* CPV: sci-biology/vienna-rna-1.8.4-r1  * REPO: gentoo  * Maintainer: sci-biology@gentoo.org  * USE: amd64 elibc_glibc kernel_linux multilib userland_GNU >>> 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/RNAforester/g2-0.70/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/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-1.8.4/Kinfold/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-1.8.4/Kinfold/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-1.8.4/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-1.8.4/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --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... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking if malloc debugging is wanted... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-gcc... x86_64-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 x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3 checking whether x86_64-pc-linux-gnu-gcc accepts -fpic... yes checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking whether x86_64-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... x86_64-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=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib64' '--with-cluster' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CFLAGS=-march=nocona -O2 -pipe -fomit-frame-pointer' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' --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... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for x86_64-pc-linux-gnu-g++... x86_64-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 x86_64-pc-linux-gnu-g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-g++... gcc3 checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3 using (to be built) libRNA.a in ../lib checking how to run the C++ preprocessor... x86_64-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=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib64' '--with-cluster' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CFLAGS=-march=nocona -O2 -pipe -fomit-frame-pointer' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CXXFLAGS=-march=nocona -O2 -pipe -fomit-frame-pointer' --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... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-gcc... x86_64-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 x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking for x86_64-pc-linux-gnu-ranlib... x86_64-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=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib64' '--with-cluster' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CFLAGS=-march=nocona -O2 -pipe -fomit-frame-pointer' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' --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... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking if malloc debugging is wanted... no checking for x86_64-pc-linux-gnu-gcc... x86_64-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 x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-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... x86_64-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/lib64 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 -j1 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 -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 -j1 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' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 mv -f .deps/libRNA_a-dist_vars.Tpo .deps/libRNA_a-dist_vars.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 mv -f .deps/libRNA_a-fold_vars.Tpo .deps/libRNA_a-fold_vars.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 mv -f .deps/libRNA_a-part_func.Tpo .deps/libRNA_a-part_func.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 mv -f .deps/libRNA_a-read_epars.Tpo .deps/libRNA_a-read_epars.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 mv -f .deps/libRNA_a-treedist.Tpo .deps/libRNA_a-treedist.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 mv -f .deps/libRNA_a-energy_par.Tpo .deps/libRNA_a-energy_par.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 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 *’ mv -f .deps/libRNA_a-inverse.Tpo .deps/libRNA_a-inverse.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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-ProfileDist.Tpo .deps/libRNA_a-ProfileDist.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 mv -f .deps/libRNA_a-RNAstruct.Tpo .deps/libRNA_a-RNAstruct.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 mv -f .deps/libRNA_a-utils.Tpo .deps/libRNA_a-utils.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 mv -f .deps/libRNA_a-fold.Tpo .deps/libRNA_a-fold.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 naview.c: In function ‘dump_loops’: naview.c:334: warning: format ‘%d’ expects type ‘int’, but argument 2 has type ‘long int’ mv -f .deps/libRNA_a-naview.Tpo .deps/libRNA_a-naview.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 mv -f .deps/libRNA_a-PS_dot.Tpo .deps/libRNA_a-PS_dot.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 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 mv -f .deps/libRNA_a-stringdist.Tpo .deps/libRNA_a-stringdist.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 mv -f .deps/libRNA_a-params.Tpo .deps/libRNA_a-params.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 mv -f .deps/libRNA_a-subopt.Tpo .deps/libRNA_a-subopt.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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-list.Tpo .deps/libRNA_a-list.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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-Lfold.Tpo .deps/libRNA_a-Lfold.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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-cofold.Tpo .deps/libRNA_a-cofold.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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-part_func_co.Tpo .deps/libRNA_a-part_func_co.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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-ProfileAln.Tpo .deps/libRNA_a-ProfileAln.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 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-duplex.Tpo .deps/libRNA_a-duplex.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 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-alifold.Tpo .deps/libRNA_a-alifold.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 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-alipfold.Tpo .deps/libRNA_a-alipfold.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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-aln_util.Tpo .deps/libRNA_a-aln_util.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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-LPfold.Tpo .deps/libRNA_a-LPfold.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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 In file included from /usr/include/stdio.h:930, from part_func_up.c:56: In function ‘sprintf’, inlined from ‘plot_free_pu_out’ at part_func_up.c:1449: /usr/include/bits/stdio2.h:34: warning: call to __builtin___sprintf_chk will always overflow destination buffer mv -f .deps/libRNA_a-part_func_up.Tpo .deps/libRNA_a-part_func_up.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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-ribo.Tpo .deps/libRNA_a-ribo.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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-findpath.Tpo .deps/libRNA_a-findpath.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -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-MEA.Tpo .deps/libRNA_a-MEA.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 x86_64-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' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAfold.o -MD -MP -MF .deps/RNAfold.Tpo -c -o RNAfold.o RNAfold.c mv -f .deps/RNAfold.Tpo .deps/RNAfold.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAfold RNAfold.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAeval.o -MD -MP -MF .deps/RNAeval.Tpo -c -o RNAeval.o RNAeval.c mv -f .deps/RNAeval.Tpo .deps/RNAeval.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAeval RNAeval.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAheat.o -MD -MP -MF .deps/RNAheat.Tpo -c -o RNAheat.o RNAheat.c mv -f .deps/RNAheat.Tpo .deps/RNAheat.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAheat RNAheat.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNApdist.o -MD -MP -MF .deps/RNApdist.Tpo -c -o RNApdist.o RNApdist.c mv -f .deps/RNApdist.Tpo .deps/RNApdist.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNApdist RNApdist.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAdistance.o -MD -MP -MF .deps/RNAdistance.Tpo -c -o RNAdistance.o RNAdistance.c mv -f .deps/RNAdistance.Tpo .deps/RNAdistance.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAdistance RNAdistance.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAinverse.o -MD -MP -MF .deps/RNAinverse.Tpo -c -o RNAinverse.o RNAinverse.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 mv -f .deps/RNAinverse.Tpo .deps/RNAinverse.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAinverse RNAinverse.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAplot.o -MD -MP -MF .deps/RNAplot.Tpo -c -o RNAplot.o RNAplot.c mv -f .deps/RNAplot.Tpo .deps/RNAplot.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAplot RNAplot.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAsubopt.o -MD -MP -MF .deps/RNAsubopt.Tpo -c -o RNAsubopt.o RNAsubopt.c mv -f .deps/RNAsubopt.Tpo .deps/RNAsubopt.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAsubopt RNAsubopt.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNALfold.o -MD -MP -MF .deps/RNALfold.Tpo -c -o RNALfold.o RNALfold.c mv -f .deps/RNALfold.Tpo .deps/RNALfold.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNALfold RNALfold.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAcofold.o -MD -MP -MF .deps/RNAcofold.Tpo -c -o RNAcofold.o RNAcofold.c mv -f .deps/RNAcofold.Tpo .deps/RNAcofold.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAcofold RNAcofold.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNApaln.o -MD -MP -MF .deps/RNApaln.Tpo -c -o RNApaln.o RNApaln.c mv -f .deps/RNApaln.Tpo .deps/RNApaln.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNApaln RNApaln.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAduplex.o -MD -MP -MF .deps/RNAduplex.Tpo -c -o RNAduplex.o RNAduplex.c RNAduplex.c: In function ‘main’: RNAduplex.c:158: warning: format ‘%d’ expects type ‘int’, but argument 2 has type ‘size_t’ RNAduplex.c:158: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘size_t’ RNAduplex.c: In function ‘print_struc’: RNAduplex.c:188: warning: format ‘%-3d’ expects type ‘int’, but argument 6 has type ‘size_t’ mv -f .deps/RNAduplex.Tpo .deps/RNAduplex.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAduplex RNAduplex.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAalifold.o -MD -MP -MF .deps/RNAalifold.Tpo -c -o RNAalifold.o RNAalifold.c mv -f .deps/RNAalifold.Tpo .deps/RNAalifold.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAalifold RNAalifold.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAplfold.o -MD -MP -MF .deps/RNAplfold.Tpo -c -o RNAplfold.o RNAplfold.c mv -f .deps/RNAplfold.Tpo .deps/RNAplfold.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAplfold RNAplfold.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAup.o -MD -MP -MF .deps/RNAup.Tpo -c -o RNAup.o RNAup.c RNAup.c: In function ‘main’: RNAup.c:110: warning: format ‘%100s’ expects type ‘char *’, but argument 3 has type ‘char (*)[201]’ mv -f .deps/RNAup.Tpo .deps/RNAup.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAup RNAup.o ../lib/libRNA.a -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAaliduplex.o -MD -MP -MF .deps/RNAaliduplex.Tpo -c -o RNAaliduplex.o RNAaliduplex.c 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 **’ RNAaliduplex.c: In function ‘print_struc’: RNAaliduplex.c:150: warning: format ‘%-3d’ expects type ‘int’, but argument 6 has type ‘size_t’ mv -f .deps/RNAaliduplex.Tpo .deps/RNAaliduplex.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o RNAaliduplex RNAaliduplex.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' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT b2ct.o -MD -MP -MF .deps/b2ct.Tpo -c -o b2ct.o b2ct.c mv -f .deps/b2ct.Tpo .deps/b2ct.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o b2ct b2ct.o -L../lib -lRNA -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT popt.o -MD -MP -MF .deps/popt.Tpo -c -o popt.o popt.c mv -f .deps/popt.Tpo .deps/popt.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o popt popt.o -L../lib -lRNA -lm 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 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 -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 x86_64-pc-linux-gnu-gcc -c -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -march=nocona -O2 -pipe -fomit-frame-pointer -DVERSION=\"0.2\" -DXS_VERSION=\"0.2\" -fPIC "-I/usr/lib64/perl5/5.12.2/x86_64-linux-thread-multi/CORE" RNA_wrap.c In file included from RNA_wrap.c:1501: ../H/part_func_co.h:28: warning: ‘struct plist’ declared inside parameter list ../H/part_func_co.h:28: warning: its scope is only this definition or declaration, which is probably not what you want Running Mkbootstrap for RNA () chmod 644 RNA.bs rm -f blib/arch/auto/RNA/RNA.so x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -shared RNA_wrap.o -o blib/arch/auto/RNA/RNA.so ../lib/libRNA.a \ -lm \ chmod 755 blib/arch/auto/RNA/RNA.so cp RNA.bs blib/arch/auto/RNA/RNA.bs chmod 644 blib/arch/auto/RNA/RNA.bs 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' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=nocona -O2 -pipe -fomit-frame-pointer -MT split.o -MD -MP -MF .deps/split.Tpo -c -o split.o split.c mv -f .deps/split.Tpo .deps/split.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=nocona -O2 -pipe -fomit-frame-pointer -MT distance_matrix.o -MD -MP -MF .deps/distance_matrix.Tpo -c -o distance_matrix.o distance_matrix.c mv -f .deps/distance_matrix.Tpo .deps/distance_matrix.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=nocona -O2 -pipe -fomit-frame-pointer -MT cluster.o -MD -MP -MF .deps/cluster.Tpo -c -o cluster.o cluster.c mv -f .deps/cluster.Tpo .deps/cluster.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=nocona -O2 -pipe -fomit-frame-pointer -MT treeplot.o -MD -MP -MF .deps/treeplot.Tpo -c -o treeplot.o treeplot.c mv -f .deps/treeplot.Tpo .deps/treeplot.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=nocona -O2 -pipe -fomit-frame-pointer -MT AD_main.o -MD -MP -MF .deps/AD_main.Tpo -c -o AD_main.o AD_main.c mv -f .deps/AD_main.Tpo .deps/AD_main.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=nocona -O2 -pipe -fomit-frame-pointer -c ./../lib/utils.c x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o utils.o -lm x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=nocona -O2 -pipe -fomit-frame-pointer -MT statgeom.o -MD -MP -MF .deps/statgeom.Tpo -c -o statgeom.o statgeom.c mv -f .deps/statgeom.Tpo .deps/statgeom.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=nocona -O2 -pipe -fomit-frame-pointer -MT AS_main.o -MD -MP -MF .deps/AS_main.Tpo -c -o AS_main.o AS_main.c AS_main.c: In function ‘main’: AS_main.c:229: warning: attempt to free a non-heap object ‘ss’ mv -f .deps/AS_main.Tpo .deps/AS_main.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -march=nocona -O2 -pipe -fomit-frame-pointer -MT PS3D.o -MD -MP -MF .deps/PS3D.Tpo -c -o PS3D.o PS3D.c mv -f .deps/PS3D.Tpo .deps/PS3D.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -Wl,-O1 -Wl,--as-needed -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' x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 src/FIG/g2_FIG.c: In function ‘g2_FIG_draw_string’: src/FIG/g2_FIG.c:478: warning: format ‘%d’ expects type ‘int’, but argument 6 has type ‘size_t’ x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer -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 "x86_64-pc-linux-gnu-ranlib" || x86_64-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' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT Arguments.o -MD -MP -MF .deps/Arguments.Tpo -c -o Arguments.o Arguments.cpp mv -f .deps/Arguments.Tpo .deps/Arguments.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT glib.o -MD -MP -MF .deps/glib.Tpo -c -o glib.o glib.c glib.c: In function ‘ReadGraph’: glib.c:161: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result glib.c:170: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result glib.c:176: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result glib.c: In function ‘ReadEuclid’: glib.c:225: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result glib.c:234: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result glib.c: In function ‘ReadMatrix’: glib.c:272: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result glib.c:282: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result mv -f .deps/glib.Tpo .deps/glib.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp In file included from rnaforest.h:22, from rna_alignment.h:24, from main.cpp:52: rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration mv -f .deps/main.Tpo .deps/main.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT ppforestbase.o -MD -MP -MF .deps/ppforestbase.Tpo -c -o ppforestbase.o ppforestbase.cpp mv -f .deps/ppforestbase.Tpo .deps/ppforestbase.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT progressive_align.o -MD -MP -MF .deps/progressive_align.Tpo -c -o progressive_align.o progressive_align.cpp progressive_align.cpp: In function ‘node_entry* makePairsGraph(const RNAProfileAliMapType&, const DoubleScoreProfileAlgebraType*, const Matrix*, double)’: progressive_align.cpp:341: warning: deprecated conversion from string constant to ‘char*’ mv -f .deps/progressive_align.Tpo .deps/progressive_align.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT rna_profile_alignment.o -MD -MP -MF .deps/rna_profile_alignment.Tpo -c -o rna_profile_alignment.o rna_profile_alignment.cpp In file included from rna_profile_alignment.cpp:37: rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration mv -f .deps/rna_profile_alignment.Tpo .deps/rna_profile_alignment.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT rna_alignment.o -MD -MP -MF .deps/rna_alignment.Tpo -c -o rna_alignment.o rna_alignment.cpp In file included from rnaforest.h:22, from rna_alignment.h:24, from rna_alignment.cpp:22: rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration mv -f .deps/rna_alignment.Tpo .deps/rna_alignment.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT rna_algebra.o -MD -MP -MF .deps/rna_algebra.Tpo -c -o rna_algebra.o rna_algebra.cpp mv -f .deps/rna_algebra.Tpo .deps/rna_algebra.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT rna_alphabet.o -MD -MP -MF .deps/rna_alphabet.Tpo -c -o rna_alphabet.o rna_alphabet.cpp mv -f .deps/rna_alphabet.Tpo .deps/rna_alphabet.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT rnaforest.o -MD -MP -MF .deps/rnaforest.Tpo -c -o rnaforest.o rnaforest.cpp In file included from rnaforest.h:22, from rnaforest.cpp:24: rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration mv -f .deps/rnaforest.Tpo .deps/rnaforest.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT rnaforestsz.o -MD -MP -MF .deps/rnaforestsz.Tpo -c -o rnaforestsz.o rnaforestsz.cpp In file included from rnaforestsz.cpp:15: rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration mv -f .deps/rnaforestsz.Tpo .deps/rnaforestsz.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT rnafuncs.o -MD -MP -MF .deps/rnafuncs.Tpo -c -o rnafuncs.o rnafuncs.cpp In file included from rnafuncs.cpp:23: rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration mv -f .deps/rnafuncs.Tpo .deps/rnafuncs.Po x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT rnaforester_options.o -MD -MP -MF .deps/rnaforester_options.Tpo -c -o rnaforester_options.o rnaforester_options.cpp mv -f .deps/rnaforester_options.Tpo .deps/rnaforester_options.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=nocona -O2 -pipe -fomit-frame-pointer -MT wmatch.o -MD -MP -MF .deps/wmatch.Tpo -c -o wmatch.o wmatch.c mv -f .deps/wmatch.Tpo .deps/wmatch.Po x86_64-pc-linux-gnu-g++ -march=nocona -O2 -pipe -fomit-frame-pointer -L../g2-0.70 -L../../lib -Wl,-O1 -Wl,--as-needed -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]: Nothing to be done for `all-am'. 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' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT baum.o -MD -MP -MF .deps/baum.Tpo -c -o baum.o baum.c mv -f .deps/baum.Tpo .deps/baum.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT cache.o -MD -MP -MF .deps/cache.Tpo -c -o cache.o cache.c mv -f .deps/cache.Tpo .deps/cache.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT globals.o -MD -MP -MF .deps/globals.Tpo -c -o globals.o globals.c globals.c: In function ‘process_options_gg’: globals.c:320: warning: format ‘%g’ expects type ‘float *’, but argument 3 has type ‘double *’ globals.c:320: warning: format ‘%g’ expects type ‘float *’, but argument 4 has type ‘double *’ globals.c:320: warning: format ‘%g’ expects type ‘float *’, but argument 5 has type ‘double *’ globals.c: In function ‘process_options’: globals.c:406: warning: format ‘%g’ expects type ‘float *’, but argument 3 has type ‘double *’ globals.c:406: warning: format ‘%g’ expects type ‘float *’, but argument 4 has type ‘double *’ globals.c:406: warning: format ‘%g’ expects type ‘float *’, but argument 5 has type ‘double *’ mv -f .deps/globals.Tpo .deps/globals.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c mv -f .deps/main.Tpo .deps/main.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT nachbar.o -MD -MP -MF .deps/nachbar.Tpo -c -o nachbar.o nachbar.c nachbar.c: In function ‘sel_nb’: nachbar.c:301: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘size_t’ mv -f .deps/nachbar.Tpo .deps/nachbar.Po x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=nocona -O2 -pipe -fomit-frame-pointer -MT cmdline.o -MD -MP -MF .deps/cmdline.Tpo -c -o cmdline.o cmdline.c mv -f .deps/cmdline.Tpo .deps/cmdline.Po x86_64-pc-linux-gnu-gcc -march=nocona -O2 -pipe -fomit-frame-pointer -L../lib -Wl,-O1 -Wl,--as-needed -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]: Nothing to be done for `all-am'. 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 -j1 -C Readseq make: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Readseq' Compiling readseq... x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -march=nocona -O2 -pipe -fomit-frame-pointer -o readseq readseq.c ureadseq.c readseq.c: In function ‘formatstr’: readseq.c:261: warning: return discards qualifiers from pointer target type readseq.c:263: warning: return discards qualifiers from pointer target type readseq.c:267: warning: return discards qualifiers from pointer target type readseq.c: In function ‘usage’: readseq.c:332: warning: format not a string literal and no format arguments readseq.c: In function ‘chooseFormat’: readseq.c:423: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result readseq.c: In function ‘main’: readseq.c:772: warning: format not a string literal and no format arguments readseq.c:914: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:916: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ readseq.c:959: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ readseq.c:959: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:959: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ readseq.c:969: warning: format not a string literal and no format arguments readseq.c:976: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ readseq.c:976: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:977: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ readseq.c:977: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:1080: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:1080: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘long unsigned int’ readseq.c:1091: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:1092: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:1116: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ readseq.c:761: warning: ignoring return value of ‘tmpnam’, declared with attribute warn_unused_result readseq.c:779: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result readseq.c:843: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result readseq.c:889: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result readseq.c:915: warning: ignoring return value of ‘freopen’, declared with attribute warn_unused_result ureadseq.c: In function ‘seqFileFormatFp’: ureadseq.c:1346: warning: format ‘%d’ expects type ‘int *’, but argument 3 has type ‘long int *’ ureadseq.c:1346: warning: format ‘%d’ expects type ‘int *’, but argument 4 has type ‘long int *’ ureadseq.c: In function ‘writeSeq’: ureadseq.c:1595: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ ureadseq.c:1624: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1625: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1625: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1639: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1639: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1649: warning: format ‘%10d’ expects type ‘int’, but argument 3 has type ‘long int’ ureadseq.c:1659: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1659: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1668: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1668: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1669: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’ ureadseq.c:1680: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1680: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1689: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1689: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1695: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1695: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1726: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1748: warning: format ‘%6d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1748: warning: format ‘%8X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1765: warning: format ‘%6d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1765: warning: format ‘%8X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1772: warning: format ‘%6d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1772: warning: format ‘%5d’ expects type ‘int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1783: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1783: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1791: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1791: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1797: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’ ureadseq.c:1797: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ ureadseq.c:1838: warning: format ‘%-9d’ expects type ‘int’, but argument 3 has type ‘long int’ In file included from /usr/include/string.h:642, from ureadseq.c:22: In function ‘strcpy’, inlined from ‘writeSeq’ at ureadseq.c:1736: /usr/include/bits/string3.h:107: warning: call to __builtin___strcpy_chk will always overflow destination buffer /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/temp/cc1u8i6k.o: In function `main': readseq.c:(.text+0x19b4): warning: the use of `tmpnam' is dangerous, better use `mkstemp' /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/temp/cc1u8i6k.o: In function `chooseFormat': readseq.c:(.text+0x83c): 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. >>> Test phase [not enabled]: sci-biology/vienna-rna-1.8.4-r1 >>> Install vienna-rna-1.8.4-r1 into /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/ category sci-biology 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/lib64" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib64" /usr/bin/install -c -m 644 libRNA.a '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib64' ( cd '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib64' && x86_64-pc-linux-gnu-ranlib libRNA.a ) make[2]: Nothing to be done for `install-data-am'. 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" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin" /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]: Nothing to be done for `install-data-am'. 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" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/info" /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' test -z "/usr/share/man/man1" || /usr/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' 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" || /usr/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' test -z "/usr/bin" || /usr/bin/mkdir -p "/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" || /usr/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[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' 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/lib64/perl5/site_perl/5.12.2/x86_64-linux-thread-multi/auto/RNA/RNA.so Installing /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/usr/lib64/perl5/site_perl/5.12.2/x86_64-linux-thread-multi/auto/RNA/RNA.bs Installing /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/usr/lib64/perl5/site_perl/5.12.2/x86_64-linux-thread-multi/RNA.pm Installing /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/usr/share/man/man3/RNA.3pm Appending installation info to /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib64/perl5/5.12.2/x86_64-linux-thread-multi/perllocal.pod make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl' make[2]: Nothing to be done for `install-data-am'. 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" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin" /usr/bin/install -c AnalyseDists AnalyseSeqs '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin' test -z "/usr/share/man/man1" || /usr/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 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/lib64 || mkdir -p /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib64 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/lib64 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" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin" /usr/bin/install -c RNAforester '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin' 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/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" || /usr/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' test -z "/usr/bin" || /usr/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]: 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' 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" || /usr/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/ strip: x86_64-pc-linux-gnu-strip --strip-unneeded -R .comment usr/lib64/perl5/site_perl/5.12.2/x86_64-linux-thread-multi/auto/RNA/RNA.so usr/bin/RNAfold usr/bin/RNAeval usr/bin/RNAheat usr/bin/RNApdist usr/bin/RNAdistance usr/bin/RNAinverse usr/bin/RNAplot usr/bin/RNAsubopt usr/bin/RNALfold usr/bin/RNAcofold usr/bin/RNApaln usr/bin/RNAduplex usr/bin/RNAalifold usr/bin/RNAplfold usr/bin/RNAup usr/bin/RNAaliduplex usr/bin/b2ct usr/bin/popt usr/bin/AnalyseDists usr/bin/AnalyseSeqs usr/bin/RNAforester usr/bin/Kinfold usr/bin/readseq-vienna usr/lib64/libRNA.a usr/lib64/libg2.a ecompressdir: bzip2 -9 /usr/share/man ecompressdir: bzip2 -9 /usr/share/info * QA Notice: Package has poor programming practices which may compile * fine but exhibit random runtime failures. * AS_main.c:229: 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: warning: call to __builtin___sprintf_chk will always overflow destination buffer * /usr/include/bits/string3.h:107: warning: call to __builtin___strcpy_chk will always overflow destination buffer * * Please file a bug about this at http://bugs.gentoo.org/ * with the maintaining herd of the package. * * ERROR: sci-biology/vienna-rna-1.8.4-r1 failed: * install aborted due to poor programming practices shown above * * Call stack: * misc-functions.sh, line 975: Called install_qa_check * misc-functions.sh, line 660: Called die * The specific snippet of code: * die "install aborted due to" \ * * If you need support, post the output of 'emerge --info =sci-biology/vienna-rna-1.8.4-r1', * the complete build log and the output of 'emerge -pqv =sci-biology/vienna-rna-1.8.4-r1'. * The complete build log is located at '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/temp/environment'. * S: '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'