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Gentoo's Bugzilla – Attachment 250657 Details for
Bug 341089
sci-biology/vienna-rna _FORTIFY_SOURCE indicates presence of overflow
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Build log
vienna-rna-1.8.4-r1:20101015-021251.log (text/plain), 90.51 KB, created by
Diego Elio Pettenò (RETIRED)
on 2010-10-15 06:17:44 UTC
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Description:
Build log
Filename:
MIME Type:
Creator:
Diego Elio Pettenò (RETIRED)
Created:
2010-10-15 06:17:44 UTC
Size:
90.51 KB
patch
obsolete
> * 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 âpf_costâ: >inverse.c:488:4: warning: passing argument 1 of âpf_foldâ discards qualifiers from pointer target type >./../H/part_func.h:6:15: note: expected âchar *â but argument is of type âconst char *â >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 âaliduplexfoldâ: >duplex.c:385:3: warning: passing argument 3 of âalibacktrackâ from incompatible pointer type >duplex.c:37:16: note: expected âconst short int **â but argument is of type âshort int **â >duplex.c:385:3: warning: passing argument 4 of âalibacktrackâ from incompatible pointer type >duplex.c:37:16: note: expected âconst short int **â but argument is of type âshort int **â >duplex.c: In function âaliduplex_suboptâ: >duplex.c:462:7: warning: passing argument 3 of âalibacktrackâ from incompatible pointer type >duplex.c:37:16: note: expected âconst short int **â but argument is of type âshort int **â >duplex.c:462:7: warning: passing argument 4 of âalibacktrackâ from incompatible pointer type >duplex.c:37:16: note: expected âconst short int **â but argument is of type âshort int **â >alifold.c: In function âmake_pscoresâ: >alifold.c:722:5: warning: passing argument 1 of âget_ribosumâ from incompatible pointer type >./../H/ribo.h:1:16: note: expected âchar **â but argument is of type âconst char * const*â >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 âmake_pscoresâ: >alipfold.c:1154:5: warning: passing argument 1 of âget_ribosumâ from incompatible pointer type >./../H/ribo.h:1:16: note: expected âchar **â but argument is of type âconst char * const*â >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 âsprintfâ, > inlined from âplot_free_pu_outâ 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 âmainâ: >RNAup.c:110:5: warning: format â%100sâ expects type âchar *â, but argument 3 has type âchar (*)[201]â >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 âmainâ: >RNAaliduplex.c:128:5: warning: passing argument 1 of âaliduplex_suboptâ from incompatible pointer type >./../H/duplex.h:14:17: note: expected âconst char **â but argument is of type âchar **â >RNAaliduplex.c:128:5: warning: passing argument 2 of âaliduplex_suboptâ from incompatible pointer type >./../H/duplex.h:14:17: note: expected âconst char **â but argument is of type âchar **â >RNAaliduplex.c:135:5: warning: passing argument 1 of âaliduplexfoldâ from incompatible pointer type >RNAaliduplex.c:22:16: note: expected âconst char **â but argument is of type âchar **â >RNAaliduplex.c:135:5: warning: passing argument 2 of âaliduplexfoldâ from incompatible pointer type >RNAaliduplex.c:22:16: note: expected âconst char **â but argument is of type âchar **â >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: âstruct plistâ 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 âmainâ: >AS_main.c:229:7: warning: attempt to free a non-heap object âssâ >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 âReadMatrixâ: >glib.c:272:8: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result >glib.c:282:10: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result >glib.c: In function âReadEuclidâ: >glib.c:225:8: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result >glib.c:234:9: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result >glib.c: In function âReadGraphâ: >glib.c:161:8: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result >glib.c:170:9: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result >glib.c:176:10: warning: ignoring return value of âfscanfâ, 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: âtypedefâ was ignored in this declaration >In file included from rna_profile_alignment.cpp:37:0: >rnafuncs.h:42:3: warning: âtypedefâ was ignored in this declaration >In file included from rnaforest.h:22:0, > from rnaforest.cpp:24: >rnafuncs.h:42:3: warning: âtypedefâ was ignored in this declaration >In file included from rnafuncs.cpp:23:0: >rnafuncs.h:42:3: warning: âtypedefâ was ignored in this declaration >In file included from rnaforestsz.cpp:15:0: >rnafuncs.h:42:3: warning: âtypedefâ 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: âtypedefâ was ignored in this declaration >progressive_align.cpp: In function ânode_entry* makePairsGraph(const RNAProfileAliMapType&, const DoubleScoreProfileAlgebraType*, const Matrix<double>*, double)â: >progressive_align.cpp:341:30: warning: deprecated conversion from string constant to âchar*â >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 âprocess_options_ggâ: >globals.c:320:9: warning: format â%gâ expects type âfloat *â, but argument 3 has type âdouble *â >globals.c:320:9: warning: format â%gâ expects type âfloat *â, but argument 4 has type âdouble *â >globals.c:320:9: warning: format â%gâ expects type âfloat *â, but argument 5 has type âdouble *â >globals.c: In function âprocess_optionsâ: >globals.c:406:8: warning: format â%gâ expects type âfloat *â, but argument 3 has type âdouble *â >globals.c:406:8: warning: format â%gâ expects type âfloat *â, but argument 4 has type âdouble *â >globals.c:406:8: warning: format â%gâ expects type âfloat *â, but argument 5 has type âdouble *â >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 âformatstrâ: >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 âusageâ: >readseq.c:332:3: warning: format not a string literal and no format arguments >readseq.c: In function âmainâ: >readseq.c:772:3: warning: format not a string literal and no format arguments >readseq.c:914:13: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >readseq.c:916:13: warning: format â%dâ expects type âintâ, but argument 3 has type âlong intâ >readseq.c:959:17: warning: format â%dâ expects type âintâ, but argument 3 has type âlong intâ >readseq.c:959:17: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >readseq.c:959:17: warning: format â%Xâ expects type âunsigned intâ, but argument 5 has type âlong unsigned intâ >readseq.c:969:15: warning: format not a string literal and no format arguments >readseq.c:976:19: warning: format â%dâ expects type âintâ, but argument 3 has type âlong intâ >readseq.c:976:19: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >readseq.c:977:19: warning: format â%dâ expects type âintâ, but argument 3 has type âlong intâ >readseq.c:977:19: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >readseq.c:1080:19: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >readseq.c:1080:19: warning: format â%dâ expects type âintâ, but argument 5 has type âlong unsigned intâ >readseq.c:1091:5: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >readseq.c:1092:5: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >readseq.c:1116:9: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >readseq.c:761:11: warning: ignoring return value of âtmpnamâ, declared with attribute warn_unused_result >readseq.c:779:9: warning: ignoring return value of âgetsâ, declared with attribute warn_unused_result >readseq.c:843:11: warning: ignoring return value of âgetsâ, declared with attribute warn_unused_result >readseq.c:889:13: warning: ignoring return value of âgetsâ, declared with attribute warn_unused_result >readseq.c:915:20: warning: ignoring return value of âfreopenâ, declared with attribute warn_unused_result >readseq.c: In function âchooseFormatâ: >readseq.c:423:11: warning: ignoring return value of âgetsâ, declared with attribute warn_unused_result >ureadseq.c: In function âseqFileFormatFpâ: >ureadseq.c:1346:5: warning: format â%dâ expects type âint *â, but argument 3 has type âlong int *â >ureadseq.c:1346:5: warning: format â%dâ expects type âint *â, but argument 4 has type âlong int *â >ureadseq.c: In function âwriteSeqâ: >ureadseq.c:1595:3: warning: format â%dâ expects type âintâ, but argument 3 has type âlong intâ >ureadseq.c:1624:7: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1625:7: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1625:7: warning: format â%Xâ expects type âunsigned intâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1639:7: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1639:7: warning: format â%Xâ expects type âunsigned intâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1649:7: warning: format â%10dâ expects type âintâ, but argument 3 has type âlong intâ >ureadseq.c:1659:7: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1659:7: warning: format â%Xâ expects type âunsigned intâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1668:7: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1668:7: warning: format â%Xâ expects type âunsigned intâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1669:7: warning: format â%dâ expects type âintâ, but argument 3 has type âlong intâ >ureadseq.c:1680:7: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1680:7: warning: format â%dâ expects type âintâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1689:7: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1689:7: warning: format â%Xâ expects type âunsigned intâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1695:7: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1695:7: warning: format â%Xâ expects type âunsigned intâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1726:7: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1748:7: warning: format â%6dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1748:7: warning: format â%8Xâ expects type âunsigned intâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1765:9: warning: format â%6dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1765:9: warning: format â%8Xâ expects type âunsigned intâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1772:21: warning: format â%6dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1772:21: warning: format â%5dâ expects type âintâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1783:7: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1783:7: warning: format â%Xâ expects type âunsigned intâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1791:7: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1791:7: warning: format â%Xâ expects type âunsigned intâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1797:7: warning: format â%dâ expects type âintâ, but argument 4 has type âlong intâ >ureadseq.c:1797:7: warning: format â%Xâ expects type âunsigned intâ, but argument 5 has type âlong unsigned intâ >ureadseq.c:1838:9: warning: format â%-9dâ expects type âintâ, but argument 3 has type âlong intâ >In file included from /usr/include/string.h:642:0, > from ureadseq.c:22: >In function âstrcpyâ, > inlined from âwriteSeqâ 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 âssâ > > > * 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
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