/var/tmp/portage/sci-biology/vienna-rna-2.1.1/temp/build.log

build.log (text/plain), 109.15 KB, created by Juergen Rose on 2013-03-01 19:20:54 UTC

[32;01m * [39;49;00mPackage:    sci-biology/vienna-rna-2.1.1
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail]
[32;01m * [39;49;00mUSE:        amd64 doc elibc_glibc kernel_linux openmp python python_targets_python2_7 userland_GNU
[32;01m * [39;49;00mFEATURES:   sandbox
>>> Unpacking source...
>>> Unpacking ViennaRNA-2.1.1.tar.gz to /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work
>>> Preparing source in /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1 ...
 [32;01m*[0m Applying vienna-rna-2.1.1-bindir.patch ...
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 [32;01m*[0m Applying vienna-rna-2.1.1-prll.patch ...
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 [32;01m*[0m Applying vienna-rna-2.1.1-impl-decl.patch ...
[A[137C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1' ...
 [32;01m*[0m Running aclocal ...
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Kinfold' ...
 [32;01m*[0m Running aclocal ...
 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester/g2-0.70' ...
 [32;01m*[0m Running aclocal ...
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 [32;01m*[0m Running autoconf ...
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 [32;01m*[0m Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester' ...
 [32;01m*[0m Running aclocal ...
 [32;01m*[0m Running autoconf ...
 [32;01m*[0m Running autoconf ...
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 [32;01m*[0m Running autoheader ...
 [32;01m*[0m Running autoheader ...
[A[137C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
[A[137C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
 [32;01m*[0m Running autoconf ...
[A[137C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running autoheader ...
[A[137C [34;01m[ [32;01mok[34;01m ][0m
[A[137C [34;01m[ [32;01mok[34;01m ][0m
 [32;01m*[0m Running automake --add-missing --copy ...
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>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1"
 * econf: updating ViennaRNA-2.1.1/RNAforester/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating ViennaRNA-2.1.1/RNAforester/g2-0.70/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating ViennaRNA-2.1.1/RNAforester/g2-0.70/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating ViennaRNA-2.1.1/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating ViennaRNA-2.1.1/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating ViennaRNA-2.1.1/config/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating ViennaRNA-2.1.1/config/config.sub with /usr/share/gnuconfig/config.sub
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/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 --disable-silent-rules --disable-dependency-tracking --docdir=/usr/share/doc/vienna-rna-2.1.1 --enable-shared --disable-static --with-cluster --enable-openmp
configure: loading site script /usr/share/config.site
checking whether make supports nested variables... yes
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... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
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++... none
checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
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... none
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
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 make sets $(MAKE)... (cached) yes
checking for grep that handles long lines and -e... /bin/grep
checking whether x86_64-pc-linux-gnu-gcc and cc understand -c and -o together... yes
checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp
checking for exp in -lm... yes
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 stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.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 for unistd.h... (cached) yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... 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 working strtod... yes
checking for floor... yes
checking for strdup... yes
checking for strstr... yes
checking for strchr... yes
checking for strrchr... yes
checking for strstr... (cached) yes
checking for strtol... yes
checking for strtoul... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for erand48... yes
checking for memset... yes
checking for memmove... yes
checking for erand48... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking for inline... inline
checking for Perl/Makefile.am... yes
checking for Kinfold/Makefile.am... yes
checking for RNAforester/Makefile.am... yes
checking for Cluster/Makefile.am... yes
checking for libsvm-2.91/svm.cpp... yes
checking for libsvm-2.91/svm.h... yes
checking for perl... /usr/bin/perl
checking whether float precision is used for partition function arrays instead of double precision... no
checking for doxygen... /usr/bin/doxygen
checking for pdflatex... /usr/bin/pdflatex
checking for latex... /usr/bin/latex
checking for makeindex... /usr/bin/makeindex
checking for dot... /usr/bin/dot
checking for egrep... /bin/egrep
checking for perl... /usr/bin/perl
configure: WARNING: due to a bug in older versions of doxygen, latex will be used for reference manual generation even if pdflatex is available
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Perl/Makefile
config.status: creating Perl/Makefile.PL
config.status: creating Cluster/Makefile
config.status: creating doc/doxygen.conf
config.status: creating Makefile
config.status: creating misc/Makefile
config.status: creating misc/ViennaRNA.spec
config.status: creating RNAlib2.pc
config.status: creating Utils/Makefile
config.status: creating Progs/Makefile
config.status: creating lib/Makefile
config.status: creating man/Makefile
config.status: creating H/Makefile
config.status: creating doc/Makefile
config.status: creating man/cmdlopt.sh
config.status: creating config.h
config.status: executing depfiles commands
=== configuring in Kinfold (/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/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' '--disable-silent-rules' '--disable-dependency-tracking' '--docdir=/usr/share/doc/vienna-rna-2.1.1' '--enable-shared' '--disable-static' '--with-cluster' '--enable-openmp' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-march=native -O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-march=native -O2 -pipe' --cache-file=/dev/null --srcdir=.
configure: loading site script /usr/share/config.site
checking whether make supports nested variables... yes
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 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... none
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 x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp
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
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Example/Makefile
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
=== configuring in RNAforester (/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/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' '--disable-silent-rules' '--disable-dependency-tracking' '--docdir=/usr/share/doc/vienna-rna-2.1.1' '--enable-shared' '--disable-static' '--with-cluster' '--enable-openmp' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-march=native -O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-march=native -O2 -pipe' --cache-file=/dev/null --srcdir=.
configure: loading site script /usr/share/config.site
checking whether make supports nested variables... yes
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 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++... none
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... none
checking for x86_64-pc-linux-gnu-g++ option to support OpenMP... -fopenmp
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... 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
checking that generated files are newer than configure... done
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-2.1.1/work/ViennaRNA-2.1.1/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' '--disable-silent-rules' '--disable-dependency-tracking' '--docdir=/usr/share/doc/vienna-rna-2.1.1' '--enable-shared' '--disable-static' '--with-cluster' '--enable-openmp' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-march=native -O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-march=native -O2 -pipe' --cache-file=/dev/null --srcdir=.
configure: loading site script /usr/share/config.site
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.

configure:
Configure successful with the following options:

  Perl Extension:       yes
  Analyse{Dists,Seqs}:  yes
  Kinfold:              yes
  RNAforester:          yes
  SVM:                  yes
  Documentation:        yes
    (HTML):             yes
    (PDF):              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
  Documentation:  /usr/share/doc/vienna-rna-2.1.1
    (HTML):       /usr/share/doc/vienna-rna-2.1.1/html
    (PDF):        /usr/share/doc/vienna-rna-2.1.1

>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1 ...
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1"
make -j9 
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/config/missing --run autoheader)
rm -f stamp-h1
touch config.h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make  all-recursive
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1'
Making all in lib
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/lib'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-utils.o `test -f 'utils.c' || echo './'`utils.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-fold.o `test -f 'fold.c' || echo './'`fold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-naview.o `test -f 'naview.c' || echo './'`naview.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c
naview.c: In function ‘dump_loops’:
naview.c:341:3: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat]
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-params.o `test -f 'params.c' || echo './'`params.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-list.o `test -f 'list.c' || echo './'`list.c
params.c: In function ‘copy_pf_param’:
params.c:578:3: warning: ‘scale_pf_parameters’ is deprecated (declared at ./../H/params.h:128) [-Wdeprecated-declarations]
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c
LPfold.c: In function ‘putoutpU_splitup’:
LPfold.c:1012:3: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ [-Wformat]
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-ribo.o `test -f 'ribo.c' || echo './'`ribo.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-findpath.o `test -f 'findpath.c' || echo './'`findpath.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-convert_epars.o `test -f 'convert_epars.c' || echo './'`convert_epars.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-MEA.o `test -f 'MEA.c' || echo './'`MEA.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-aliLfold.o `test -f 'aliLfold.c' || echo './'`aliLfold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-mm.o `test -f 'mm.c' || echo './'`mm.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-2Dfold.o `test -f '2Dfold.c' || echo './'`2Dfold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-2Dpfold.o `test -f '2Dpfold.c' || echo './'`2Dpfold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-plex_functions.o `test -f 'plex_functions.c' || echo './'`plex_functions.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-plot_layouts.o `test -f 'plot_layouts.c' || echo './'`plot_layouts.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-ali_plex.o `test -f 'ali_plex.c' || echo './'`ali_plex.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-c_plex.o `test -f 'c_plex.c' || echo './'`c_plex.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-plex.o `test -f 'plex.c' || echo './'`plex.c
c_plex.c: In function ‘find_max_C’:
c_plex.c:1076:20: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
c_plex.c: In function ‘plot_max_C’:
c_plex.c:1114:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-snofold.o `test -f 'snofold.c' || echo './'`snofold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-snoop.o `test -f 'snoop.c' || echo './'`snoop.c
plex.c: In function ‘find_max_XS’:
plex.c:1518:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
plex.c: In function ‘plot_max_XS’:
plex.c:1613:12: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
plex.c: In function ‘find_max’:
plex.c:2676:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
plex.c:2723:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
plex.c: In function ‘plot_max’:
plex.c:2758:12: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
plex.c:2780:12: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
snoop.c: In function ‘find_max_snoop’:
snoop.c:1091:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat]
snoop.c: In function ‘snoop_subopt_XS’:
snoop.c:1604:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat]
snoop.c: In function ‘find_max_snoop_XS’:
snoop.c:2100:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat]
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-move_set.o `test -f 'move_set.c' || echo './'`move_set.c
ali_plex.c: In function ‘alifind_max’:
ali_plex.c:599:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
ali_plex.c: In function ‘aliplot_max’:
ali_plex.c:649:12: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-gquad.o `test -f 'gquad.c' || echo './'`gquad.c
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -march=native -O2 -pipe -c -o svm.o `test -f '../libsvm-2.91/svm.cpp' || echo './'`../libsvm-2.91/svm.cpp
../libsvm-2.91/svm.cpp: In function ‘svm_model* svm_load_model(const char*)’:
../libsvm-2.91/svm.cpp:2730:24: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
../libsvm-2.91/svm.cpp:2734:25: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
../libsvm-2.91/svm.cpp:2756:25: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
../libsvm-2.91/svm.cpp:2777:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
../libsvm-2.91/svm.cpp:2779:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
../libsvm-2.91/svm.cpp:2781:33: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
../libsvm-2.91/svm.cpp:2783:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
../libsvm-2.91/svm.cpp:2785:29: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
../libsvm-2.91/svm.cpp:2791:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
../libsvm-2.91/svm.cpp:2798:37: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
../libsvm-2.91/svm.cpp:2805:38: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
../libsvm-2.91/svm.cpp:2812:38: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
../libsvm-2.91/svm.cpp:2819:35: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../libsvm-2.91 -fpic   -fopenmp -fpic -march=native -O2 -pipe -c -o libRNA_a-svm_utils.o `test -f 'svm_utils.c' || echo './'`svm_utils.c
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-convert_epars.o libRNA_a-MEA.o libRNA_a-aliLfold.o libRNA_a-mm.o libRNA_a-2Dfold.o libRNA_a-2Dpfold.o libRNA_a-plex_functions.o libRNA_a-plot_layouts.o libRNA_a-ali_plex.o libRNA_a-c_plex.o libRNA_a-plex.o libRNA_a-snofold.o libRNA_a-snoop.o libRNA_a-move_set.o libRNA_a-gquad.o svm.o libRNA_a-svm_utils.o 
x86_64-pc-linux-gnu-ranlib libRNA.a
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/lib'
Making all in Progs
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Progs'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAfold_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAfold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAeval_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAeval.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAheat_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAheat.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNApdist_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNApdist.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAdistance_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAdistance.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAinverse_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAinverse.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAplot_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAplot.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAsubopt_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAsubopt.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNALfold_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNALfold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAcofold_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAcofold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNApaln_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNApaln.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAduplex_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAduplex.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAalifold_cmdl.c
RNAduplex.c: In function ‘main’:
RNAduplex.c:161:5: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ [-Wformat]
RNAduplex.c:161:5: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ [-Wformat]
RNAduplex.c: In function ‘print_struc’:
RNAduplex.c:203:10: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAalifold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAplfold_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAplfold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAup_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAup.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAaliduplex_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAaliduplex.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNALalifold_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNALalifold.c
RNAaliduplex.c: In function ‘print_struc’:
RNAaliduplex.c:171:10: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNA2Dfold_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNA2Dfold.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAparconv_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAparconv.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAPKplex_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAPKplex.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAplex_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAplex.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAsnoop_cmdl.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H -I./../lib  -fopenmp -march=native -O2 -pipe -c RNAsnoop.c
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAfold RNAfold_cmdl.o RNAfold.o -fopenmp ../lib/libRNA.a -lm -lm 
RNAsnoop.c: In function ‘print_struc’:
RNAsnoop.c:546:10: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat]
RNAsnoop.c: In function ‘aliprint_struc’:
RNAsnoop.c:627:11: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ [-Wformat]
RNAplex.c: In function ‘main’:
RNAplex.c:1100:9: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ [-Wformat]
RNAplex.c:1100:9: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ [-Wformat]
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAeval RNAeval_cmdl.o RNAeval.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAheat RNAheat_cmdl.o RNAheat.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNApdist RNApdist_cmdl.o RNApdist.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAdistance RNAdistance_cmdl.o RNAdistance.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAinverse RNAinverse_cmdl.o RNAinverse.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAplot RNAplot_cmdl.o RNAplot.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAsubopt RNAsubopt_cmdl.o RNAsubopt.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-g++  -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNALfold RNALfold_cmdl.o RNALfold.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAcofold RNAcofold_cmdl.o RNAcofold.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNApaln RNApaln_cmdl.o RNApaln.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAduplex RNAduplex_cmdl.o RNAduplex.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAalifold RNAalifold_cmdl.o RNAalifold.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAplfold RNAplfold_cmdl.o RNAplfold.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAup RNAup_cmdl.o RNAup.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNALalifold RNALalifold_cmdl.o RNALalifold.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAparconv RNAparconv_cmdl.o RNAparconv.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAsnoop RNAsnoop_cmdl.o RNAsnoop.o -fopenmp ../lib/libRNA.a -lm -lm 
x86_64-pc-linux-gnu-gcc -fopenmp -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o RNAplex RNAplex_cmdl.o RNAplex.o -fopenmp ../lib/libRNA.a -lm -lm 
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Progs'
Making all in man
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/man'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/man'
Making all in Utils
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Utils'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H   -march=native -O2 -pipe -c b2ct.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H   -march=native -O2 -pipe -c 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
if test -n "/usr/bin/perl"; then \
  /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' switch.pl ; \
fi
x86_64-pc-linux-gnu-gcc  -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o popt popt.o -L../lib -lRNA -lm -lm 
x86_64-pc-linux-gnu-gcc  -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o b2ct b2ct.o -L../lib -lRNA -lm -lm 
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Utils'
Making all in H
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H'
Making all in misc
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/misc'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/misc'
Making all in doc
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/doc'
/usr/bin/doxygen doxygen.conf
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/fold.h:50: group mfe_fold: ignoring title "Calculating Minimum Free Energy Structures" that does not match old title "Calculating Minimum Free Energy (MFE) Structures"

/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/svm_utils.h:4: warning: Compound svm_model is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/data_structures.h:373: warning: Compound interact is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/data_structures.h:347: warning: Compound path_t is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/data_structures.h:327: warning: Compound move_t is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/data_structures.h:265: warning: Compound cofoldF is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/data_structures.h:277: warning: Compound ConcEnt is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/lib/list.h:21: warning: Compound LIST is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/dist_vars.h:46: warning: Compound swString is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/dist_vars.h:41: warning: Compound Tree is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/data_structures.h:337: warning: Compound intermediate_t is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/data_structures.h:485: warning: Compound dupVar is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/data_structures.h:290: warning: Compound pairpro is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/dist_vars.h:33: warning: Compound Postorder_list is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/move_set.h:5: warning: Compound struct_en is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/lib/list.h:16: warning: Compound LST_BUCKET is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/data_structures.h:442: warning: Compound folden is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/data_structures.h:451: warning: Compound snoopT is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/data_structures.h:414: warning: Compound duplexT is not documented.
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/gquad.h:225: warning: The following parameters of backtrack_GQuad_IntLoop_L(int c, int i, int j, int type, short *S, int **ggg, int maxdist, int *p, int *q, paramT *P) are not documented:
  parameter 'maxdist'
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/plot_layouts.h:54: warning: unable to resolve reference to `bruccoleri_88' for \ref command
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/utils.h:293: warning: The following parameters of hamming_bound(const char *s1, const char *s2, int n) are not documented:
  parameter 'n'
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/utils.h:324: warning: explicit link request to 'VRNA_INPUT_NOPRINT_COMMENTS' could not be resolved
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/utils.h:324: warning: explicit link request to 'VRNA_INPUT_NOELIM_WS_SUFFIX' could not be resolved
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/utils.h:480: warning: argument 'str1' of command @param is not found in the argument list of make_loop_index_pt(short *pt)
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/utils.h:480: warning: argument 'str2' of command @param is not found in the argument list of make_loop_index_pt(short *pt)
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/utils.h:480: warning: The following parameters of make_loop_index_pt(short *pt) are not documented:
  parameter 'pt'
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/utils.h:591: warning: The following parameters of constrain_ptypes(const char *constraint, unsigned int length, char *ptype, int *BP, int min_loop_size, unsigned int idx_type) are not documented:
  parameter 'BP'
citelist:4: warning: Unexpected new line character
citelist:12: warning: Unexpected new line character
citelist:20: warning: Unexpected new line character
citelist:21: warning: Unexpected new line character
citelist:37: warning: Unexpected new line character
citelist:62: warning: Unexpected new line character
citelist:63: warning: Unexpected new line character
citelist:73: warning: Unexpected new line character
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/fold.h:21: warning: unable to resolve reference to `zuker_81' for \ref command
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/alifold.h:350: warning: The following parameters of get_alipf_arrays(short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p, short **pscore) are not documented:
  parameter 'pscore'
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H/data_structures.h:652: warning: explicit link request to 'FLT_OR_DBL' could not be resolved
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/doc/mainpage.h:137: warning: unable to resolve reference to `mp_ref' for \ref command
/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/doc/mainpage.h:137: warning: unable to resolve reference to `mp_ref' for \ref command
cd latex; \
make; \
mv refman.pdf ../RNAlib-2.1.1.pdf
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/doc/latex'
make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.
rm -f *.ps *.dvi *.aux *.toc *.idx *.ind *.ilg *.log *.out *.brf *.blg *.bbl refman.pdf
pdflatex refman
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
 restricted \write18 enabled.
entering extended mode
(./refman.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, bu
lgarian, russian, ukrainian, basque, french, german-x-2012-05-30, ngerman-x-201
2-05-30, german, ngerman, swissgerman, loaded.

/usr/bin/makeindex refman.idx
This is makeindex, version 2.15 [TeX Live 2012] (kpathsea + Thai support).
Scanning input file refman.idx....done (572 entries accepted, 73 rejected).
Sorting entries.......done (5798 comparisons).
Generating output file refman.ind....done (1322 lines written, 0 warnings).
Output written in refman.ind.
Transcript written in refman.ilg.
bibtex refman
This is BibTeX, Version 0.99d (TeX Live 2012)
The top-level auxiliary file: refman.aux
A level-1 auxiliary file: group__mfe__fold.aux
A level-1 auxiliary file: group__pf__fold.aux
A level-1 auxiliary file: group__mea__fold.aux
A level-1 auxiliary file: group__centroid__fold.aux
A level-1 auxiliary file: group__subopt__fold.aux
A level-1 auxiliary file: group__subopt__zuker.aux
A level-1 auxiliary file: group__subopt__wuchty.aux
A level-1 auxiliary file: group__subopt__stochbt.aux
A level-1 auxiliary file: group__cofold.aux
A level-1 auxiliary file: group__mfe__cofold.aux
A level-1 auxiliary file: group__pf__cofold.aux
A level-1 auxiliary file: group__up__cofold.aux
A level-1 auxiliary file: group__consensus__fold.aux
A level-1 auxiliary file: group__consensus__mfe__fold.aux
A level-1 auxiliary file: group__consensus__pf__fold.aux
A level-1 auxiliary file: group__consensus__stochbt.aux
A level-1 auxiliary file: group__local__fold.aux
A level-1 auxiliary file: group__local__mfe__fold.aux
A level-1 auxiliary file: group__local__pf__fold.aux
A level-1 auxiliary file: group__local__consensus__fold.aux
A level-1 auxiliary file: group__energy__parameters.aux
A level-1 auxiliary file: group__energy__parameters__rw.aux
A level-1 auxiliary file: group__energy__parameters__convert.aux
A level-1 auxiliary file: group__eval.aux
A level-1 auxiliary file: group__inverse__fold.aux
A level-1 auxiliary file: group__class__fold.aux
A level-1 auxiliary file: group__kl__neighborhood.aux
A level-1 auxiliary file: group__kl__neighborhood__mfe.aux
A level-1 auxiliary file: group__kl__neighborhood__pf.aux
A level-1 auxiliary file: group__kl__neighborhood__stochbt.aux
A level-1 auxiliary file: group__dos.aux
A level-1 auxiliary file: group__parse.aux
The style file: plain.bst
Database file #1: viennarna.bib
pdflatex refman
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
 restricted \write18 enabled.
entering extended mode
(./refman.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, bu
lgarian, russian, ukrainian, basque, french, german-x-2012-05-30, ngerman-x-201
2-05-30, german, ngerman, swissgerman, loaded.

pdflatex refman
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012)
 restricted \write18 enabled.
entering extended mode
(./refman.tex
LaTeX2e <2011/06/27>
Babel <v3.8m> and hyphenation patterns for english, dumylang, nohyphenation, bu
lgarian, russian, ukrainian, basque, french, german-x-2012-05-30, ngerman-x-201
2-05-30, german, ngerman, swissgerman, loaded.

latex_count=5 ; \
while egrep -s 'Rerun (LaTeX|to get cross-references right)' refman.log && [ $latex_count -gt 0 ] ;\
    do \
      echo "Rerunning latex...." ;\
      pdflatex refman ;\
      latex_count=`expr $latex_count - 1` ;\
    done
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/doc/latex'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/doc'
Making all in Perl
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Perl'
/usr/bin/perl Makefile.PL INSTALLDIRS=vendor LDDLFLAGS="-Wl,-O1 -Wl,--as-needed -shared"
Writing Makefile.perl for RNA
Writing MYMETA.yml and MYMETA.json
make -f Makefile.perl
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Perl'
x86_64-pc-linux-gnu-gcc -c   -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64  -march=native -O2 -pipe -O2 -pipe   -DVERSION=\"2.1.1\" -DXS_VERSION=\"2.1.1\" -fPIC "-I/usr/lib64/perl5/5.16.2/x86_64-linux-thread-multi/CORE"   RNA_wrap.c
Running Mkbootstrap for RNA ()
chmod 644 RNA.bs
cp RNA.bs blib/arch/auto/RNA/RNA.bs
chmod 644 blib/arch/auto/RNA/RNA.bs
cp RNA.pm blib/lib/RNA.pm
RNA_wrap.c: In function ‘my_alifold’:
RNA_wrap.c:2327:5: warning: passing argument 1 of ‘alifold’ from incompatible pointer type [enabled by default]
../H/alifold.h:86:8: note: expected ‘const char **’ but argument is of type ‘char **’
RNA_wrap.c: In function ‘_wrap_LoopEnergy’:
RNA_wrap.c:6561:5: warning: ‘LoopEnergy’ is deprecated (declared at ../H/fold.h:518) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_HairpinE’:
RNA_wrap.c:6636:5: warning: ‘HairpinE’ is deprecated (declared at ../H/fold.h:531) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_initialize_fold’:
RNA_wrap.c:6671:5: warning: ‘initialize_fold’ is deprecated (declared at ../H/fold.h:542) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_energy_of_struct’:
RNA_wrap.c:6709:5: warning: ‘energy_of_struct’ is deprecated (declared at ../H/fold.h:558) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_energy_of_struct_pt’:
RNA_wrap.c:6764:5: warning: ‘energy_of_struct_pt’ is deprecated (declared at ../H/fold.h:577) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_energy_of_circ_struct’:
RNA_wrap.c:6808:5: warning: ‘energy_of_circ_struct’ is deprecated (declared at ../H/fold.h:596) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_initialize_cofold’:
RNA_wrap.c:7332:5: warning: ‘initialize_cofold’ is deprecated (declared at ../H/cofold.h:180) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_init_pf_fold’:
RNA_wrap.c:8240:5: warning: ‘init_pf_fold’ is deprecated (declared at ../H/part_func.h:399) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_centroid’:
RNA_wrap.c:8276:5: warning: ‘centroid’ is deprecated (declared at ../H/part_func.h:405) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_mean_bp_dist’:
RNA_wrap.c:8306:5: warning: ‘mean_bp_dist’ is deprecated (declared at ../H/part_func.h:413) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_expLoopEnergy’:
RNA_wrap.c:8390:5: warning: ‘expLoopEnergy’ is deprecated (declared at ../H/part_func.h:418) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_expHairpinEnergy’:
RNA_wrap.c:8465:5: warning: ‘expHairpinEnergy’ is deprecated (declared at ../H/part_func.h:430) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_Make_bp_profile’:
RNA_wrap.c:11671:5: warning: ‘Make_bp_profile’ is deprecated (declared at ../H/profiledist.h:56) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_copy_parameters’:
RNA_wrap.c:13220:5: warning: ‘copy_parameters’ is deprecated (declared at ../H/params.h:126) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_set_parameters’:
RNA_wrap.c:13246:5: warning: ‘set_parameters’ is deprecated (declared at ../H/params.h:127) [-Wdeprecated-declarations]
RNA_wrap.c: In function ‘_wrap_PS_dot_plot’:
RNA_wrap.c:14913:5: warning: ‘PS_dot_plot’ is deprecated (declared at ../H/PS_dot.h:195) [-Wdeprecated-declarations]
rm -f blib/arch/auto/RNA/RNA.so
g++  -Wl,-O1 -Wl,--as-needed -shared RNA_wrap.o  -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -fopenmp -o blib/arch/auto/RNA/RNA.so ../lib/libRNA.a	\
   -lm  	\
  
chmod 755 blib/arch/auto/RNA/RNA.so
Manifying blib/man3/RNA.3pm
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Perl'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Perl'
Making all in Cluster
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Cluster'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H   -march=native -O2 -pipe -c split.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H   -march=native -O2 -pipe -c distance_matrix.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H   -march=native -O2 -pipe -c cluster.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H   -march=native -O2 -pipe -c treeplot.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H   -march=native -O2 -pipe -c AD_main.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H   -march=native -O2 -pipe -c ./../lib/utils.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H   -march=native -O2 -pipe -c statgeom.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H   -march=native -O2 -pipe -c AS_main.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..  -I./../H   -march=native -O2 -pipe -c PS3D.c
x86_64-pc-linux-gnu-gcc  -march=native -O2 -pipe  -Wl,-O1 -Wl,--as-needed -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o utils.o -lm -lm 
x86_64-pc-linux-gnu-gcc  -march=native -O2 -pipe  -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 -lm 
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Cluster'
Making all in Kinfold
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Kinfold'
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/missing --run autoheader)
rm -f stamp-h1
touch config.h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make  all-recursive
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Kinfold'
Making all in Example
make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Kinfold/Example'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Kinfold/Example'
make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Kinfold'
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -march=native -O2 -pipe -c baum.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -march=native -O2 -pipe -c cache.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -march=native -O2 -pipe -c globals.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -march=native -O2 -pipe -c main.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -march=native -O2 -pipe -c nachbar.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.   -I../H  -march=native -O2 -pipe -c cmdline.c
globals.c: In function ‘process_options_gg’:
globals.c:298:3: warning: passing argument 2 of ‘strncpy’ makes pointer from integer without a cast [enabled by default]
/usr/include/bits/string3.h:117:1: note: expected ‘const char * __restrict__’ but argument is of type ‘int’
globals.c:298:3: warning: passing argument 3 of ‘strncpy’ makes integer from pointer without a cast [enabled by default]
/usr/include/bits/string3.h:117:1: note: expected ‘size_t’ but argument is of type ‘char *’
globals.c:334:9: warning: format ‘%g’ expects argument of type ‘float *’, but argument 3 has type ‘double *’ [-Wformat]
globals.c:334:9: warning: format ‘%g’ expects argument of type ‘float *’, but argument 4 has type ‘double *’ [-Wformat]
globals.c:334:9: warning: format ‘%g’ expects argument of type ‘float *’, but argument 5 has type ‘double *’ [-Wformat]
globals.c: In function ‘process_options’:
globals.c:423:8: warning: format ‘%g’ expects argument of type ‘float *’, but argument 3 has type ‘double *’ [-Wformat]
globals.c:423:8: warning: format ‘%g’ expects argument of type ‘float *’, but argument 4 has type ‘double *’ [-Wformat]
globals.c:423:8: warning: format ‘%g’ expects argument of type ‘float *’, but argument 5 has type ‘double *’ [-Wformat]
nachbar.c: In function ‘sel_nb’:
nachbar.c:302:2: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ [-Wformat]
x86_64-pc-linux-gnu-gcc  -march=native -O2 -pipe -fopenmp -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-2.1.1/work/ViennaRNA-2.1.1/Kinfold'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Kinfold'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Kinfold'
Making all in RNAforester
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester'
(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester/missing --run autoheader)
rm -f stamp-h1
touch config.h.in
cd . && /bin/sh ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make  all-recursive
make[3]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester'
Making all in g2-0.70
make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester/g2-0.70'
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_device.c -o src/g2_device.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_control.c -o src/g2_ui_control.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_util.c -o src/g2_util.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_fif.c -o src/g2_fif.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_virtual_device.c -o src/g2_virtual_device.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_physical_device.c -o src/g2_physical_device.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_graphic_pd.c -o src/g2_graphic_pd.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_control_pd.c -o src/g2_control_pd.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_graphic.c -o src/g2_ui_graphic.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_virtual_device.c -o src/g2_ui_virtual_device.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_device.c -o src/g2_ui_device.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_splines.c -o src/g2_splines.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/PS/g2_PS.c -o src/PS/g2_PS.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/FIG/g2_FIG.c -o src/FIG/g2_FIG.o
x86_64-pc-linux-gnu-gcc  -I./src -march=native -O2 -pipe  -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/X11/g2_X11.c -o src/X11/g2_X11.o
src/FIG/g2_FIG.c: In function ‘g2_FIG_draw_string’:
src/FIG/g2_FIG.c:478:6: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ [-Wformat]
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-2.1.1/work/ViennaRNA-2.1.1/RNAforester/g2-0.70'
Making all in src
make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester/src'
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c -o Arguments.o Arguments.cpp
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c glib.c
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c -o main.o main.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c -o ppforestbase.o ppforestbase.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c -o progressive_align.o progressive_align.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c -o rna_profile_alignment.o rna_profile_alignment.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c -o rna_alignment.o rna_alignment.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c -o rna_algebra.o rna_algebra.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c -o rna_alphabet.o rna_alphabet.cpp
glib.c: In function ‘ReadMatrix’:
glib.c:272:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
glib.c:282:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
glib.c: In function ‘ReadEuclid’:
glib.c:225:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
glib.c:234:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
glib.c: In function ‘ReadGraph’:
glib.c:161:8: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
glib.c:170:9: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
glib.c:176:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c -o rnaforest.o rnaforest.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c -o rnaforestsz.o rnaforestsz.cpp
In file included from rnaforest.h:22:0,
                 from rnaforest.cpp:24:
rnafuncs.h:42:3: warning: ‘typedef’ was ignored in this declaration [enabled by default]
In file included from rnaforest.h:22:0,
                 from rna_alignment.h:24,
                 from rna_alignment.cpp:22:
rnafuncs.h:42:3: warning: ‘typedef’ was ignored in this declaration [enabled by default]
In file included from rnaforestsz.cpp:15:0:
rnafuncs.h:42:3: warning: ‘typedef’ was ignored in this declaration [enabled by default]
In file included from rnaforest.h:22:0,
                 from rna_alignment.h:24,
                 from main.cpp:52:
rnafuncs.h:42:3: warning: ‘typedef’ was ignored in this declaration [enabled by default]
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c -o rnafuncs.o rnafuncs.cpp
x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c -o rnaforester_options.o rnaforester_options.cpp
progressive_align.cpp: In function ‘node_entry* makePairsGraph(const RNAProfileAliMapType&, const DoubleScoreProfileAlgebraType*, const Matrix<double>*, double)’:
progressive_align.cpp:341:30: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings]
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..   -I../g2-0.70/include/   -march=native -O2 -pipe -c wmatch.c
In file included from rna_profile_alignment.cpp:37:0:
rnafuncs.h:42:3: warning: ‘typedef’ was ignored in this declaration [enabled by default]
In file included from rnafuncs.cpp:23:0:
rnafuncs.h:42:3: warning: ‘typedef’ was ignored in this declaration [enabled by default]
x86_64-pc-linux-gnu-g++  -march=native -O2 -pipe  -L../g2-0.70 -L../../lib -L../../ViennaRNA -Wl,-O1 -Wl,--as-needed -fopenmp -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-2.1.1/work/ViennaRNA-2.1.1/RNAforester/src'
Making all in man
make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester/man'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester/man'
make[4]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester'
make[4]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester'
make[3]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/RNAforester'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1'
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1"
make -j9 -C Readseq build CC=x86_64-pc-linux-gnu-gcc 
make: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Readseq'
Compiling readseq...
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -march=native -O2 -pipe -o readseq readseq.c ureadseq.c ureadasn.c
readseq.c: In function ‘formatstr’:
readseq.c:257:27: warning: return discards ‘const’ qualifier from pointer target type [enabled by default]
readseq.c:259:31: warning: return discards ‘const’ qualifier from pointer target type [enabled by default]
readseq.c:263:8: warning: return discards ‘const’ qualifier from pointer target type [enabled by default]
readseq.c: In function ‘usage’:
readseq.c:328:3: warning: format not a string literal and no format arguments [-Wformat-security]
readseq.c: In function ‘chooseFormat’:
readseq.c:419:7: warning: ‘gets’ is deprecated (declared at /usr/include/bits/stdio2.h:233) [-Wdeprecated-declarations]
readseq.c: In function ‘main’:
readseq.c:768:3: warning: format not a string literal and no format arguments [-Wformat-security]
readseq.c:775:5: warning: ‘gets’ is deprecated (declared at /usr/include/bits/stdio2.h:233) [-Wdeprecated-declarations]
readseq.c:839:7: warning: ‘gets’ is deprecated (declared at /usr/include/bits/stdio2.h:233) [-Wdeprecated-declarations]
readseq.c:885:9: warning: ‘gets’ is deprecated (declared at /usr/include/bits/stdio2.h:233) [-Wdeprecated-declarations]
readseq.c:910:13: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
readseq.c:912:13: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat]
readseq.c:955:17: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat]
readseq.c:955:17: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
readseq.c:955:17: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
readseq.c:965:15: warning: format not a string literal and no format arguments [-Wformat-security]
readseq.c:972:19: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat]
readseq.c:972:19: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
readseq.c:973:19: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat]
readseq.c:973:19: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
readseq.c:1076:19: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
readseq.c:1076:19: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
readseq.c:1087:5: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
readseq.c:1088:5: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
readseq.c:1112:9: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
readseq.c:757:11: warning: ignoring return value of ‘tmpnam’, declared with attribute warn_unused_result [-Wunused-result]
readseq.c:775:9: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result [-Wunused-result]
readseq.c:839:11: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result [-Wunused-result]
readseq.c:885:13: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result [-Wunused-result]
readseq.c:911:20: warning: ignoring return value of ‘freopen’, declared with attribute warn_unused_result [-Wunused-result]
readseq.c: In function ‘chooseFormat’:
readseq.c:419:11: warning: ignoring return value of ‘gets’, declared with attribute warn_unused_result [-Wunused-result]
ureadseq.c: In function ‘seqFileFormatFp’:
ureadseq.c:1346:5: warning: format ‘%d’ expects argument of type ‘int *’, but argument 3 has type ‘long int *’ [-Wformat]
ureadseq.c:1346:5: warning: format ‘%d’ expects argument of type ‘int *’, but argument 4 has type ‘long int *’ [-Wformat]
ureadseq.c: In function ‘writeSeq’:
ureadseq.c:1595:3: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat]
ureadseq.c:1624:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1625:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1625:7: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
ureadseq.c:1639:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1639:7: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
ureadseq.c:1649:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat]
ureadseq.c:1659:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1659:7: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
ureadseq.c:1668:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1668:7: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
ureadseq.c:1669:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat]
ureadseq.c:1680:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1680:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
ureadseq.c:1689:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1689:7: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
ureadseq.c:1695:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1695:7: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
ureadseq.c:1726:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1748:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1748:7: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
ureadseq.c:1765:9: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1765:9: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
ureadseq.c:1772:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1772:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
ureadseq.c:1783:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1783:7: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
ureadseq.c:1792:7: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat]
ureadseq.c:1792:7: warning: format ‘%X’ expects argument of type ‘unsigned int’, but argument 5 has type ‘long unsigned int’ [-Wformat]
ureadseq.c:1833:9: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat]
make: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Readseq'
RNA.i:238: Warning 303: %extend defined for an undeclared class bondT.
../H/fold_vars.h:150: Warning 454: Setting a pointer/reference variable may leak memory.
../H/fold_vars.h:157: Warning 454: Setting a pointer/reference variable may leak memory.
../H/fold_vars.h:165: Warning 454: Setting a pointer/reference variable may leak memory.
 [32;01m*[0m python2.7: running distutils-r1_run_phase distutils-r1_python_compile
/usr/bin/python2.7 setup.py build build --build-base /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1-python2_7 --build-lib /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1-python2_7/lib --build-scripts /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1-python2_7/scripts
running build
running build_py
creating /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1-python2_7
creating /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1-python2_7/lib
creating /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1-python2_7/lib/RNA
copying Perl/__init__.py -> /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1-python2_7/lib/RNA
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
building '_RNA' extension
creating /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1-python2_7/temp.linux-x86_64-2.7
creating /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1-python2_7/temp.linux-x86_64-2.7/Perl
x86_64-pc-linux-gnu-gcc -pthread -march=native -O2 -pipe -fPIC -I/usr/include/python2.7 -c Perl/RNA_wrap.c -o /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1-python2_7/temp.linux-x86_64-2.7/Perl/RNA_wrap.o
Perl/RNA_wrap.c: In function ‘my_alifold’:
Perl/RNA_wrap.c:3800:5: warning: passing argument 1 of ‘alifold’ from incompatible pointer type [enabled by default]
Perl/../H/alifold.h:86:8: note: expected ‘const char **’ but argument is of type ‘char **’
Perl/RNA_wrap.c: In function ‘_wrap_LoopEnergy’:
Perl/RNA_wrap.c:6573:3: warning: ‘LoopEnergy’ is deprecated (declared at Perl/../H/fold.h:518) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_HairpinE’:
Perl/RNA_wrap.c:6632:3: warning: ‘HairpinE’ is deprecated (declared at Perl/../H/fold.h:531) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_initialize_fold’:
Perl/RNA_wrap.c:6655:3: warning: ‘initialize_fold’ is deprecated (declared at Perl/../H/fold.h:542) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_energy_of_struct’:
Perl/RNA_wrap.c:6688:3: warning: ‘energy_of_struct’ is deprecated (declared at Perl/../H/fold.h:558) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_energy_of_struct_pt’:
Perl/RNA_wrap.c:6742:3: warning: ‘energy_of_struct_pt’ is deprecated (declared at Perl/../H/fold.h:577) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_energy_of_circ_struct’:
Perl/RNA_wrap.c:6777:3: warning: ‘energy_of_circ_struct’ is deprecated (declared at Perl/../H/fold.h:596) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_initialize_cofold’:
Perl/RNA_wrap.c:7212:3: warning: ‘initialize_cofold’ is deprecated (declared at Perl/../H/cofold.h:180) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_assign_plist_from_pr’:
Perl/RNA_wrap.c:7569:3: warning: passing argument 2 of ‘assign_plist_from_pr’ from incompatible pointer type [enabled by default]
Perl/../H/part_func.h:258:7: note: expected ‘double *’ but argument is of type ‘float *’
Perl/RNA_wrap.c: In function ‘_wrap_get_pf_arrays’:
Perl/RNA_wrap.c:7715:3: warning: passing argument 4 of ‘get_pf_arrays’ from incompatible pointer type [enabled by default]
Perl/../H/part_func.h:286:5: note: expected ‘double **’ but argument is of type ‘float **’
Perl/RNA_wrap.c:7715:3: warning: passing argument 5 of ‘get_pf_arrays’ from incompatible pointer type [enabled by default]
Perl/../H/part_func.h:286:5: note: expected ‘double **’ but argument is of type ‘float **’
Perl/RNA_wrap.c:7715:3: warning: passing argument 6 of ‘get_pf_arrays’ from incompatible pointer type [enabled by default]
Perl/../H/part_func.h:286:5: note: expected ‘double **’ but argument is of type ‘float **’
Perl/RNA_wrap.c:7715:3: warning: passing argument 7 of ‘get_pf_arrays’ from incompatible pointer type [enabled by default]
Perl/../H/part_func.h:286:5: note: expected ‘double **’ but argument is of type ‘float **’
Perl/RNA_wrap.c: In function ‘_wrap_get_centroid_struct_pr’:
Perl/RNA_wrap.c:7832:3: warning: passing argument 3 of ‘get_centroid_struct_pr’ from incompatible pointer type [enabled by default]
Perl/../H/part_func.h:335:8: note: expected ‘double *’ but argument is of type ‘float *’
Perl/RNA_wrap.c: In function ‘_wrap_mean_bp_distance_pr’:
Perl/RNA_wrap.c:7885:3: warning: passing argument 2 of ‘mean_bp_distance_pr’ from incompatible pointer type [enabled by default]
Perl/../H/part_func.h:370:9: note: expected ‘double *’ but argument is of type ‘float *’
Perl/RNA_wrap.c: In function ‘_wrap_bppm_to_structure’:
Perl/RNA_wrap.c:7925:3: warning: passing argument 2 of ‘bppm_to_structure’ from incompatible pointer type [enabled by default]
Perl/../H/part_func.h:376:7: note: expected ‘double *’ but argument is of type ‘float *’
Perl/RNA_wrap.c: In function ‘_wrap_init_pf_fold’:
Perl/RNA_wrap.c:7992:3: warning: ‘init_pf_fold’ is deprecated (declared at Perl/../H/part_func.h:399) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_centroid’:
Perl/RNA_wrap.c:8023:3: warning: ‘centroid’ is deprecated (declared at Perl/../H/part_func.h:405) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_mean_bp_dist’:
Perl/RNA_wrap.c:8045:3: warning: ‘mean_bp_dist’ is deprecated (declared at Perl/../H/part_func.h:413) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_expLoopEnergy’:
Perl/RNA_wrap.c:8130:3: warning: ‘expLoopEnergy’ is deprecated (declared at Perl/../H/part_func.h:418) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_expHairpinEnergy’:
Perl/RNA_wrap.c:8189:3: warning: ‘expHairpinEnergy’ is deprecated (declared at Perl/../H/part_func.h:430) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘Swig_var_pr_set’:
Perl/RNA_wrap.c:9344:8: warning: assignment from incompatible pointer type [enabled by default]
Perl/RNA_wrap.c: In function ‘_wrap_get_alipf_arrays’:
Perl/RNA_wrap.c:10362:3: warning: passing argument 6 of ‘get_alipf_arrays’ from incompatible pointer type [enabled by default]
Perl/../H/alifold.h:367:5: note: expected ‘double **’ but argument is of type ‘float **’
Perl/RNA_wrap.c:10362:3: warning: passing argument 7 of ‘get_alipf_arrays’ from incompatible pointer type [enabled by default]
Perl/../H/alifold.h:367:5: note: expected ‘double **’ but argument is of type ‘float **’
Perl/RNA_wrap.c:10362:3: warning: passing argument 8 of ‘get_alipf_arrays’ from incompatible pointer type [enabled by default]
Perl/../H/alifold.h:367:5: note: expected ‘double **’ but argument is of type ‘float **’
Perl/RNA_wrap.c:10362:3: warning: passing argument 9 of ‘get_alipf_arrays’ from incompatible pointer type [enabled by default]
Perl/../H/alifold.h:367:5: note: expected ‘double **’ but argument is of type ‘float **’
Perl/RNA_wrap.c: In function ‘_wrap_Make_bp_profile_bppm’:
Perl/RNA_wrap.c:11608:3: warning: passing argument 1 of ‘Make_bp_profile_bppm’ from incompatible pointer type [enabled by default]
Perl/../H/profiledist.h:33:8: note: expected ‘double *’ but argument is of type ‘float *’
Perl/RNA_wrap.c: In function ‘_wrap_Make_bp_profile’:
Perl/RNA_wrap.c:11672:3: warning: ‘Make_bp_profile’ is deprecated (declared at Perl/../H/profiledist.h:56) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_copy_parameters’:
Perl/RNA_wrap.c:13008:3: warning: ‘copy_parameters’ is deprecated (declared at Perl/../H/params.h:126) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_set_parameters’:
Perl/RNA_wrap.c:13030:3: warning: ‘set_parameters’ is deprecated (declared at Perl/../H/params.h:127) [-Wdeprecated-declarations]
Perl/RNA_wrap.c: In function ‘_wrap_PS_dot_plot’:
Perl/RNA_wrap.c:14535:3: warning: ‘PS_dot_plot’ is deprecated (declared at Perl/../H/PS_dot.h:195) [-Wdeprecated-declarations]
x86_64-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -march=native -O2 -pipe /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1-python2_7/temp.linux-x86_64-2.7/Perl/RNA_wrap.o -Llib -L/usr/lib64 -lRNA -lpython2.7 -o /var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1-python2_7/lib/_RNA.so
>>> Source compiled.
>>> Test phase [not enabled]: sci-biology/vienna-rna-2.1.1

>>> Install vienna-rna-2.1.1 into /var/tmp/portage/sci-biology/vienna-rna-2.1.1/image/ category sci-biology
>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1"
make -j9 DESTDIR=/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image/ install 
Making install in lib
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/lib'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/lib'
make[2]: Nothing to be done for `install-data-am'.
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/lib64'
 /usr/bin/install -c -m 644  libRNA.a '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/lib64'
 ( cd '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/lib64' && x86_64-pc-linux-gnu-ranlib libRNA.a )
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/lib'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/lib'
Making install in Progs
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Progs'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Progs'
make[2]: Nothing to be done for `install-data-am'.
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/bin'
  /usr/bin/install -c RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex RNALalifold RNA2Dfold RNAparconv RNAPKplex RNAplex RNAsnoop '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/bin'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Progs'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Progs'
Making install in man
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/man'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/man'
make[2]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/man/man1'
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/info'
 /usr/bin/install -c -m 644 RNA2Dfold.1 RNAaliduplex.1 RNAalifold.1 RNAcofold.1 RNAduplex.1 RNAeval.1 RNAfold.1 RNAheat.1 RNAinverse.1 RNALalifold.1 RNALfold.1 RNApaln.1 RNAparconv.1 RNAplfold.1 RNAplot.1 RNAsubopt.1 RNAup.1 RNAPKplex.1 RNAsnoop.1 RNAplex.1 RNAdistance.1 RNApdist.1 '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/man/man1'
 /usr/bin/install -c -m 644 ./RNAlib.info '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/info'
 install-info --info-dir='/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/info' '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/info/RNAlib.info'
install-info: warning: no info dir entry in `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/info/RNAlib.info'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/man'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/man'
Making install in Utils
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Utils'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Utils'
make[2]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/bin'
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/bin'
  /usr/bin/install -c b2ct popt '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/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 switch.pl Fold '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/bin'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Utils'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/Utils'
Making install in H
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H'
make[2]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/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 loop_energies.h data_structures.h MEA.h mm.h naview.h 2Dfold.h 2Dpfold.h read_epars.h convert_epars.h PKplex.h plot_layouts.h ali_plex.h '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/include/ViennaRNA'
 /usr/bin/install -c -m 644 plex.h snofold.h snoop.h move_set.h gquad.h svm_utils.h '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/include/ViennaRNA'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/H'
Making install in misc
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/misc'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/misc'
make[2]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/ViennaRNA'
 /usr/bin/install -c -m 644 rna_turner1999.par rna_turner2004.par rna_andronescu2007.par dna_mathews1999.par dna_mathews2004.par 2Dlandscape_mfe.gri 2Dlandscape_pf.gri '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/ViennaRNA'
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/misc'
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/misc'
Making install in doc
make[1]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/doc'
make[2]: Entering directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/doc'
make[2]: Nothing to be done for `install-exec-am'.
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1'
 /usr/bin/install -c -m 644 RNAlib-2.1.1.tag RNAlib-2.1.1.pdf '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1'
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1/html'
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1/html'
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1'
 /bin/mkdir -p '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/ViennaRNA'
 /usr/bin/install -c -m 644 RNAlib-2.1.1.tag RNAlib-2.1.1.pdf '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1'
 /usr/bin/install -c -m 644 viennarna.bib '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/ViennaRNA'
 /usr/bin/install -c -m 644 html/1_88_84__epars_8h.html html/1_88_84__epars_8h.js html/1_88_84__epars_8h_source.html html/1_88_84__intloops_8h.html html/1_88_84__intloops_8h.js html/1_88_84__intloops_8h_source.html html/2Dfold_8h.html html/2Dfold_8h__incl.map html/2Dfold_8h__incl.md5 html/2Dfold_8h__incl.png html/2Dfold_8h.js html/2Dfold_8h_source.html html/2Dpfold_8h.html html/2Dpfold_8h__incl.map html/2Dpfold_8h__incl.md5 html/2Dpfold_8h__incl.png html/2Dpfold_8h.js html/2Dpfold_8h_source.html html/alifold_8h.html html/alifold_8h__incl.map html/alifold_8h__incl.md5 html/alifold_8h__incl.png html/alifold_8h.js html/alifold_8h_source.html html/ali__plex_8h_source.html html/aln__util_8h_source.html html/annotated.html html/annotated.js html/bc_s.png html/bdwn.png html/citelist.html html/classes.html html/closed.png html/cofold_8h.html html/cofold_8h__incl.map html/cofold_8h__incl.md5 html/cofold_8h__incl.png html/cofold_8h.js html/cofold_8h_source.html html/convert__epars_8h.html '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1/html'
 /usr/bin/install -c -m 644 html/1_88_84__epars_8h.html html/1_88_84__epars_8h.js html/1_88_84__epars_8h_source.html html/1_88_84__intloops_8h.html html/1_88_84__intloops_8h.js html/1_88_84__intloops_8h_source.html html/2Dfold_8h.html html/2Dfold_8h__incl.map html/2Dfold_8h__incl.md5 html/2Dfold_8h__incl.png html/2Dfold_8h.js html/2Dfold_8h_source.html html/2Dpfold_8h.html html/2Dpfold_8h__incl.map html/2Dpfold_8h__incl.md5 html/2Dpfold_8h__incl.png html/2Dpfold_8h.js html/2Dpfold_8h_source.html html/alifold_8h.html html/alifold_8h__incl.map html/alifold_8h__incl.md5 html/alifold_8h__incl.png html/alifold_8h.js html/alifold_8h_source.html html/ali__plex_8h_source.html html/aln__util_8h_source.html html/annotated.html html/annotated.js html/bc_s.png html/bdwn.png html/citelist.html html/classes.html html/closed.png html/cofold_8h.html html/cofold_8h__incl.map html/cofold_8h__incl.md5 html/cofold_8h__incl.png html/cofold_8h.js html/cofold_8h_source.html html/convert__epars_8h.html '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1/html'
/usr/bin/install: cannot create regular file ‘/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1/html/1_88_84__epars_8h.html’: File exists
/usr/bin/install: cannot create regular file ‘/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1/html/1_88_84__epars_8h.js’: File exists
/usr/bin/install: cannot create regular file ‘/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1/html/1_88_84__epars_8h_source.html’: File exists
/usr/bin/install: cannot create regular file ‘/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1/html/1_88_84__intloops_8h.html’: File exists
/usr/bin/install: cannot create regular file ‘/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1/html/1_88_84__intloops_8h.js’: File exists
/usr/bin/install: cannot create regular file ‘/var/tmp/portage/sci-biology/vienna-rna-2.1.1/image//usr/share/doc/vienna-rna-2.1.1/html/1_88_84__intloops_8h_source.html’: File exists
make[2]: *** [install-docdir_htmlDATA] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: *** [install-dist_docdir_htmlDATA] Error 1
make[2]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/doc'
make[1]: *** [install-am] Error 2
make[1]: Leaving directory `/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1/doc'
make: *** [install-recursive] Error 1
 [31;01m*[0m ERROR: sci-biology/vienna-rna-2.1.1 failed (install phase):
 [31;01m*[0m   emake failed
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of `emerge --info '=sci-biology/vienna-rna-2.1.1'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-biology/vienna-rna-2.1.1'`.
 [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/temp/environment'.
 [31;01m*[0m Working directory: '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1'
 [31;01m*[0m S: '/var/tmp/portage/sci-biology/vienna-rna-2.1.1/work/ViennaRNA-2.1.1'
[33;01m * [39;49;00mQA Notice: make jobserver unavailable:
[33;01m * [39;49;00m
[33;01m * [39;49;00m	make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make rule.