m-pir -otest.m-msf ./readseq -p -f=paup test.m-msf -otest.m-paup ./readseq -p -f=ig test.m-paup -otest.m-ig-b diff -w test.m-ig test.m-ig-b 1,2c1,2 < ;acarr58sst , 183 bases, 64754A4D checksum. < acarr58sst --- > ;acarr58ss, 183 bases, 64754A4D checksum. > acarr58ss 25,26c25,26 < ;ddirr58sst , 183 bases, 1E3D23B8 checksum. < ddirr58sst --- > ;ddirr58ss, 183 bases, 1E3D23B8 checksum. > ddirr58ss make: [test] Error 1 (ignored) Expect differences in the header lines due to different format headers. If any sequence lines differ, or if the checksums differ, there is a problem. ---------------------- To clean up test files, command me: make clean >>> Install vienna-rna-1.8.4-r1 into /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/ category sci-biology * Tinderbox QA Notice: 'make' called by src_install make -j14 install DESTDIR=/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/ Making install in lib make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib' make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib' test -z "/usr/lib" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib" make[2]: Nothing to be done for `install-data-am'. /usr/bin/install -c -m 644 libRNA.a '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib' ( cd '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib' && i686-pc-linux-gnu-ranlib libRNA.a ) make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib' Making install in Progs make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs' make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs' test -z "/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin" make[2]: Nothing to be done for `install-data-am'. /usr/bin/install -c RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs' Making install in man make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man' make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man' make[2]: Nothing to be done for `install-exec-am'. test -z "/usr/share/info" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/info" test -z "/usr/share/man/man1" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/man/man1" /usr/bin/install -c -m 644 RNAheat.1 RNAsubopt.1 RNAdistance.1 RNAinverse.1 RNAcofold.1 RNAeval.1 RNAfold.1 RNApdist.1 RNAplot.1 RNAalifold.1 RNALfold.1 RNAduplex.1 RNAplfold.1 RNAup.1 RNApaln.1 RNAaliduplex.1 '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/man/man1' /usr/bin/install -c -m 644 ./RNAlib.info '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/info' install-info --info-dir='/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/info' '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/info/RNAlib.info' install-info: warning: no info dir entry in `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/info/RNAlib.info' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man' Making install in Utils make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils' make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils' make[2]: Nothing to be done for `install-exec-am'. test -z "/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin" test -z "/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin" /usr/bin/install -c b2ct popt '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin' /usr/bin/install -c b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl Fold '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils' Making install in H make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H' make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H' make[2]: Nothing to be done for `install-exec-am'. test -z "/usr/include/ViennaRNA" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/include/ViennaRNA" /usr/bin/install -c -m 644 energy_par.h pair_mat.h RNAstruct.h dist_vars.h fold.h part_func.h stringdist.h edit_cost.h fold_vars.h profiledist.h treedist.h energy_const.h inverse.h PS_dot.h utils.h params.h subopt.h cofold.h duplex.h alifold.h aln_util.h part_func_co.h ProfileAln.h LPfold.h Lfold.h part_func_up.h ribo.h findpath.h MEA.h '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/include/ViennaRNA' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H' Making install in Perl make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make -f Makefile.perl make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make -f Makefile.perl make[2]: Nothing to be done for `install-data-am'. make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make -f Makefile.perl install make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' Appending installation info to /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib/perl5/5.12.2/i686-linux-thread-multi/perllocal.pod Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/usr/lib/perl5/site_perl/5.12.2/i686-linux-thread-multi/auto/RNA/RNA.bs Installing /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/usr/lib/perl5/site_perl/5.12.2/i686-linux-thread-multi/auto/RNA/RNA.so Installing /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/usr/lib/perl5/site_perl/5.12.2/i686-linux-thread-multi/RNA.pm Installing /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/usr/share/man/man3/RNA.3pm make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' Making install in Cluster make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster' make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster' test -z "/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin" test -z "/usr/share/man/man1" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/man/man1" /usr/bin/install -c AnalyseDists AnalyseSeqs '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin' /usr/bin/install -c -m 644 AnalyseDists.1 AnalyseSeqs.1 '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/man/man1' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster' Making install in RNAforester make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' Making install in g2-0.70 make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70' test -d /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib || mkdir -p /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib test -d /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/include || mkdir -p /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/include /usr/bin/install -c -m 644 libg2.a /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib for IFILE in ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ; do \ /usr/bin/install -c -m 644 $IFILE /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/include; \ done make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70' Making install in src make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src' make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src' test -z "/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin" make[3]: Nothing to be done for `install-data-am'. /usr/bin/install -c RNAforester '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin' make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src' Making install in man make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man' make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man' make[3]: Nothing to be done for `install-exec-am'. test -z "/usr/share/man/man1" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/man/man1" /usr/bin/install -c -m 644 RNAforester.1 '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/man/man1' make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man' make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' Making install in Kinfold make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' Making install in Example make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example' make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example' make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' make[3]: Nothing to be done for `install-data-am'. test -z "/usr/bin" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin" /usr/bin/install -c Kinfold '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin' make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4' make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4' make[2]: Nothing to be done for `install-exec-am'. test -z "/usr/share/ViennaRNA" || /bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/ViennaRNA" /usr/bin/install -c -m 644 vienna13.par default.par '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/ViennaRNA' make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4' make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4' >>> Completed installing vienna-rna-1.8.4-r1 into /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/ * Tinderbox QA Warning! Perl files installed in site_dir /usr/lib/perl5/site_perl/5.12.2 /usr/lib/perl5/site_perl/5.12.2/i686-linux-thread-multi /usr/lib/perl5/site_perl/5.12.2/i686-linux-thread-multi/RNA.pm /usr/lib/perl5/site_perl/5.12.2/i686-linux-thread-multi/auto /usr/lib/perl5/site_perl/5.12.2/i686-linux-thread-multi/auto/RNA /usr/lib/perl5/site_perl/5.12.2/i686-linux-thread-multi/auto/RNA/RNA.bs /usr/lib/perl5/site_perl/5.12.2/i686-linux-thread-multi/auto/RNA/RNA.so /usr/lib/perl5/site_perl/5.12.2/i686-linux-thread-multi/auto/RNA/.packlist * Tinderbox QA Warning (end)! Perl files installed in site_dir * Tinderbox QA Notice! Insecure functions used tmpnam@@GLIBC_2.0 /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/usr/bin/readseq-vienna * Tinderbox QA Notice (end)! Insecure functions used strip: i686-pc-linux-gnu-strip --strip-unneeded -R .comment usr/lib/perl5/site_perl/5.12.2/i686-linux-thread-multi/auto/RNA/RNA.so usr/bin/RNALfold usr/bin/RNApdist usr/bin/RNAcofold usr/bin/Kinfold usr/bin/RNAinverse usr/bin/popt usr/bin/RNAheat usr/bin/AnalyseSeqs usr/bin/RNAup usr/bin/RNAforester usr/bin/RNAaliduplex usr/bin/RNAplot usr/bin/RNAeval usr/bin/RNAdistance usr/bin/RNAalifold usr/bin/readseq-vienna usr/bin/AnalyseDists usr/bin/RNAplfold usr/bin/RNAduplex usr/bin/RNApaln usr/bin/RNAsubopt usr/bin/RNAfold usr/bin/b2ct usr/lib/libRNA.a usr/lib/libg2.a * QA Notice: Package has poor programming practices which may compile * fine but exhibit random runtime failures. * AS_main.c:229:7: warning: attempt to free a non-heap object ‘ss’ * QA Notice: Package has poor programming practices which may compile * fine but exhibit random runtime failures. * /usr/include/bits/stdio2.h:34:3: warning: call to __builtin___sprintf_chk will always overflow destination buffer * /usr/include/bits/string3.h:107:3: warning: call to __builtin___strcpy_chk will always overflow destination buffer * Please do not file a Gentoo bug and instead report the above QA * issues directly to the upstream developers of this software. * Homepage: http://www.tbi.univie.ac.at/~ivo/RNA