build log failure

build.log (text/plain), 46.00 KB, created by Brent Baude (RETIRED) on 2012-03-07 20:42:13 UTC

[32;01m * [39;49;00mPackage:    sci-biology/vienna-rna-1.8.5
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail]
[32;01m * [39;49;00mUSE:        elibc_glibc kernel_linux ppc test userland_GNU
[32;01m * [39;49;00mFEATURES:   sandbox test
>>> Unpacking source...
>>> Unpacking ViennaRNA-1.8.5.tar.gz to /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work
>>> Source unpacked in /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work
>>> Preparing source in /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5 ...
 [32;01m*[0m Applying vienna-rna-1.6.5-c-fixes.patch ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying vienna-rna-1.7.2-LDFLAGS.patch ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying vienna-rna-1.8.3-gcc4.3.patch ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying vienna-rna-1.8.3-disable-gd.patch ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying vienna-rna-1.8.4-jobserver-fix.patch ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying vienna-rna-1.8.4-bindir.patch ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying vienna-rna-1.8.4-overflows.patch ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Applying vienna-rna-1.8.4-implicits.patch ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70' ...
 [32;01m*[0m Running aclocal ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester' ...
 [32;01m*[0m Running aclocal ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoheader ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold' ...
 [32;01m*[0m Running aclocal ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoheader ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5' ...
 [32;01m*[0m Running aclocal ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoheader ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70' ...
 [32;01m*[0m Running aclocal ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester' ...
 [32;01m*[0m Running aclocal ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoconf ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoheader ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
[A[91C [34;01m[ [32;01mok[34;01m ][0m
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5 ...
 * econf: updating ViennaRNA-1.8.5/RNAforester/g2-0.70/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating ViennaRNA-1.8.5/RNAforester/g2-0.70/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating ViennaRNA-1.8.5/RNAforester/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating ViennaRNA-1.8.5/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating ViennaRNA-1.8.5/config.guess with /usr/share/gnuconfig/config.guess
./configure --prefix=/usr --build=powerpc-unknown-linux-gnu --host=powerpc-unknown-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib --with-cluster
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking if malloc debugging is wanted... no
checking build system type... powerpc-unknown-linux-gnu
checking host system type... powerpc-unknown-linux-gnu
checking for powerpc-unknown-linux-gnu-gcc... powerpc-unknown-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether powerpc-unknown-linux-gnu-gcc accepts -g... yes
checking for powerpc-unknown-linux-gnu-gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of powerpc-unknown-linux-gnu-gcc... gcc3
checking whether powerpc-unknown-linux-gnu-gcc accepts -fpic... yes
checking for powerpc-unknown-linux-gnu-ranlib... powerpc-unknown-linux-gnu-ranlib
checking whether powerpc-unknown-linux-gnu-gcc and cc understand -c and -o together... yes
checking for perl... /usr/bin/perl
checking how to run the C preprocessor... powerpc-unknown-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for inline... inline
checking for strdup... yes
checking for strstr... yes
checking for strchr... yes
checking for erand48... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating ViennaRNA.spec
config.status: creating Utils/Makefile
config.status: creating Progs/Makefile
config.status: creating lib/Makefile
config.status: creating man/Makefile
config.status: creating Cluster/Makefile
config.status: creating H/Makefile
config.status: creating Perl/Makefile
config.status: creating man/RNAheat.1
config.status: creating man/RNAsubopt.1
config.status: creating man/RNAdistance.1
config.status: creating man/RNAinverse.1
config.status: creating man/RNAeval.1
config.status: creating man/RNAfold.1
config.status: creating man/RNApdist.1
config.status: creating man/RNAplot.1
config.status: creating man/RNALfold.1
config.status: creating man/RNAalifold.1
config.status: creating man/RNAduplex.1
config.status: creating man/RNAcofold.1
config.status: creating man/RNAplfold.1
config.status: creating man/RNAup.1
config.status: creating man/RNApaln.1
config.status: creating man/RNAaliduplex.1
config.status: creating config.h
config.status: executing depfiles commands
=== configuring in RNAforester (/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr'  '--build=powerpc-unknown-linux-gnu' '--host=powerpc-unknown-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib' '--with-cluster' 'build_alias=powerpc-unknown-linux-gnu' 'host_alias=powerpc-unknown-linux-gnu' 'CFLAGS=-O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for powerpc-unknown-linux-gnu-g++... powerpc-unknown-linux-gnu-g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether powerpc-unknown-linux-gnu-g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of powerpc-unknown-linux-gnu-g++... gcc3
checking for powerpc-unknown-linux-gnu-gcc... powerpc-unknown-linux-gnu-gcc
checking whether we are using the GNU C compiler... yes
checking whether powerpc-unknown-linux-gnu-gcc accepts -g... yes
checking for powerpc-unknown-linux-gnu-gcc option to accept ISO C89... none needed
checking dependency style of powerpc-unknown-linux-gnu-gcc... gcc3
using (to be built) libRNA.a in ../lib
checking how to run the C++ preprocessor... powerpc-unknown-linux-gnu-g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking g2.h usability... yes
checking g2.h presence... yes
checking for g2.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating man/Makefile
config.status: creating config.h
config.status: executing depfiles commands
=== configuring in g2-0.70 (/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr'  '--build=powerpc-unknown-linux-gnu' '--host=powerpc-unknown-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib' '--with-cluster' 'build_alias=powerpc-unknown-linux-gnu' 'host_alias=powerpc-unknown-linux-gnu' 'CFLAGS=-O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CXXFLAGS=-O2 -pipe' --cache-file=/dev/null --srcdir=.
checking build system type... powerpc-unknown-linux-gnu
checking host system type... powerpc-unknown-linux-gnu
checking for powerpc-unknown-linux-gnu-gcc... powerpc-unknown-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether powerpc-unknown-linux-gnu-gcc accepts -g... yes
checking for powerpc-unknown-linux-gnu-gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... powerpc-unknown-linux-gnu-gcc -E
checking for powerpc-unknown-linux-gnu-g++... powerpc-unknown-linux-gnu-g++
checking whether we are using the GNU C++ compiler... yes
checking whether powerpc-unknown-linux-gnu-g++ accepts -g... yes
checking for powerpc-unknown-linux-gnu-ranlib... powerpc-unknown-linux-gnu-ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking for find... find
checking for makedepend... makedepend
checking for dlopen in -ldl... yes
checking for X... libraries , headers 
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for main in -lm... yes
checking for main in -lX11... yes
checking for main in -lgd... yes
checking for gdImagePng... no
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes

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

Supported devices:
    PostScript
    FIG
    X11

Unsupported devices:
    Win32
    GD

Run 'make depend' to create dependencies.

=== configuring in Kinfold (/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold)
configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr'  '--build=powerpc-unknown-linux-gnu' '--host=powerpc-unknown-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--libdir=/usr/lib' '--with-cluster' 'build_alias=powerpc-unknown-linux-gnu' 'host_alias=powerpc-unknown-linux-gnu' 'CFLAGS=-O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' --cache-file=/dev/null --srcdir=.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking if malloc debugging is wanted... no
checking for powerpc-unknown-linux-gnu-gcc... powerpc-unknown-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether powerpc-unknown-linux-gnu-gcc accepts -g... yes
checking for powerpc-unknown-linux-gnu-gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of powerpc-unknown-linux-gnu-gcc... gcc3
checking build system type... powerpc-unknown-linux-gnu
checking host system type... powerpc-unknown-linux-gnu
checking for strdup... yes
checking for memset... yes
checking for strchr... yes
checking for ViennaRNA package...  headers in "../H" and library... "../lib"
checking how to run the C preprocessor... powerpc-unknown-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking fold.h usability... yes
checking fold.h presence... yes
checking for fold.h... yes
checking for exp in -lm... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for an ANSI C-conforming const... yes
configure: creating ./config.status
config.status: creating Example/Makefile
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure:
Configure successful with the following options:

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

Files will be installed in the following directories:

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

>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5 ...
make -j20 clean 
Making clean in Kinfold
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
Making clean in Example
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold/Example'
make[2]: Nothing to be done for `clean'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold/Example'
Making clean in .
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
test -z "Kinfold" || rm -f Kinfold
rm -f *.o
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
Making clean in RNAforester
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
Making clean in man
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/man'
make[2]: Nothing to be done for `clean'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/man'
Making clean in src
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/src'
test -z "RNAforester" || rm -f RNAforester
rm -f *.o
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/src'
Making clean in g2-0.70
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70'
(cd ./demo ; make clean)
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70/demo'
rm g2_test g2_arc g2_splines_demo demo_cpp simple_PS simple_FIG simple_X11 pointer handles   g2testf g2testf.f demo_f *~ core *.ps *.fig *.eps *.png *.jpg *.fig.bak
rm: cannot remove `g2_test': No such file or directory
rm: cannot remove `g2_arc': No such file or directory
rm: cannot remove `g2_splines_demo': No such file or directory
rm: cannot remove `demo_cpp': No such file or directory
rm: cannot remove `simple_PS': No such file or directory
rm: cannot remove `simple_FIG': No such file or directory
rm: cannot remove `simple_X11': No such file or directory
rm: cannot remove `pointer': No such file or directory
rm: cannot remove `handles': No such file or directory
rm: cannot remove `g2testf': No such file or directory
rm: cannot remove `g2testf.f': No such file or directory
rm: cannot remove `demo_f': No such file or directory
rm: cannot remove `*~': No such file or directory
rm: cannot remove `core': No such file or directory
rm: cannot remove `*.ps': No such file or directory
rm: cannot remove `*.fig': No such file or directory
rm: cannot remove `*.eps': No such file or directory
rm: cannot remove `*.png': No such file or directory
rm: cannot remove `*.jpg': No such file or directory
rm: cannot remove `*.fig.bak': No such file or directory
make[3]: [clean] Error 1 (ignored)
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70/demo'
rm -f ./src/g2_device.o ./src/g2_ui_control.o ./src/g2_util.o ./src/g2_fif.o ./src/g2_virtual_device.o ./src/g2_physical_device.o ./src/g2_graphic_pd.o ./src/g2_control_pd.o ./src/g2_ui_graphic.o ./src/g2_ui_virtual_device.o ./src/g2_ui_device.o ./src/g2_splines.o ./src/PS/g2_PS.o ./src/FIG/g2_FIG.o ./src/X11/g2_X11.o
rm -f libg2.a config.cache config.log Makefile.bak config.status
rm -f ./include/*.h
find . -name "*~" -exec rm -f {} \;
(cd ./g2_perl ; make clean)
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70/g2_perl'
make[3]: *** No rule to make target `clean'.  Stop.
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70/g2_perl'
make[2]: [clean] Error 2 (ignored)
rm -f ./g2_perl/test.ps
rm -f ./g2_perl/test.png
rm -f ./g2_perl/test.jpg
rm -f ./g2_perl/test.fig
rm -f ./g2_perl/Makefile.old
rm -f ./libg2.so.0.0.70
rm -f libg2.0.70.a
rm -f a.out
rm -fr doc/html/ doc/latex/ doc/g2_refman.ps doc/g2_refman.pdf
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70'
Making clean in .
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
make[2]: Nothing to be done for `clean-am'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
Making clean in Cluster
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Cluster'
test -z "AnalyseDists AnalyseSeqs" || rm -f AnalyseDists AnalyseSeqs
rm -f *.o
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Cluster'
Making clean in Perl
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
/usr/bin/perl Makefile.PL INSTALLDIRS=vendor LDDLFLAGS="-Wl,-O1 -Wl,--as-needed -shared"
Writing Makefile.perl for RNA
make -f Makefile.perl clean
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
rm -f \
  *.a core \
  core.[0-9] blib/arch/auto/RNA/extralibs.all \
  core.[0-9][0-9] RNA.bso \
  pm_to_blib.ts core.[0-9][0-9][0-9][0-9] \
  RNA.x RNA.bs \
  perl tmon.out \
  *.o pm_to_blib \
  blib/arch/auto/RNA/extralibs.ld blibdirs.ts \
  core.[0-9][0-9][0-9][0-9][0-9] *perl.core \
  core.*perl.*.? Makefile.perl.aperl \
  perl RNA.def \
  core.[0-9][0-9][0-9] mon.out \
  libRNA.def perlmain.c \
  perl.exe so_locations \
  RNA.exp 
rm -rf \
  blib 
mv Makefile.perl Makefile.perl.old > /dev/null 2>&1
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
Making clean in H
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H'
make[1]: Nothing to be done for `clean'.
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H'
Making clean in Utils
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils'
test -z "b2ct popt" || rm -f b2ct popt
rm -f *.o
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils'
Making clean in man
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man'
test -z "RNAlib.dvi RNAlib.pdf RNAlib.ps RNAlib.html" \
|| rm -rf RNAlib.dvi RNAlib.pdf RNAlib.ps RNAlib.html
rm -rf RNAlib.aux RNAlib.cp RNAlib.cps RNAlib.fn RNAlib.fns RNAlib.ky \
  RNAlib.kys RNAlib.log RNAlib.pg RNAlib.pgs RNAlib.tmp \
  RNAlib.toc RNAlib.tp RNAlib.tps RNAlib.vr RNAlib.vrs
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man'
Making clean in Progs
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs'
test -z "RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex" || rm -f RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex
rm -f *.o
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs'
Making clean in lib
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib'
test -z "libRNA.a" || rm -f libRNA.a
rm -f *.o
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib'
Making clean in .
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
make[1]: Nothing to be done for `clean-am'.
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
make -j20 
make  all-recursive
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
Making all in lib
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib'
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-dist_vars.o -MD -MP -MF .deps/libRNA_a-dist_vars.Tpo -c -o libRNA_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-fold_vars.o -MD -MP -MF .deps/libRNA_a-fold_vars.Tpo -c -o libRNA_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-part_func.o -MD -MP -MF .deps/libRNA_a-part_func.Tpo -c -o libRNA_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-read_epars.o -MD -MP -MF .deps/libRNA_a-read_epars.Tpo -c -o libRNA_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-treedist.o -MD -MP -MF .deps/libRNA_a-treedist.Tpo -c -o libRNA_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-energy_par.o -MD -MP -MF .deps/libRNA_a-energy_par.Tpo -c -o libRNA_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-inverse.o -MD -MP -MF .deps/libRNA_a-inverse.Tpo -c -o libRNA_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-ProfileDist.o -MD -MP -MF .deps/libRNA_a-ProfileDist.Tpo -c -o libRNA_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-RNAstruct.o -MD -MP -MF .deps/libRNA_a-RNAstruct.Tpo -c -o libRNA_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-utils.o -MD -MP -MF .deps/libRNA_a-utils.Tpo -c -o libRNA_a-utils.o `test -f 'utils.c' || echo './'`utils.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-fold.o -MD -MP -MF .deps/libRNA_a-fold.Tpo -c -o libRNA_a-fold.o `test -f 'fold.c' || echo './'`fold.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-naview.o -MD -MP -MF .deps/libRNA_a-naview.Tpo -c -o libRNA_a-naview.o `test -f 'naview.c' || echo './'`naview.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-PS_dot.o -MD -MP -MF .deps/libRNA_a-PS_dot.Tpo -c -o libRNA_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-stringdist.o -MD -MP -MF .deps/libRNA_a-stringdist.Tpo -c -o libRNA_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-params.o -MD -MP -MF .deps/libRNA_a-params.Tpo -c -o libRNA_a-params.o `test -f 'params.c' || echo './'`params.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-subopt.o -MD -MP -MF .deps/libRNA_a-subopt.Tpo -c -o libRNA_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-list.o -MD -MP -MF .deps/libRNA_a-list.Tpo -c -o libRNA_a-list.o `test -f 'list.c' || echo './'`list.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-Lfold.o -MD -MP -MF .deps/libRNA_a-Lfold.Tpo -c -o libRNA_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-cofold.o -MD -MP -MF .deps/libRNA_a-cofold.Tpo -c -o libRNA_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-part_func_co.o -MD -MP -MF .deps/libRNA_a-part_func_co.Tpo -c -o libRNA_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c
mv -f .deps/libRNA_a-dist_vars.Tpo .deps/libRNA_a-dist_vars.Po
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-ProfileAln.o -MD -MP -MF .deps/libRNA_a-ProfileAln.Tpo -c -o libRNA_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c
mv -f .deps/libRNA_a-fold_vars.Tpo .deps/libRNA_a-fold_vars.Po
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-duplex.o -MD -MP -MF .deps/libRNA_a-duplex.Tpo -c -o libRNA_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c
stringdist.c:24:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from stringdist.c:12:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
inverse.c: In function 'pf_cost':
inverse.c:488: warning: passing argument 1 of 'pf_fold' discards qualifiers from pointer target type
./../H/part_func.h:6: note: expected 'char *' but argument is of type 'const char *'
duplex.c: In function 'aliduplexfold':
duplex.c:385: warning: passing argument 3 of 'alibacktrack' from incompatible pointer type
duplex.c:37: note: expected 'const short int **' but argument is of type 'short int **'
duplex.c:385: warning: passing argument 4 of 'alibacktrack' from incompatible pointer type
duplex.c:37: note: expected 'const short int **' but argument is of type 'short int **'
duplex.c: In function 'aliduplex_subopt':
duplex.c:462: warning: passing argument 3 of 'alibacktrack' from incompatible pointer type
duplex.c:37: note: expected 'const short int **' but argument is of type 'short int **'
duplex.c:462: warning: passing argument 4 of 'alibacktrack' from incompatible pointer type
duplex.c:37: note: expected 'const short int **' but argument is of type 'short int **'
mv -f .deps/libRNA_a-list.Tpo .deps/libRNA_a-list.Po
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-alifold.o -MD -MP -MF .deps/libRNA_a-alifold.Tpo -c -o libRNA_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c
mv -f .deps/libRNA_a-utils.Tpo .deps/libRNA_a-utils.Po
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-alipfold.o -MD -MP -MF .deps/libRNA_a-alipfold.Tpo -c -o libRNA_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c
alifold.c: In function 'make_pscores':
alifold.c:722: warning: passing argument 1 of 'get_ribosum' from incompatible pointer type
./../H/ribo.h:1: note: expected 'char **' but argument is of type 'const char * const*'
mv -f .deps/libRNA_a-ProfileAln.Tpo .deps/libRNA_a-ProfileAln.Po
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-aln_util.o -MD -MP -MF .deps/libRNA_a-aln_util.Tpo -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c
mv -f .deps/libRNA_a-ProfileDist.Tpo .deps/libRNA_a-ProfileDist.Po
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-LPfold.o -MD -MP -MF .deps/libRNA_a-LPfold.Tpo -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c
mv -f .deps/libRNA_a-stringdist.Tpo .deps/libRNA_a-stringdist.Po
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-part_func_up.o -MD -MP -MF .deps/libRNA_a-part_func_up.Tpo -c -o libRNA_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.c
alipfold.c: In function 'make_pscores':
alipfold.c:1154: warning: passing argument 1 of 'get_ribosum' from incompatible pointer type
./../H/ribo.h:1: note: expected 'char **' but argument is of type 'const char * const*'
mv -f .deps/libRNA_a-energy_par.Tpo .deps/libRNA_a-energy_par.Po
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-ribo.o -MD -MP -MF .deps/libRNA_a-ribo.Tpo -c -o libRNA_a-ribo.o `test -f 'ribo.c' || echo './'`ribo.c
mv -f .deps/libRNA_a-params.Tpo .deps/libRNA_a-params.Po
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-findpath.o -MD -MP -MF .deps/libRNA_a-findpath.Tpo -c -o libRNA_a-findpath.o `test -f 'findpath.c' || echo './'`findpath.c
mv -f .deps/libRNA_a-aln_util.Tpo .deps/libRNA_a-aln_util.Po
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -fpic -O2 -pipe -MT libRNA_a-MEA.o -MD -MP -MF .deps/libRNA_a-MEA.Tpo -c -o libRNA_a-MEA.o `test -f 'MEA.c' || echo './'`MEA.c
mv -f .deps/libRNA_a-treedist.Tpo .deps/libRNA_a-treedist.Po
mv -f .deps/libRNA_a-inverse.Tpo .deps/libRNA_a-inverse.Po
mv -f .deps/libRNA_a-RNAstruct.Tpo .deps/libRNA_a-RNAstruct.Po
mv -f .deps/libRNA_a-naview.Tpo .deps/libRNA_a-naview.Po
mv -f .deps/libRNA_a-read_epars.Tpo .deps/libRNA_a-read_epars.Po
mv -f .deps/libRNA_a-MEA.Tpo .deps/libRNA_a-MEA.Po
mv -f .deps/libRNA_a-PS_dot.Tpo .deps/libRNA_a-PS_dot.Po
mv -f .deps/libRNA_a-findpath.Tpo .deps/libRNA_a-findpath.Po
mv -f .deps/libRNA_a-Lfold.Tpo .deps/libRNA_a-Lfold.Po
mv -f .deps/libRNA_a-subopt.Tpo .deps/libRNA_a-subopt.Po
mv -f .deps/libRNA_a-duplex.Tpo .deps/libRNA_a-duplex.Po
mv -f .deps/libRNA_a-ribo.Tpo .deps/libRNA_a-ribo.Po
mv -f .deps/libRNA_a-part_func_co.Tpo .deps/libRNA_a-part_func_co.Po
mv -f .deps/libRNA_a-part_func.Tpo .deps/libRNA_a-part_func.Po
mv -f .deps/libRNA_a-part_func_up.Tpo .deps/libRNA_a-part_func_up.Po
mv -f .deps/libRNA_a-alifold.Tpo .deps/libRNA_a-alifold.Po
mv -f .deps/libRNA_a-LPfold.Tpo .deps/libRNA_a-LPfold.Po
mv -f .deps/libRNA_a-cofold.Tpo .deps/libRNA_a-cofold.Po
mv -f .deps/libRNA_a-alipfold.Tpo .deps/libRNA_a-alipfold.Po
mv -f .deps/libRNA_a-fold.Tpo .deps/libRNA_a-fold.Po
rm -f libRNA.a
ar cru libRNA.a libRNA_a-dist_vars.o libRNA_a-fold_vars.o libRNA_a-part_func.o libRNA_a-read_epars.o libRNA_a-treedist.o libRNA_a-energy_par.o libRNA_a-inverse.o libRNA_a-ProfileDist.o libRNA_a-RNAstruct.o libRNA_a-utils.o libRNA_a-fold.o libRNA_a-naview.o libRNA_a-PS_dot.o libRNA_a-stringdist.o libRNA_a-params.o libRNA_a-subopt.o libRNA_a-list.o libRNA_a-Lfold.o libRNA_a-cofold.o libRNA_a-part_func_co.o libRNA_a-ProfileAln.o libRNA_a-duplex.o libRNA_a-alifold.o libRNA_a-alipfold.o libRNA_a-aln_util.o libRNA_a-LPfold.o libRNA_a-part_func_up.o libRNA_a-ribo.o libRNA_a-findpath.o libRNA_a-MEA.o 
powerpc-unknown-linux-gnu-ranlib libRNA.a
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib'
Making all in Progs
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs'
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAfold.o -MD -MP -MF .deps/RNAfold.Tpo -c -o RNAfold.o RNAfold.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAeval.o -MD -MP -MF .deps/RNAeval.Tpo -c -o RNAeval.o RNAeval.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAheat.o -MD -MP -MF .deps/RNAheat.Tpo -c -o RNAheat.o RNAheat.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNApdist.o -MD -MP -MF .deps/RNApdist.Tpo -c -o RNApdist.o RNApdist.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAdistance.o -MD -MP -MF .deps/RNAdistance.Tpo -c -o RNAdistance.o RNAdistance.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAinverse.o -MD -MP -MF .deps/RNAinverse.Tpo -c -o RNAinverse.o RNAinverse.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAplot.o -MD -MP -MF .deps/RNAplot.Tpo -c -o RNAplot.o RNAplot.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAsubopt.o -MD -MP -MF .deps/RNAsubopt.Tpo -c -o RNAsubopt.o RNAsubopt.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNALfold.o -MD -MP -MF .deps/RNALfold.Tpo -c -o RNALfold.o RNALfold.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAcofold.o -MD -MP -MF .deps/RNAcofold.Tpo -c -o RNAcofold.o RNAcofold.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNApaln.o -MD -MP -MF .deps/RNApaln.Tpo -c -o RNApaln.o RNApaln.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAduplex.o -MD -MP -MF .deps/RNAduplex.Tpo -c -o RNAduplex.o RNAduplex.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAalifold.o -MD -MP -MF .deps/RNAalifold.Tpo -c -o RNAalifold.o RNAalifold.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAplfold.o -MD -MP -MF .deps/RNAplfold.Tpo -c -o RNAplfold.o RNAplfold.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAup.o -MD -MP -MF .deps/RNAup.Tpo -c -o RNAup.o RNAup.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT RNAaliduplex.o -MD -MP -MF .deps/RNAaliduplex.Tpo -c -o RNAaliduplex.o RNAaliduplex.c
RNAinverse.c:31:1: warning: "INFINITY" redefined
In file included from /usr/include/math.h:40,
                 from RNAinverse.c:9:
/usr/include/bits/inf.h:27:1: warning: this is the location of the previous definition
RNAup.c: In function 'main':
RNAup.c:110: warning: format '%100s' expects type 'char *', but argument 3 has type 'char (*)[201]'
RNAaliduplex.c: In function 'main':
RNAaliduplex.c:128: warning: passing argument 1 of 'aliduplex_subopt' from incompatible pointer type
./../H/duplex.h:14: note: expected 'const char **' but argument is of type 'char **'
RNAaliduplex.c:128: warning: passing argument 2 of 'aliduplex_subopt' from incompatible pointer type
./../H/duplex.h:14: note: expected 'const char **' but argument is of type 'char **'
RNAaliduplex.c:135: warning: passing argument 1 of 'aliduplexfold' from incompatible pointer type
RNAaliduplex.c:22: note: expected 'const char **' but argument is of type 'char **'
RNAaliduplex.c:135: warning: passing argument 2 of 'aliduplexfold' from incompatible pointer type
RNAaliduplex.c:22: note: expected 'const char **' but argument is of type 'char **'
mv -f .deps/RNAplot.Tpo .deps/RNAplot.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAplot RNAplot.o ../lib/libRNA.a -lm 
mv -f .deps/RNAeval.Tpo .deps/RNAeval.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAeval RNAeval.o ../lib/libRNA.a -lm 
mv -f .deps/RNAduplex.Tpo .deps/RNAduplex.Po
mv -f .deps/RNAaliduplex.Tpo .deps/RNAaliduplex.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAduplex RNAduplex.o ../lib/libRNA.a -lm 
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAaliduplex RNAaliduplex.o ../lib/libRNA.a -lm 
mv -f .deps/RNAheat.Tpo .deps/RNAheat.Po
mv -f .deps/RNALfold.Tpo .deps/RNALfold.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAheat RNAheat.o ../lib/libRNA.a -lm 
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNALfold RNALfold.o ../lib/libRNA.a -lm 
mv -f .deps/RNAinverse.Tpo .deps/RNAinverse.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAinverse RNAinverse.o ../lib/libRNA.a -lm 
mv -f .deps/RNApdist.Tpo .deps/RNApdist.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNApdist RNApdist.o ../lib/libRNA.a -lm 
mv -f .deps/RNAfold.Tpo .deps/RNAfold.Po
mv -f .deps/RNApaln.Tpo .deps/RNApaln.Po
mv -f .deps/RNAsubopt.Tpo .deps/RNAsubopt.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAfold RNAfold.o ../lib/libRNA.a -lm 
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNApaln RNApaln.o ../lib/libRNA.a -lm 
mv -f .deps/RNAplfold.Tpo .deps/RNAplfold.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAsubopt RNAsubopt.o ../lib/libRNA.a -lm 
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAplfold RNAplfold.o ../lib/libRNA.a -lm 
mv -f .deps/RNAcofold.Tpo .deps/RNAcofold.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAcofold RNAcofold.o ../lib/libRNA.a -lm 
mv -f .deps/RNAdistance.Tpo .deps/RNAdistance.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAdistance RNAdistance.o ../lib/libRNA.a -lm 
mv -f .deps/RNAalifold.Tpo .deps/RNAalifold.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAalifold RNAalifold.o ../lib/libRNA.a -lm 
mv -f .deps/RNAup.Tpo .deps/RNAup.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAup RNAup.o ../lib/libRNA.a -lm 
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs'
Making all in man
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man'
Making all in Utils
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils'
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT b2ct.o -MD -MP -MF .deps/b2ct.Tpo -c -o b2ct.o b2ct.c
powerpc-unknown-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H    -O2 -pipe -MT popt.o -MD -MP -MF .deps/popt.Tpo -c -o popt.o popt.c
if test -n "/usr/bin/perl"; then \
  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' b2mt.pl ; \
fi
if test -n "/usr/bin/perl"; then \
  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' ct2b.pl ; \
fi
if test -n "/usr/bin/perl"; then \
  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' dpzoom.pl ; \
fi
if test -n "/usr/bin/perl"; then \
  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' mountain.pl ; \
fi
if test -n "/usr/bin/perl"; then \
  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' relplot.pl ; \
fi
if test -n "/usr/bin/perl"; then \
  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' rotate_ss.pl ; \
fi
if test -n "/usr/bin/perl"; then \
  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' cmount.pl ; \
fi
if test -n "/usr/bin/perl"; then \
  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' colorrna.pl ; \
fi
if test -n "/usr/bin/perl"; then \
  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' coloraln.pl ; \
fi
if test -n "/usr/bin/perl"; then \
  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' refold.pl ; \
fi
mv -f .deps/popt.Tpo .deps/popt.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o popt popt.o -L../lib -lRNA -lm 
mv -f .deps/b2ct.Tpo .deps/b2ct.Po
powerpc-unknown-linux-gnu-gcc  -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o b2ct b2ct.o -L../lib -lRNA -lm 
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils'
Making all in H
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H'
Making all in Perl
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
/usr/bin/perl Makefile.PL INSTALLDIRS=vendor LDDLFLAGS="-Wl,-O1 -Wl,--as-needed -shared"
Writing Makefile.perl for RNA
make -f Makefile.perl
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
powerpc-unknown-linux-gnu-gcc -c   -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O1 -pipe   -DVERSION=\"0.2\" -DXS_VERSION=\"0.2\" -fPIC "-I/usr/lib/perl5/5.12.4/powerpc-linux/CORE"   RNA_wrap.c
Running Mkbootstrap for RNA ()
cp RNA.pm blib/lib/RNA.pm
chmod 644 RNA.bs
cp RNA.bs blib/arch/auto/RNA/RNA.bs
chmod 644 blib/arch/auto/RNA/RNA.bs
In file included from RNA_wrap.c:1547:
../H/part_func_co.h:28: warning: 'struct plist' declared inside parameter list
../H/part_func_co.h:33: error: expected identifier or '(' before numeric constant
../H/part_func_co.h:34: error: expected ';' before 'double'
RNA_wrap.c:2169: error: expected ';', ',' or ')' before numeric constant
make[3]: *** [RNA_wrap.o] Error 1
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
make[2]: *** [all-local] Error 2
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
make: *** [all] Error 2
emake failed
 [31;01m*[0m ERROR: sci-biology/vienna-rna-1.8.5 failed (compile phase):
 [31;01m*[0m   (no error message)
 [31;01m*[0m 
 [31;01m*[0m Call stack:
 [31;01m*[0m     ebuild.sh, line  85:  Called src_compile
 [31;01m*[0m   environment, line 5889:  Called die
 [31;01m*[0m The specific snippet of code:
 [31;01m*[0m       emake || die;
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of 'emerge --info =sci-biology/vienna-rna-1.8.5',
 [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-biology/vienna-rna-1.8.5'.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/temp/environment'.
 [31;01m*[0m S: '/var/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'