/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/temp/build.log

build.log (text/plain), 93.52 KB, created by Juergen Rose on 2010-09-11 09:26:35 UTC

[32;01m * [39;49;00mCPV:  sci-biology/vienna-rna-1.8.4-r1
[32;01m * [39;49;00mREPO: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail]
[32;01m * [39;49;00mUSE:  amd64 elibc_glibc kernel_linux multilib userland_GNU
>>> Unpacking source...
>>> Unpacking ViennaRNA-1.8.4.tar.gz to /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work
>>> Preparing source in /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4 ...
 [32;01m*[0m Applying vienna-rna-1.6.5-c-fixes.patch ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying vienna-rna-1.7.2-LDFLAGS.patch ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying vienna-rna-1.8.3-gcc4.3.patch ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying vienna-rna-1.8.3-disable-gd.patch ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying vienna-rna-1.8.4-jobserver-fix.patch ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying vienna-rna-1.8.4-bindir.patch ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70' ...
 [32;01m*[0m Running aclocal ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' ...
 [32;01m*[0m Running aclocal ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoheader ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold' ...
 [32;01m*[0m Running aclocal ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoheader ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4' ...
 [32;01m*[0m Running aclocal ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoheader ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70' ...
 [32;01m*[0m Running aclocal ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester' ...
 [32;01m*[0m Running aclocal ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoheader ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
[A[127C [34;01m[ [32;01mok[34;01m ][0m
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4 ...
 * econf: updating ViennaRNA-1.8.4/RNAforester/g2-0.70/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating ViennaRNA-1.8.4/RNAforester/g2-0.70/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating ViennaRNA-1.8.4/RNAforester/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating ViennaRNA-1.8.4/Kinfold/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating ViennaRNA-1.8.4/Kinfold/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating ViennaRNA-1.8.4/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating ViennaRNA-1.8.4/config.sub with /usr/share/gnuconfig/config.sub
./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --with-cluster
configure: loading site script /usr/share/config.site
configure: loading site script /usr/share/crossdev/include/site/linux
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking if malloc debugging is wanted... no
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3
checking whether x86_64-pc-linux-gnu-gcc accepts -fpic... yes
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking whether x86_64-pc-linux-gnu-gcc and cc understand -c and -o together... yes
checking for perl... /usr/bin/perl
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for inline... inline
checking for strdup... yes
checking for strstr... yes
checking for strchr... yes
checking for erand48... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ViennaRNA.spec
config.status: creating Utils/Makefile
config.status: creating Progs/Makefile
config.status: creating lib/Makefile
config.status: creating man/Makefile
config.status: creating Cluster/Makefile
config.status: creating H/Makefile
config.status: creating Perl/Makefile
config.status: creating man/RNAheat.1
config.status: creating man/RNAsubopt.1
config.status: creating man/RNAdistance.1
config.status: creating man/RNAinverse.1
config.status: creating man/RNAeval.1
config.status: creating man/RNAfold.1
config.status: creating man/RNApdist.1
config.status: creating man/RNAplot.1
config.status: creating man/RNALfold.1
config.status: creating man/RNAalifold.1
config.status: creating man/RNAduplex.1
config.status: creating man/RNAcofold.1
config.status: creating man/RNAplfold.1
config.status: creating man/RNAup.1
config.status: creating man/RNApaln.1
config.status: creating man/RNAaliduplex.1
config.status: creating config.h
config.status: executing depfiles commands
=== configuring in RNAforester (/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr'  '--build=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib64' '--with-cluster' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CFLAGS=-march=nocona -O2 -pipe -fomit-frame-pointer' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' --cache-file=/dev/null --srcdir=.
configure: loading site script /usr/share/config.site
configure: loading site script /usr/share/crossdev/include/site/linux
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of x86_64-pc-linux-gnu-g++... gcc3
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3
using (to be built) libRNA.a in ../lib
checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking g2.h usability... yes
checking g2.h presence... yes
checking for g2.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating man/Makefile
config.status: creating config.h
config.status: executing depfiles commands
=== configuring in g2-0.70 (/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr'  '--build=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib64' '--with-cluster' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CFLAGS=-march=nocona -O2 -pipe -fomit-frame-pointer' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CXXFLAGS=-march=nocona -O2 -pipe -fomit-frame-pointer' --cache-file=/dev/null --srcdir=.
configure: loading site script /usr/share/config.site
configure: loading site script /usr/share/crossdev/include/site/linux
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking for find... find
checking for makedepend... makedepend
checking for dlopen in -ldl... yes
checking for X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for main in -lm... yes
checking for main in -lX11... yes
checking for main in -lgd... yes
checking for gdImagePng... no
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes

configure: creating ./config.status
config.status: creating Makefile
config.status: creating demo/Makefile
config.status: creating g2_perl/Makefile.PL

Supported devices:
    PostScript
    FIG
    X11

Unsupported devices:
    Win32
    GD

Run 'make depend' to create dependencies.

=== configuring in Kinfold (/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr'  '--build=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib64' '--with-cluster' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CFLAGS=-march=nocona -O2 -pipe -fomit-frame-pointer' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' --cache-file=/dev/null --srcdir=.
configure: loading site script /usr/share/config.site
configure: loading site script /usr/share/crossdev/include/site/linux
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking if malloc debugging is wanted... no
checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for strdup... yes
checking for memset... yes
checking for strchr... yes
checking for ViennaRNA package...  headers in "../H" and library... "../lib"
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking fold.h usability... yes
checking fold.h presence... yes
checking for fold.h... yes
checking for exp in -lm... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for an ANSI C-conforming const... yes
configure: creating ./config.status
config.status: creating Example/Makefile
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure:
Configure successful with the following options:

  Perl Extension:      yes
  Analyse{Dists,Seqs}: yes
  Kinfold:             yes
  RNAforester:         yes

Files will be installed in the following directories:

  Executables:  /usr/bin
  Libraries:    /usr/lib64
  Header files: /usr/include
  Extra Data:   /usr/share
  Man pages:    /usr/share/man

>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4 ...
make -j1 clean 
Making clean in Kinfold
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
Making clean in Example
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example'
make[2]: Nothing to be done for `clean'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example'
Making clean in .
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
test -z "Kinfold" || rm -f Kinfold
rm -f *.o
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
Making clean in RNAforester
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
Making clean in man
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man'
make[2]: Nothing to be done for `clean'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man'
Making clean in src
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src'
test -z "RNAforester" || rm -f RNAforester
rm -f *.o
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src'
Making clean in g2-0.70
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70'
(cd ./demo ; make clean)
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70/demo'
rm g2_test g2_arc g2_splines_demo demo_cpp simple_PS simple_FIG simple_X11 pointer handles   g2testf g2testf.f demo_f *~ core *.ps *.fig *.eps *.png *.jpg *.fig.bak
rm: cannot remove `g2_test': No such file or directory
rm: cannot remove `g2_arc': No such file or directory
rm: cannot remove `g2_splines_demo': No such file or directory
rm: cannot remove `demo_cpp': No such file or directory
rm: cannot remove `simple_PS': No such file or directory
rm: cannot remove `simple_FIG': No such file or directory
rm: cannot remove `simple_X11': No such file or directory
rm: cannot remove `pointer': No such file or directory
rm: cannot remove `handles': No such file or directory
rm: cannot remove `g2testf': No such file or directory
rm: cannot remove `g2testf.f': No such file or directory
rm: cannot remove `demo_f': No such file or directory
rm: cannot remove `*~': No such file or directory
rm: cannot remove `core': No such file or directory
rm: cannot remove `*.ps': No such file or directory
rm: cannot remove `*.fig': No such file or directory
rm: cannot remove `*.eps': No such file or directory
rm: cannot remove `*.png': No such file or directory
rm: cannot remove `*.jpg': No such file or directory
rm: cannot remove `*.fig.bak': No such file or directory
make[3]: [clean] Error 1 (ignored)
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70/demo'
rm -f ./src/g2_device.o ./src/g2_ui_control.o ./src/g2_util.o ./src/g2_fif.o ./src/g2_virtual_device.o ./src/g2_physical_device.o ./src/g2_graphic_pd.o ./src/g2_control_pd.o ./src/g2_ui_graphic.o ./src/g2_ui_virtual_device.o ./src/g2_ui_device.o ./src/g2_splines.o ./src/PS/g2_PS.o ./src/FIG/g2_FIG.o ./src/X11/g2_X11.o
rm -f libg2.a config.cache config.log Makefile.bak config.status
rm -f ./include/*.h
find . -name "*~" -exec rm -f {} \;
(cd ./g2_perl ; make clean)
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70/g2_perl'
make[3]: *** No rule to make target `clean'.  Stop.
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70/g2_perl'
make[2]: [clean] Error 2 (ignored)
rm -f ./g2_perl/test.ps
rm -f ./g2_perl/test.png
rm -f ./g2_perl/test.jpg
rm -f ./g2_perl/test.fig
rm -f ./g2_perl/Makefile.old
rm -f ./libg2.so.0.0.70
rm -f libg2.0.70.a
rm -f a.out
rm -fr doc/html/ doc/latex/ doc/g2_refman.ps doc/g2_refman.pdf
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70'
Making clean in .
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
make[2]: Nothing to be done for `clean-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
Making clean in Cluster
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster'
test -z "AnalyseDists AnalyseSeqs" || rm -f AnalyseDists AnalyseSeqs
rm -f *.o
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster'
Making clean in Perl
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
/usr/bin/perl Makefile.PL LDDLFLAGS="-Wl,-O1 -Wl,--as-needed -shared"
Writing Makefile.perl for RNA
make -f Makefile.perl clean
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
rm -f \
	  *.a core \
	  core.[0-9] blib/arch/auto/RNA/extralibs.all \
	  core.[0-9][0-9] RNA.bso \
	  pm_to_blib.ts core.[0-9][0-9][0-9][0-9] \
	  RNA.x RNA.bs \
	  perl tmon.out \
	  *.o pm_to_blib \
	  blib/arch/auto/RNA/extralibs.ld blibdirs.ts \
	  core.[0-9][0-9][0-9][0-9][0-9] *perl.core \
	  core.*perl.*.? Makefile.perl.aperl \
	  perl RNA.def \
	  core.[0-9][0-9][0-9] mon.out \
	  libRNA.def perlmain.c \
	  perl.exe so_locations \
	  RNA.exp 
rm -rf \
	  blib 
mv Makefile.perl Makefile.perl.old > /dev/null 2>&1
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
Making clean in H
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H'
make[1]: Nothing to be done for `clean'.
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H'
Making clean in Utils
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils'
test -z "b2ct popt" || rm -f b2ct popt
rm -f *.o
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils'
Making clean in man
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man'
test -z "RNAlib.dvi RNAlib.pdf RNAlib.ps RNAlib.html" \
	|| rm -rf RNAlib.dvi RNAlib.pdf RNAlib.ps RNAlib.html
rm -rf RNAlib.aux RNAlib.cp RNAlib.cps RNAlib.fn RNAlib.fns RNAlib.ky \
	  RNAlib.kys RNAlib.log RNAlib.pg RNAlib.pgs RNAlib.tmp \
	  RNAlib.toc RNAlib.tp RNAlib.tps RNAlib.vr RNAlib.vrs
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man'
Making clean in Progs
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs'
test -z "RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex" || rm -f RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex
rm -f *.o
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs'
Making clean in lib
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib'
test -z "libRNA.a" || rm -f libRNA.a
rm -f *.o
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib'
Making clean in .
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'
make[1]: Nothing to be done for `clean-am'.
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'
make -j1 
make  all-recursive
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'
Making all in lib
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-dist_vars.o -MD -MP -MF .deps/libRNA_a-dist_vars.Tpo -c -o libRNA_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c
mv -f .deps/libRNA_a-dist_vars.Tpo .deps/libRNA_a-dist_vars.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-fold_vars.o -MD -MP -MF .deps/libRNA_a-fold_vars.Tpo -c -o libRNA_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c
mv -f .deps/libRNA_a-fold_vars.Tpo .deps/libRNA_a-fold_vars.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-part_func.o -MD -MP -MF .deps/libRNA_a-part_func.Tpo -c -o libRNA_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c
mv -f .deps/libRNA_a-part_func.Tpo .deps/libRNA_a-part_func.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-read_epars.o -MD -MP -MF .deps/libRNA_a-read_epars.Tpo -c -o libRNA_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c
mv -f .deps/libRNA_a-read_epars.Tpo .deps/libRNA_a-read_epars.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-treedist.o -MD -MP -MF .deps/libRNA_a-treedist.Tpo -c -o libRNA_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c
mv -f .deps/libRNA_a-treedist.Tpo .deps/libRNA_a-treedist.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-energy_par.o -MD -MP -MF .deps/libRNA_a-energy_par.Tpo -c -o libRNA_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c
mv -f .deps/libRNA_a-energy_par.Tpo .deps/libRNA_a-energy_par.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-inverse.o -MD -MP -MF .deps/libRNA_a-inverse.Tpo -c -o libRNA_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c
inverse.c: In function ‘pf_cost’:
inverse.c:488: warning: passing argument 1 of ‘pf_fold’ discards qualifiers from pointer target type
./../H/part_func.h:6: note: expected ‘char *’ but argument is of type ‘const char *’
mv -f .deps/libRNA_a-inverse.Tpo .deps/libRNA_a-inverse.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-ProfileDist.o -MD -MP -MF .deps/libRNA_a-ProfileDist.Tpo -c -o libRNA_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c
mv -f .deps/libRNA_a-ProfileDist.Tpo .deps/libRNA_a-ProfileDist.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-RNAstruct.o -MD -MP -MF .deps/libRNA_a-RNAstruct.Tpo -c -o libRNA_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c
mv -f .deps/libRNA_a-RNAstruct.Tpo .deps/libRNA_a-RNAstruct.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-utils.o -MD -MP -MF .deps/libRNA_a-utils.Tpo -c -o libRNA_a-utils.o `test -f 'utils.c' || echo './'`utils.c
mv -f .deps/libRNA_a-utils.Tpo .deps/libRNA_a-utils.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-fold.o -MD -MP -MF .deps/libRNA_a-fold.Tpo -c -o libRNA_a-fold.o `test -f 'fold.c' || echo './'`fold.c
mv -f .deps/libRNA_a-fold.Tpo .deps/libRNA_a-fold.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-naview.o -MD -MP -MF .deps/libRNA_a-naview.Tpo -c -o libRNA_a-naview.o `test -f 'naview.c' || echo './'`naview.c
naview.c: In function ‘dump_loops’:
naview.c:334: warning: format ‘%d’ expects type ‘int’, but argument 2 has type ‘long int’
mv -f .deps/libRNA_a-naview.Tpo .deps/libRNA_a-naview.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-PS_dot.o -MD -MP -MF .deps/libRNA_a-PS_dot.Tpo -c -o libRNA_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c
mv -f .deps/libRNA_a-PS_dot.Tpo .deps/libRNA_a-PS_dot.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-stringdist.o -MD -MP -MF .deps/libRNA_a-stringdist.Tpo -c -o libRNA_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c
stringdist.c:24:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from stringdist.c:12:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
mv -f .deps/libRNA_a-stringdist.Tpo .deps/libRNA_a-stringdist.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-params.o -MD -MP -MF .deps/libRNA_a-params.Tpo -c -o libRNA_a-params.o `test -f 'params.c' || echo './'`params.c
mv -f .deps/libRNA_a-params.Tpo .deps/libRNA_a-params.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-subopt.o -MD -MP -MF .deps/libRNA_a-subopt.Tpo -c -o libRNA_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c
mv -f .deps/libRNA_a-subopt.Tpo .deps/libRNA_a-subopt.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-list.o -MD -MP -MF .deps/libRNA_a-list.Tpo -c -o libRNA_a-list.o `test -f 'list.c' || echo './'`list.c
mv -f .deps/libRNA_a-list.Tpo .deps/libRNA_a-list.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-Lfold.o -MD -MP -MF .deps/libRNA_a-Lfold.Tpo -c -o libRNA_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c
mv -f .deps/libRNA_a-Lfold.Tpo .deps/libRNA_a-Lfold.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-cofold.o -MD -MP -MF .deps/libRNA_a-cofold.Tpo -c -o libRNA_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c
mv -f .deps/libRNA_a-cofold.Tpo .deps/libRNA_a-cofold.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-part_func_co.o -MD -MP -MF .deps/libRNA_a-part_func_co.Tpo -c -o libRNA_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c
mv -f .deps/libRNA_a-part_func_co.Tpo .deps/libRNA_a-part_func_co.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-ProfileAln.o -MD -MP -MF .deps/libRNA_a-ProfileAln.Tpo -c -o libRNA_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c
mv -f .deps/libRNA_a-ProfileAln.Tpo .deps/libRNA_a-ProfileAln.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-duplex.o -MD -MP -MF .deps/libRNA_a-duplex.Tpo -c -o libRNA_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c
duplex.c: In function ‘aliduplexfold’:
duplex.c:385: warning: passing argument 3 of ‘alibacktrack’ from incompatible pointer type
duplex.c:37: note: expected ‘const short int **’ but argument is of type ‘short int **’
duplex.c:385: warning: passing argument 4 of ‘alibacktrack’ from incompatible pointer type
duplex.c:37: note: expected ‘const short int **’ but argument is of type ‘short int **’
duplex.c: In function ‘aliduplex_subopt’:
duplex.c:462: warning: passing argument 3 of ‘alibacktrack’ from incompatible pointer type
duplex.c:37: note: expected ‘const short int **’ but argument is of type ‘short int **’
duplex.c:462: warning: passing argument 4 of ‘alibacktrack’ from incompatible pointer type
duplex.c:37: note: expected ‘const short int **’ but argument is of type ‘short int **’
mv -f .deps/libRNA_a-duplex.Tpo .deps/libRNA_a-duplex.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-alifold.o -MD -MP -MF .deps/libRNA_a-alifold.Tpo -c -o libRNA_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c
alifold.c: In function ‘make_pscores’:
alifold.c:722: warning: passing argument 1 of ‘get_ribosum’ from incompatible pointer type
./../H/ribo.h:1: note: expected ‘char **’ but argument is of type ‘const char * const*’
mv -f .deps/libRNA_a-alifold.Tpo .deps/libRNA_a-alifold.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-alipfold.o -MD -MP -MF .deps/libRNA_a-alipfold.Tpo -c -o libRNA_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c
alipfold.c: In function ‘make_pscores’:
alipfold.c:1154: warning: passing argument 1 of ‘get_ribosum’ from incompatible pointer type
./../H/ribo.h:1: note: expected ‘char **’ but argument is of type ‘const char * const*’
mv -f .deps/libRNA_a-alipfold.Tpo .deps/libRNA_a-alipfold.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-aln_util.o -MD -MP -MF .deps/libRNA_a-aln_util.Tpo -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c
mv -f .deps/libRNA_a-aln_util.Tpo .deps/libRNA_a-aln_util.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-LPfold.o -MD -MP -MF .deps/libRNA_a-LPfold.Tpo -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c
mv -f .deps/libRNA_a-LPfold.Tpo .deps/libRNA_a-LPfold.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-part_func_up.o -MD -MP -MF .deps/libRNA_a-part_func_up.Tpo -c -o libRNA_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.c
In file included from /usr/include/stdio.h:930,
                 from part_func_up.c:56:
In function ‘sprintf’,
    inlined from ‘plot_free_pu_out’ at part_func_up.c:1449:
/usr/include/bits/stdio2.h:34: warning: call to __builtin___sprintf_chk will always overflow destination buffer
mv -f .deps/libRNA_a-part_func_up.Tpo .deps/libRNA_a-part_func_up.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-ribo.o -MD -MP -MF .deps/libRNA_a-ribo.Tpo -c -o libRNA_a-ribo.o `test -f 'ribo.c' || echo './'`ribo.c
mv -f .deps/libRNA_a-ribo.Tpo .deps/libRNA_a-ribo.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-findpath.o -MD -MP -MF .deps/libRNA_a-findpath.Tpo -c -o libRNA_a-findpath.o `test -f 'findpath.c' || echo './'`findpath.c
mv -f .deps/libRNA_a-findpath.Tpo .deps/libRNA_a-findpath.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -march=nocona -O2 -pipe -fomit-frame-pointer -MT libRNA_a-MEA.o -MD -MP -MF .deps/libRNA_a-MEA.Tpo -c -o libRNA_a-MEA.o `test -f 'MEA.c' || echo './'`MEA.c
mv -f .deps/libRNA_a-MEA.Tpo .deps/libRNA_a-MEA.Po
rm -f libRNA.a
ar cru libRNA.a libRNA_a-dist_vars.o libRNA_a-fold_vars.o libRNA_a-part_func.o libRNA_a-read_epars.o libRNA_a-treedist.o libRNA_a-energy_par.o libRNA_a-inverse.o libRNA_a-ProfileDist.o libRNA_a-RNAstruct.o libRNA_a-utils.o libRNA_a-fold.o libRNA_a-naview.o libRNA_a-PS_dot.o libRNA_a-stringdist.o libRNA_a-params.o libRNA_a-subopt.o libRNA_a-list.o libRNA_a-Lfold.o libRNA_a-cofold.o libRNA_a-part_func_co.o libRNA_a-ProfileAln.o libRNA_a-duplex.o libRNA_a-alifold.o libRNA_a-alipfold.o libRNA_a-aln_util.o libRNA_a-LPfold.o libRNA_a-part_func_up.o libRNA_a-ribo.o libRNA_a-findpath.o libRNA_a-MEA.o 
x86_64-pc-linux-gnu-ranlib libRNA.a
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib'
Making all in Progs
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAfold.o -MD -MP -MF .deps/RNAfold.Tpo -c -o RNAfold.o RNAfold.c
mv -f .deps/RNAfold.Tpo .deps/RNAfold.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAfold RNAfold.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAeval.o -MD -MP -MF .deps/RNAeval.Tpo -c -o RNAeval.o RNAeval.c
mv -f .deps/RNAeval.Tpo .deps/RNAeval.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAeval RNAeval.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAheat.o -MD -MP -MF .deps/RNAheat.Tpo -c -o RNAheat.o RNAheat.c
mv -f .deps/RNAheat.Tpo .deps/RNAheat.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAheat RNAheat.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNApdist.o -MD -MP -MF .deps/RNApdist.Tpo -c -o RNApdist.o RNApdist.c
mv -f .deps/RNApdist.Tpo .deps/RNApdist.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNApdist RNApdist.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAdistance.o -MD -MP -MF .deps/RNAdistance.Tpo -c -o RNAdistance.o RNAdistance.c
mv -f .deps/RNAdistance.Tpo .deps/RNAdistance.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAdistance RNAdistance.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAinverse.o -MD -MP -MF .deps/RNAinverse.Tpo -c -o RNAinverse.o RNAinverse.c
RNAinverse.c:31:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from RNAinverse.c:9:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
mv -f .deps/RNAinverse.Tpo .deps/RNAinverse.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAinverse RNAinverse.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAplot.o -MD -MP -MF .deps/RNAplot.Tpo -c -o RNAplot.o RNAplot.c
mv -f .deps/RNAplot.Tpo .deps/RNAplot.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAplot RNAplot.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAsubopt.o -MD -MP -MF .deps/RNAsubopt.Tpo -c -o RNAsubopt.o RNAsubopt.c
mv -f .deps/RNAsubopt.Tpo .deps/RNAsubopt.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAsubopt RNAsubopt.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNALfold.o -MD -MP -MF .deps/RNALfold.Tpo -c -o RNALfold.o RNALfold.c
mv -f .deps/RNALfold.Tpo .deps/RNALfold.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNALfold RNALfold.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAcofold.o -MD -MP -MF .deps/RNAcofold.Tpo -c -o RNAcofold.o RNAcofold.c
mv -f .deps/RNAcofold.Tpo .deps/RNAcofold.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAcofold RNAcofold.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNApaln.o -MD -MP -MF .deps/RNApaln.Tpo -c -o RNApaln.o RNApaln.c
mv -f .deps/RNApaln.Tpo .deps/RNApaln.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNApaln RNApaln.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAduplex.o -MD -MP -MF .deps/RNAduplex.Tpo -c -o RNAduplex.o RNAduplex.c
RNAduplex.c: In function ‘main’:
RNAduplex.c:158: warning: format ‘%d’ expects type ‘int’, but argument 2 has type ‘size_t’
RNAduplex.c:158: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘size_t’
RNAduplex.c: In function ‘print_struc’:
RNAduplex.c:188: warning: format ‘%-3d’ expects type ‘int’, but argument 6 has type ‘size_t’
mv -f .deps/RNAduplex.Tpo .deps/RNAduplex.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAduplex RNAduplex.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAalifold.o -MD -MP -MF .deps/RNAalifold.Tpo -c -o RNAalifold.o RNAalifold.c
mv -f .deps/RNAalifold.Tpo .deps/RNAalifold.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAalifold RNAalifold.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAplfold.o -MD -MP -MF .deps/RNAplfold.Tpo -c -o RNAplfold.o RNAplfold.c
mv -f .deps/RNAplfold.Tpo .deps/RNAplfold.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAplfold RNAplfold.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAup.o -MD -MP -MF .deps/RNAup.Tpo -c -o RNAup.o RNAup.c
RNAup.c: In function ‘main’:
RNAup.c:110: warning: format ‘%100s’ expects type ‘char *’, but argument 3 has type ‘char (*)[201]’
mv -f .deps/RNAup.Tpo .deps/RNAup.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAup RNAup.o ../lib/libRNA.a -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT RNAaliduplex.o -MD -MP -MF .deps/RNAaliduplex.Tpo -c -o RNAaliduplex.o RNAaliduplex.c
RNAaliduplex.c: In function ‘main’:
RNAaliduplex.c:128: warning: passing argument 1 of ‘aliduplex_subopt’ from incompatible pointer type
./../H/duplex.h:14: note: expected ‘const char **’ but argument is of type ‘char **’
RNAaliduplex.c:128: warning: passing argument 2 of ‘aliduplex_subopt’ from incompatible pointer type
./../H/duplex.h:14: note: expected ‘const char **’ but argument is of type ‘char **’
RNAaliduplex.c:135: warning: passing argument 1 of ‘aliduplexfold’ from incompatible pointer type
RNAaliduplex.c:22: note: expected ‘const char **’ but argument is of type ‘char **’
RNAaliduplex.c:135: warning: passing argument 2 of ‘aliduplexfold’ from incompatible pointer type
RNAaliduplex.c:22: note: expected ‘const char **’ but argument is of type ‘char **’
RNAaliduplex.c: In function ‘print_struc’:
RNAaliduplex.c:150: warning: format ‘%-3d’ expects type ‘int’, but argument 6 has type ‘size_t’
mv -f .deps/RNAaliduplex.Tpo .deps/RNAaliduplex.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o RNAaliduplex RNAaliduplex.o ../lib/libRNA.a -lm 
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs'
Making all in man
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man'
Making all in Utils
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT b2ct.o -MD -MP -MF .deps/b2ct.Tpo -c -o b2ct.o b2ct.c
mv -f .deps/b2ct.Tpo .deps/b2ct.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o b2ct b2ct.o -L../lib -lRNA -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -march=nocona -O2 -pipe -fomit-frame-pointer -MT popt.o -MD -MP -MF .deps/popt.Tpo -c -o popt.o popt.c
mv -f .deps/popt.Tpo .deps/popt.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o popt popt.o -L../lib -lRNA -lm 
if test -n "/usr/bin/perl"; then \
	  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' b2mt.pl ; \
	fi
if test -n "/usr/bin/perl"; then \
	  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' ct2b.pl ; \
	fi
if test -n "/usr/bin/perl"; then \
	  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' dpzoom.pl ; \
	fi
if test -n "/usr/bin/perl"; then \
	  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' mountain.pl ; \
	fi
if test -n "/usr/bin/perl"; then \
	  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' relplot.pl ; \
	fi
if test -n "/usr/bin/perl"; then \
	  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' rotate_ss.pl ; \
	fi
if test -n "/usr/bin/perl"; then \
	  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' cmount.pl ; \
	fi
if test -n "/usr/bin/perl"; then \
	  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' colorrna.pl ; \
	fi
if test -n "/usr/bin/perl"; then \
	  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' coloraln.pl ; \
	fi
if test -n "/usr/bin/perl"; then \
	  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' refold.pl ; \
	fi
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils'
Making all in H
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H'
Making all in Perl
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
/usr/bin/perl Makefile.PL LDDLFLAGS="-Wl,-O1 -Wl,--as-needed -shared"
Writing Makefile.perl for RNA
make -f Makefile.perl
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
cp RNA.pm blib/lib/RNA.pm
x86_64-pc-linux-gnu-gcc -c   -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -march=nocona -O2 -pipe -fomit-frame-pointer   -DVERSION=\"0.2\" -DXS_VERSION=\"0.2\" -fPIC "-I/usr/lib64/perl5/5.12.2/x86_64-linux-thread-multi/CORE"   RNA_wrap.c
In file included from RNA_wrap.c:1501:
../H/part_func_co.h:28: warning: ‘struct plist’ declared inside parameter list
../H/part_func_co.h:28: warning: its scope is only this definition or declaration, which is probably not what you want
Running Mkbootstrap for RNA ()
chmod 644 RNA.bs
rm -f blib/arch/auto/RNA/RNA.so
x86_64-pc-linux-gnu-gcc  -Wl,-O1 -Wl,--as-needed -shared RNA_wrap.o  -o blib/arch/auto/RNA/RNA.so ../lib/libRNA.a	\
	   -lm  	\
	  
chmod 755 blib/arch/auto/RNA/RNA.so
cp RNA.bs blib/arch/auto/RNA/RNA.bs
chmod 644 blib/arch/auto/RNA/RNA.bs
Manifying blib/man3/RNA.3pm
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
Making all in Cluster
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -march=nocona -O2 -pipe -fomit-frame-pointer -MT split.o -MD -MP -MF .deps/split.Tpo -c -o split.o split.c
mv -f .deps/split.Tpo .deps/split.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -march=nocona -O2 -pipe -fomit-frame-pointer -MT distance_matrix.o -MD -MP -MF .deps/distance_matrix.Tpo -c -o distance_matrix.o distance_matrix.c
mv -f .deps/distance_matrix.Tpo .deps/distance_matrix.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -march=nocona -O2 -pipe -fomit-frame-pointer -MT cluster.o -MD -MP -MF .deps/cluster.Tpo -c -o cluster.o cluster.c
mv -f .deps/cluster.Tpo .deps/cluster.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -march=nocona -O2 -pipe -fomit-frame-pointer -MT treeplot.o -MD -MP -MF .deps/treeplot.Tpo -c -o treeplot.o treeplot.c
mv -f .deps/treeplot.Tpo .deps/treeplot.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -march=nocona -O2 -pipe -fomit-frame-pointer -MT AD_main.o -MD -MP -MF .deps/AD_main.Tpo -c -o AD_main.o AD_main.c
mv -f .deps/AD_main.Tpo .deps/AD_main.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -march=nocona -O2 -pipe -fomit-frame-pointer -c ./../lib/utils.c
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o utils.o -lm 
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -march=nocona -O2 -pipe -fomit-frame-pointer -MT statgeom.o -MD -MP -MF .deps/statgeom.Tpo -c -o statgeom.o statgeom.c
mv -f .deps/statgeom.Tpo .deps/statgeom.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -march=nocona -O2 -pipe -fomit-frame-pointer -MT AS_main.o -MD -MP -MF .deps/AS_main.Tpo -c -o AS_main.o AS_main.c
AS_main.c: In function ‘main’:
AS_main.c:229: warning: attempt to free a non-heap object ‘ss’
mv -f .deps/AS_main.Tpo .deps/AS_main.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..     -march=nocona -O2 -pipe -fomit-frame-pointer -MT PS3D.o -MD -MP -MF .deps/PS3D.Tpo -c -o PS3D.o PS3D.c
mv -f .deps/PS3D.Tpo .deps/PS3D.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -Wl,-O1 -Wl,--as-needed -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o utils.o -lm 
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster'
Making all in RNAforester
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
make  all-recursive
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
Making all in g2-0.70
make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70'
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_device.c -o src/g2_device.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_control.c -o src/g2_ui_control.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_util.c -o src/g2_util.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_fif.c -o src/g2_fif.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_virtual_device.c -o src/g2_virtual_device.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_physical_device.c -o src/g2_physical_device.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_graphic_pd.c -o src/g2_graphic_pd.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_control_pd.c -o src/g2_control_pd.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_graphic.c -o src/g2_ui_graphic.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_virtual_device.c -o src/g2_ui_virtual_device.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_device.c -o src/g2_ui_device.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_splines.c -o src/g2_splines.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/PS/g2_PS.c -o src/PS/g2_PS.o
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/FIG/g2_FIG.c -o src/FIG/g2_FIG.o
src/FIG/g2_FIG.c: In function ‘g2_FIG_draw_string’:
src/FIG/g2_FIG.c:478: warning: format ‘%d’ expects type ‘int’, but argument 6 has type ‘size_t’
x86_64-pc-linux-gnu-gcc -I./src -march=nocona -O2 -pipe -fomit-frame-pointer  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/X11/g2_X11.c -o src/X11/g2_X11.o
ar -cr libg2.a ./src/g2_device.o ./src/g2_ui_control.o ./src/g2_util.o ./src/g2_fif.o ./src/g2_virtual_device.o ./src/g2_physical_device.o ./src/g2_graphic_pd.o ./src/g2_control_pd.o ./src/g2_ui_graphic.o ./src/g2_ui_virtual_device.o ./src/g2_ui_device.o ./src/g2_splines.o ./src/PS/g2_PS.o ./src/FIG/g2_FIG.o ./src/X11/g2_X11.o
test ! -n "x86_64-pc-linux-gnu-ranlib" || x86_64-pc-linux-gnu-ranlib libg2.a
test -d ./include || mkdir ./include
cp ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h   ./include/
make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70'
Making all in src
make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT Arguments.o -MD -MP -MF .deps/Arguments.Tpo -c -o Arguments.o Arguments.cpp
mv -f .deps/Arguments.Tpo .deps/Arguments.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT glib.o -MD -MP -MF .deps/glib.Tpo -c -o glib.o glib.c
glib.c: In function ‘ReadGraph’:
glib.c:161: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
glib.c:170: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
glib.c:176: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
glib.c: In function ‘ReadEuclid’:
glib.c:225: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
glib.c:234: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
glib.c: In function ‘ReadMatrix’:
glib.c:272: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
glib.c:282: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result
mv -f .deps/glib.Tpo .deps/glib.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp
In file included from rnaforest.h:22,
                 from rna_alignment.h:24,
                 from main.cpp:52:
rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration
mv -f .deps/main.Tpo .deps/main.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT ppforestbase.o -MD -MP -MF .deps/ppforestbase.Tpo -c -o ppforestbase.o ppforestbase.cpp
mv -f .deps/ppforestbase.Tpo .deps/ppforestbase.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT progressive_align.o -MD -MP -MF .deps/progressive_align.Tpo -c -o progressive_align.o progressive_align.cpp
progressive_align.cpp: In function ‘node_entry* makePairsGraph(const RNAProfileAliMapType&, const DoubleScoreProfileAlgebraType*, const Matrix<double>*, double)’:
progressive_align.cpp:341: warning: deprecated conversion from string constant to ‘char*’
mv -f .deps/progressive_align.Tpo .deps/progressive_align.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT rna_profile_alignment.o -MD -MP -MF .deps/rna_profile_alignment.Tpo -c -o rna_profile_alignment.o rna_profile_alignment.cpp
In file included from rna_profile_alignment.cpp:37:
rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration
mv -f .deps/rna_profile_alignment.Tpo .deps/rna_profile_alignment.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT rna_alignment.o -MD -MP -MF .deps/rna_alignment.Tpo -c -o rna_alignment.o rna_alignment.cpp
In file included from rnaforest.h:22,
                 from rna_alignment.h:24,
                 from rna_alignment.cpp:22:
rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration
mv -f .deps/rna_alignment.Tpo .deps/rna_alignment.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT rna_algebra.o -MD -MP -MF .deps/rna_algebra.Tpo -c -o rna_algebra.o rna_algebra.cpp
mv -f .deps/rna_algebra.Tpo .deps/rna_algebra.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT rna_alphabet.o -MD -MP -MF .deps/rna_alphabet.Tpo -c -o rna_alphabet.o rna_alphabet.cpp
mv -f .deps/rna_alphabet.Tpo .deps/rna_alphabet.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT rnaforest.o -MD -MP -MF .deps/rnaforest.Tpo -c -o rnaforest.o rnaforest.cpp
In file included from rnaforest.h:22,
                 from rnaforest.cpp:24:
rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration
mv -f .deps/rnaforest.Tpo .deps/rnaforest.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT rnaforestsz.o -MD -MP -MF .deps/rnaforestsz.Tpo -c -o rnaforestsz.o rnaforestsz.cpp
In file included from rnaforestsz.cpp:15:
rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration
mv -f .deps/rnaforestsz.Tpo .deps/rnaforestsz.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT rnafuncs.o -MD -MP -MF .deps/rnafuncs.Tpo -c -o rnafuncs.o rnafuncs.cpp
In file included from rnafuncs.cpp:23:
rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration
mv -f .deps/rnafuncs.Tpo .deps/rnafuncs.Po
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT rnaforester_options.o -MD -MP -MF .deps/rnaforester_options.Tpo -c -o rnaforester_options.o rnaforester_options.cpp
mv -f .deps/rnaforester_options.Tpo .deps/rnaforester_options.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=nocona -O2 -pipe -fomit-frame-pointer -MT wmatch.o -MD -MP -MF .deps/wmatch.Tpo -c -o wmatch.o wmatch.c
mv -f .deps/wmatch.Tpo .deps/wmatch.Po
x86_64-pc-linux-gnu-g++  -march=nocona -O2 -pipe -fomit-frame-pointer  -L../g2-0.70 -L../../lib -Wl,-O1 -Wl,--as-needed -o RNAforester Arguments.o glib.o main.o ppforestbase.o progressive_align.o rna_profile_alignment.o rna_alignment.o rna_algebra.o rna_alphabet.o rnaforest.o rnaforestsz.o rnafuncs.o rnaforester_options.o wmatch.o  -lg2 -lRNA 
make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src'
Making all in man
make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man'
make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
make[4]: Nothing to be done for `all-am'.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
Making all in Kinfold
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
make  all-recursive
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
Making all in Example
make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example'
make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -march=nocona -O2 -pipe -fomit-frame-pointer -MT baum.o -MD -MP -MF .deps/baum.Tpo -c -o baum.o baum.c
mv -f .deps/baum.Tpo .deps/baum.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -march=nocona -O2 -pipe -fomit-frame-pointer -MT cache.o -MD -MP -MF .deps/cache.Tpo -c -o cache.o cache.c
mv -f .deps/cache.Tpo .deps/cache.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -march=nocona -O2 -pipe -fomit-frame-pointer -MT globals.o -MD -MP -MF .deps/globals.Tpo -c -o globals.o globals.c
globals.c: In function ‘process_options_gg’:
globals.c:320: warning: format ‘%g’ expects type ‘float *’, but argument 3 has type ‘double *’
globals.c:320: warning: format ‘%g’ expects type ‘float *’, but argument 4 has type ‘double *’
globals.c:320: warning: format ‘%g’ expects type ‘float *’, but argument 5 has type ‘double *’
globals.c: In function ‘process_options’:
globals.c:406: warning: format ‘%g’ expects type ‘float *’, but argument 3 has type ‘double *’
globals.c:406: warning: format ‘%g’ expects type ‘float *’, but argument 4 has type ‘double *’
globals.c:406: warning: format ‘%g’ expects type ‘float *’, but argument 5 has type ‘double *’
mv -f .deps/globals.Tpo .deps/globals.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -march=nocona -O2 -pipe -fomit-frame-pointer -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c
mv -f .deps/main.Tpo .deps/main.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -march=nocona -O2 -pipe -fomit-frame-pointer -MT nachbar.o -MD -MP -MF .deps/nachbar.Tpo -c -o nachbar.o nachbar.c
nachbar.c: In function ‘sel_nb’:
nachbar.c:301: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘size_t’
mv -f .deps/nachbar.Tpo .deps/nachbar.Po
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -march=nocona -O2 -pipe -fomit-frame-pointer -MT cmdline.o -MD -MP -MF .deps/cmdline.Tpo -c -o cmdline.o cmdline.c
mv -f .deps/cmdline.Tpo .deps/cmdline.Po
x86_64-pc-linux-gnu-gcc  -march=nocona -O2 -pipe -fomit-frame-pointer  -L../lib -Wl,-O1 -Wl,--as-needed -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o  -lRNA -lm 
make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'
make -j1 -C Readseq 
make: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Readseq'
Compiling readseq...
x86_64-pc-linux-gnu-gcc    -Wl,-O1 -Wl,--as-needed -march=nocona -O2 -pipe -fomit-frame-pointer -o readseq readseq.c ureadseq.c
readseq.c: In function ‘formatstr’:
readseq.c:261: warning: return discards qualifiers from pointer target type
readseq.c:263: warning: return discards qualifiers from pointer target type
readseq.c:267: warning: return discards qualifiers from pointer target type
readseq.c: In function ‘usage’:
readseq.c:332: warning: format not a string literal and no format arguments
readseq.c: In function ‘chooseFormat’:
readseq.c:423: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result
readseq.c: In function ‘main’:
readseq.c:772: warning: format not a string literal and no format arguments
readseq.c:914: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
readseq.c:916: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’
readseq.c:959: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’
readseq.c:959: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
readseq.c:959: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’
readseq.c:969: warning: format not a string literal and no format arguments
readseq.c:976: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’
readseq.c:976: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
readseq.c:977: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’
readseq.c:977: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
readseq.c:1080: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
readseq.c:1080: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘long unsigned int’
readseq.c:1091: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
readseq.c:1092: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
readseq.c:1116: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
readseq.c:761: warning: ignoring return value of ‘tmpnam’, declared with attribute warn_unused_result
readseq.c:779: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result
readseq.c:843: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result
readseq.c:889: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result
readseq.c:915: warning: ignoring return value of ‘freopen’, declared with attribute warn_unused_result
ureadseq.c: In function ‘seqFileFormatFp’:
ureadseq.c:1346: warning: format ‘%d’ expects type ‘int *’, but argument 3 has type ‘long int *’
ureadseq.c:1346: warning: format ‘%d’ expects type ‘int *’, but argument 4 has type ‘long int *’
ureadseq.c: In function ‘writeSeq’:
ureadseq.c:1595: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’
ureadseq.c:1624: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1625: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1625: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1639: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1639: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1649: warning: format ‘%10d’ expects type ‘int’, but argument 3 has type ‘long int’
ureadseq.c:1659: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1659: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1668: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1668: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1669: warning: format ‘%d’ expects type ‘int’, but argument 3 has type ‘long int’
ureadseq.c:1680: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1680: warning: format ‘%d’ expects type ‘int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1689: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1689: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1695: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1695: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1726: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1748: warning: format ‘%6d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1748: warning: format ‘%8X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1765: warning: format ‘%6d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1765: warning: format ‘%8X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1772: warning: format ‘%6d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1772: warning: format ‘%5d’ expects type ‘int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1783: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1783: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1791: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1791: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1797: warning: format ‘%d’ expects type ‘int’, but argument 4 has type ‘long int’
ureadseq.c:1797: warning: format ‘%X’ expects type ‘unsigned int’, but argument 5 has type ‘long unsigned int’
ureadseq.c:1838: warning: format ‘%-9d’ expects type ‘int’, but argument 3 has type ‘long int’
In file included from /usr/include/string.h:642,
                 from ureadseq.c:22:
In function ‘strcpy’,
    inlined from ‘writeSeq’ at ureadseq.c:1736:
/usr/include/bits/string3.h:107: warning: call to __builtin___strcpy_chk will always overflow destination buffer
/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/temp/cc1u8i6k.o: In function `main':
readseq.c:(.text+0x19b4): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/temp/cc1u8i6k.o: In function `chooseFormat':
readseq.c:(.text+0x83c): warning: the `gets' function is dangerous and should not be used.
make: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Readseq'
>>> Source compiled.
>>> Test phase [not enabled]: sci-biology/vienna-rna-1.8.4-r1

>>> Install vienna-rna-1.8.4-r1 into /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/ category sci-biology
Making install in lib
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib'
test -z "/usr/lib64" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib64"
 /usr/bin/install -c -m 644  libRNA.a '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib64'
 ( cd '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib64' && x86_64-pc-linux-gnu-ranlib libRNA.a )
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/lib'
Making install in Progs
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs'
test -z "/usr/bin" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin"
  /usr/bin/install -c RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Progs'
Making install in man
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/usr/share/info" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/info"
 /usr/bin/install -c -m 644 ./RNAlib.info '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/info'
 install-info --info-dir='/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/info' '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/info/RNAlib.info'
install-info: warning: no info dir entry in `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/info/RNAlib.info'
test -z "/usr/share/man/man1" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/man/man1"
 /usr/bin/install -c -m 644 RNAheat.1 RNAsubopt.1 RNAdistance.1 RNAinverse.1 RNAcofold.1 RNAeval.1 RNAfold.1 RNApdist.1 RNAplot.1 RNAalifold.1 RNALfold.1 RNAduplex.1 RNAplfold.1 RNAup.1 RNApaln.1 RNAaliduplex.1 '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/man/man1'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/man'
Making install in Utils
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/usr/bin" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin"
  /usr/bin/install -c b2ct popt '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin'
test -z "/usr/bin" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin"
 /usr/bin/install -c b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl Fold '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Utils'
Making install in H
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/usr/include/ViennaRNA" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/include/ViennaRNA"
 /usr/bin/install -c -m 644 energy_par.h pair_mat.h RNAstruct.h dist_vars.h fold.h part_func.h stringdist.h edit_cost.h fold_vars.h profiledist.h treedist.h energy_const.h inverse.h PS_dot.h utils.h params.h subopt.h cofold.h duplex.h alifold.h aln_util.h part_func_co.h ProfileAln.h LPfold.h Lfold.h part_func_up.h ribo.h findpath.h MEA.h '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/include/ViennaRNA'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/H'
Making install in Perl
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
make -f Makefile.perl
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
make -f Makefile.perl
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
make -f Makefile.perl install
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/usr/lib64/perl5/site_perl/5.12.2/x86_64-linux-thread-multi/auto/RNA/RNA.so
Installing /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/usr/lib64/perl5/site_perl/5.12.2/x86_64-linux-thread-multi/auto/RNA/RNA.bs
Installing /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/usr/lib64/perl5/site_perl/5.12.2/x86_64-linux-thread-multi/RNA.pm
Installing /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/usr/share/man/man3/RNA.3pm
Appending installation info to /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib64/perl5/5.12.2/x86_64-linux-thread-multi/perllocal.pod
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Perl'
Making install in Cluster
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster'
test -z "/usr/bin" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin"
  /usr/bin/install -c AnalyseDists AnalyseSeqs '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin'
test -z "/usr/share/man/man1" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/man/man1"
 /usr/bin/install -c -m 644 AnalyseDists.1 AnalyseSeqs.1 '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/man/man1'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Cluster'
Making install in RNAforester
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
Making install in g2-0.70
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70'
test -d /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib64 || mkdir -p /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib64
test -d /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/include || mkdir -p /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/include
/usr/bin/install -c -m 644 libg2.a /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/lib64
for IFILE in ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h  ; do \
		/usr/bin/install -c -m 644 $IFILE  /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/include; \
	done
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/g2-0.70'
Making install in src
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src'
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src'
test -z "/usr/bin" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin"
  /usr/bin/install -c RNAforester '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin'
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/src'
Making install in man
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man'
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man'
make[3]: Nothing to be done for `install-exec-am'.
test -z "/usr/share/man/man1" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/man/man1"
 /usr/bin/install -c -m 644 RNAforester.1 '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/man/man1'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester/man'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/RNAforester'
Making install in Kinfold
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
Making install in Example
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example'
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold/Example'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
test -z "/usr/bin" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin"
  /usr/bin/install -c Kinfold '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/bin'
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4/Kinfold'
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'
make[2]: Nothing to be done for `install-exec-am'.
test -z "/usr/share/ViennaRNA" || /usr/bin/mkdir -p "/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/ViennaRNA"
 /usr/bin/install -c -m 644 vienna13.par default.par '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image//usr/share/ViennaRNA'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'
>>> Completed installing vienna-rna-1.8.4-r1 into /var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/image/

strip: x86_64-pc-linux-gnu-strip --strip-unneeded -R .comment
   usr/lib64/perl5/site_perl/5.12.2/x86_64-linux-thread-multi/auto/RNA/RNA.so
   usr/bin/RNAfold
   usr/bin/RNAeval
   usr/bin/RNAheat
   usr/bin/RNApdist
   usr/bin/RNAdistance
   usr/bin/RNAinverse
   usr/bin/RNAplot
   usr/bin/RNAsubopt
   usr/bin/RNALfold
   usr/bin/RNAcofold
   usr/bin/RNApaln
   usr/bin/RNAduplex
   usr/bin/RNAalifold
   usr/bin/RNAplfold
   usr/bin/RNAup
   usr/bin/RNAaliduplex
   usr/bin/b2ct
   usr/bin/popt
   usr/bin/AnalyseDists
   usr/bin/AnalyseSeqs
   usr/bin/RNAforester
   usr/bin/Kinfold
   usr/bin/readseq-vienna
   usr/lib64/libRNA.a
   usr/lib64/libg2.a
ecompressdir: bzip2 -9 /usr/share/man
ecompressdir: bzip2 -9 /usr/share/info

 [33;01m*[0m QA Notice: Package has poor programming practices which may compile
 [33;01m*[0m            fine but exhibit random runtime failures.
 [33;01m*[0m AS_main.c:229: warning: attempt to free a non-heap object ‘ss’

 [31;01m*[0m 
 [31;01m*[0m QA Notice: Package has poor programming practices which may compile
 [31;01m*[0m            fine but exhibit random runtime failures.
 [31;01m*[0m 
 [31;01m*[0m /usr/include/bits/stdio2.h:34: warning: call to __builtin___sprintf_chk will always overflow destination buffer
 [31;01m*[0m /usr/include/bits/string3.h:107: warning: call to __builtin___strcpy_chk will always overflow destination buffer
 [31;01m*[0m 
 [31;01m*[0m  Please file a bug about this at http://bugs.gentoo.org/
 [31;01m*[0m  with the maintaining herd of the package.
 [31;01m*[0m 
 [31;01m*[0m ERROR: sci-biology/vienna-rna-1.8.4-r1 failed:
 [31;01m*[0m   install aborted due to poor programming practices shown above
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m   misc-functions.sh, line 975:  Called install_qa_check
 [31;01m*[0m   misc-functions.sh, line 660:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m   				die "install aborted due to" \
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of 'emerge --info =sci-biology/vienna-rna-1.8.4-r1',
 [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-biology/vienna-rna-1.8.4-r1'.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/temp/environment'.
 [31;01m*[0m S: '/var/tmp/portage/sci-biology/vienna-rna-1.8.4-r1/work/ViennaRNA-1.8.4'