* Package: sci-biology/vienna-rna-2.1.8 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 doc elibc_glibc kernel_linux openmp python_targets_python2_7 userland_GNU * FEATURES: sandbox test userpriv usersandbox Installed LAPACK for library directory lib64 [1] reference * Installed BLAS for library directory lib64 [1] reference * Installed CBLAS for library directory lib64 [1] gsl [2] reference * >>> Unpacking source... >>> Unpacking ViennaRNA-2.1.8.tar.gz to /tmp/portage/sci-biology/vienna-rna-2.1.8/work >>> Source unpacked in /tmp/portage/sci-biology/vienna-rna-2.1.8/work >>> Preparing source in /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ... * Applying vienna-rna-2.1.8-bindir.patch ... [ ok ] * Applying vienna-rna-2.1.1-prll.patch ... [ ok ] * Applying vienna-rna-2.1.1-impl-decl.patch ... [ ok ] * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' ... * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' ... * Running aclocal ... * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70' ... * Running aclocal ... * Running aclocal ... [ ok ] [ ok ] [ ok ] * Running autoconf ... * Running autoconf ... [ ok ] * Running autoheader ... [ ok ] * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' ... * Running autoconf ... * Running aclocal ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] [ ok ] * Running autoconf ... [ ok ] * Running elibtoolize in: ViennaRNA-2.1.8/ * Running elibtoolize in: ViennaRNA-2.1.8/Kinfold/ * Running elibtoolize in: ViennaRNA-2.1.8/RNAforester/ [ ok ] * Running autoheader ... * Running elibtoolize in: ViennaRNA-2.1.8/RNAforester/g2-0.70/ [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] >>> Source prepared. >>> Configuring source in /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ... >>> Working in BUILD_DIR: "/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8" * econf: updating ViennaRNA-2.1.8/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-2.1.8/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-2.1.8/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-2.1.8/config/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-2.1.8/RNAforester/g2-0.70/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-2.1.8/RNAforester/g2-0.70/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-2.1.8/RNAforester/config.guess with /usr/share/gnuconfig/config.guess /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/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 --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64 --docdir=/usr/share/doc/vienna-rna-2.1.8 --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 whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes 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 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 interfaces/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 whether float precision is used for partition function arrays instead of double precision... no checking for perl... /usr/bin/perl checking for python... /usr/bin/python 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 interfaces/Perl/Makefile config.status: creating interfaces/Perl/Makefile.PL config.status: creating Cluster/Makefile config.status: creating doc/doxygen.conf config.status: creating misc/Makefile config.status: creating misc/ViennaRNA.spec config.status: creating misc/PKGBUILD config.status: creating interfaces/Makefile config.status: creating Makefile 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 (/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold) configure: running /bin/bash ./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' '--disable-dependency-tracking' '--disable-silent-rules' '--libdir=/usr/lib64' '--docdir=/usr/share/doc/vienna-rna-2.1.8' '--enable-shared' '--disable-static' '--with-cluster' '--enable-openmp' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches' --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 whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes 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 (/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester) configure: running /bin/bash ./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' '--disable-dependency-tracking' '--disable-silent-rules' '--libdir=/usr/lib64' '--docdir=/usr/share/doc/vienna-rna-2.1.8' '--enable-shared' '--disable-static' '--with-cluster' '--enable-openmp' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches' --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 whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes 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 (/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70) configure: running /bin/bash ./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' '--disable-dependency-tracking' '--disable-silent-rules' '--libdir=/usr/lib64' '--docdir=/usr/share/doc/vienna-rna-2.1.8' '--enable-shared' '--disable-static' '--with-cluster' '--enable-openmp' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches' --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: RNAlib Interfaces: Perl Interface: yes Python Interface: no Ruby Interface: no Extra Programs: Analyse{Dists,Seqs}: yes Kinfold: yes RNAforester: yes Other Options: 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-2.1.8 (HTML): /usr/share/doc/vienna-rna-2.1.8/html (PDF): /usr/share/doc/vienna-rna-2.1.8 >>> Source configured. >>> Compiling source in /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ... >>> Working in BUILD_DIR: "/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8" make -j24 make all-recursive make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' Making all in lib make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.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=] printf("\nRoot loop is #%d\n",(root-loops)+1); ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.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=] fprintf(fp,"\t%s\n",ident); ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-plex.o `test -f 'plex.c' || echo './'`plex.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-snoop.o `test -f 'snoop.c' || echo './'`snoop.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=] test.energy); ^ 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=] (begin_q -11) + test.j + strlen(test.structure)-l1-2 , test.energy); ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-move_set.o `test -f 'move_set.c' || echo './'`move_set.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-gquad.o `test -f 'gquad.c' || echo './'`gquad.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=] position[pos+delta]); ^ 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=] test.energy_backtrack + test.dG1 + test.dG2, test.energy_backtrack , test.dG1 , test.dG2); ^ 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=] test.Duplex_Er, test.Loop_E, test.Loop_D,test.fullStemEnergy, target,s4); ^ 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=] test.Duplex_Er, test.Loop_E, test.Loop_D,dE , test.fullStemEnergy, s5,s4); ^ 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=] test.energy,test.energy_backtrack); ^ plex.c:2723:18: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=] test.energy); ^ 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=] test.energy, test.energy_backtrack); ^ plex.c:2780:12: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=] test.energy); ^ 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=] test.Duplex_Er, test.Loop_E, test.Loop_D,dE ,test.fullStemEnergy, s5,s4); ^ x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o svm.o `test -f '../libsvm-2.91/svm.cpp' || echo './'`../libsvm-2.91/svm.cpp 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=] begin_q-11 + test.j +strlen(test.structure) -l1 -2 , test.energy); ^ 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=] test.energy); ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-svm_utils.o `test -f 'svm_utils.c' || echo './'`svm_utils.c ../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] fscanf(fp,"%80s",cmd); ^ ../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] fscanf(fp,"%80s",cmd); ^ ../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] fscanf(fp,"%80s",cmd); ^ ../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] fscanf(fp,"%d",&param.degree); ^ ../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] fscanf(fp,"%lf",&param.gamma); ^ ../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] fscanf(fp,"%lf",&param.coef0); ^ ../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] fscanf(fp,"%d",&model->nr_class); ^ ../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] fscanf(fp,"%d",&model->l); ^ ../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] fscanf(fp,"%lf",&model->rho[i]); ^ ../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] fscanf(fp,"%d",&model->label[i]); ^ ../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] fscanf(fp,"%lf",&model->probA[i]); ^ ../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] fscanf(fp,"%lf",&model->probB[i]); ^ ../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] fscanf(fp,"%d",&model->nSV[i]); ^ 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 '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib' Making all in Progs make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAfold_cmdl.o RNAfold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAfold.o RNAfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAeval_cmdl.o RNAeval_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAeval.o RNAeval.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAheat_cmdl.o RNAheat_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAheat.o RNAheat.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNApdist_cmdl.o RNApdist_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNApdist.o RNApdist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAdistance_cmdl.o RNAdistance_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAdistance.o RNAdistance.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAinverse_cmdl.o RNAinverse_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAinverse.o RNAinverse.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAplot_cmdl.o RNAplot_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAplot.o RNAplot.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAsubopt_cmdl.o RNAsubopt_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAsubopt.o RNAsubopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNALfold_cmdl.o RNALfold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNALfold.o RNALfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAcofold_cmdl.o RNAcofold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAcofold.o RNAcofold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNApaln_cmdl.o RNApaln_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNApaln.o RNApaln.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAduplex_cmdl.o RNAduplex_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAduplex.o RNAduplex.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=] if (istty) printf("lengths = %d,%d\n", strlen(s1), strlen(s2)); ^ 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=] dup->i, dup->j, dup->j+strlen(dup->structure)-l1-2, dup->energy); ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAalifold_cmdl.o RNAalifold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAalifold.o RNAalifold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAplfold_cmdl.o RNAplfold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAplfold.o RNAplfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAup_cmdl.o RNAup_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAup.o RNAup.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAaliduplex_cmdl.o RNAaliduplex_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAaliduplex.o RNAaliduplex.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNALalifold_cmdl.o RNALalifold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNALalifold.o 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=] dup->i, dup->j, dup->j+strlen(dup->structure)-l1-2, dup->energy); ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNA2Dfold_cmdl.o RNA2Dfold_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNA2Dfold.o RNA2Dfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAparconv_cmdl.o RNAparconv_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAparconv.o RNAparconv.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAPKplex_cmdl.o RNAPKplex_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAPKplex.o RNAPKplex.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAplex_cmdl.o RNAplex_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAplex.o RNAplex.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAsnoop_cmdl.o RNAsnoop_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAsnoop.o RNAsnoop.c x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAplot RNAplot_cmdl.o RNAplot.o -fopenmp ../lib/libRNA.a -lm -lm 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=] printf("lengths = %d,%d\n", strlen(s1), strlen(s2)); ^ 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-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNALfold RNALfold_cmdl.o RNALfold.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=] dup->Duplex_El, dup->Duplex_Er, dup->Loop_E, dup->Loop_D,dup->fullStemEnergy,target,s4); ^ 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=] dup->Duplex_El/n_seq, dup->Duplex_Er/n_seq, dup->Loop_E/n_seq, dup->Loop_D/n_seq,dup->pscd/n_seq, dup->psct/n_seq,consens ); ^ x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAfold RNAfold_cmdl.o RNAfold.o -fopenmp ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAsubopt RNAsubopt_cmdl.o RNAsubopt.o -fopenmp ../lib/libRNA.a -lm -lm x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAplex RNAplex_cmdl.o RNAplex.o -fopenmp ../lib/libRNA.a -lm -lm make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs' Making all in man make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man' Making all in Utils make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o b2ct.o b2ct.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o popt.o popt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o ct2db_cmdl.o ct2db_cmdl.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o ct2db.o ct2db.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 -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o popt popt.o -L../lib -lRNA -lm -lm x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o b2ct b2ct.o -L../lib -lRNA -lm -lm x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o ct2db ct2db_cmdl.o ct2db.o -L../lib -lRNA -lm -lm make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils' Making all in H make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H' Making all in misc make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc' Making all in doc make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc' /usr/bin/doxygen doxygen.conf Warning: Tag `SYMBOL_CACHE_SIZE' at line 336 of file doxygen.conf has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" Warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/fold.h:50: warning: group mfe_fold: ignoring title "Calculating Minimum Free Energy Structures" that does not match old title "Calculating Minimum Free Energy (MFE) Structures" /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/svm_utils.h:4: warning: Compound svm_model is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:374: warning: Compound interact is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:348: warning: Compound path_t is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:328: warning: Compound move_t is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:266: warning: Compound cofoldF is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:278: warning: Compound ConcEnt is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib/list.h:21: warning: Compound LIST is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/dist_vars.h:46: warning: Compound swString is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/dist_vars.h:41: warning: Compound Tree is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:338: warning: Compound intermediate_t is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:486: warning: Compound dupVar is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:291: warning: Compound pairpro is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/dist_vars.h:33: warning: Compound Postorder_list is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/move_set.h:5: warning: Compound struct_en is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib/list.h:16: warning: Compound LST_BUCKET is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:443: warning: Compound folden is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:452: warning: Compound snoopT is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:415: warning: Compound duplexT is not documented. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/gquad.h:244: 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' /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/plot_layouts.h:54: warning: unable to resolve reference to `bruccoleri_88' for \ref command /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:293: warning: The following parameters of hamming_bound(const char *s1, const char *s2, int n) are not documented: parameter 'n' /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:326: warning: explicit link request to 'VRNA_INPUT_NOPRINT_COMMENTS' could not be resolved /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:326: warning: explicit link request to 'VRNA_INPUT_NOELIM_WS_SUFFIX' could not be resolved /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:480: warning: argument 'str1' of command @param is not found in the argument list of make_loop_index_pt(short *pt) /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:480: warning: argument 'str2' of command @param is not found in the argument list of make_loop_index_pt(short *pt) /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:480: warning: The following parameters of make_loop_index_pt(short *pt) are not documented: parameter 'pt' /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/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 /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/fold.h:21: warning: unable to resolve reference to `zuker_81' for \ref command /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/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' /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:653: warning: explicit link request to 'FLT_OR_DBL' could not be resolved /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc/mainpage.h:139: warning: unable to resolve reference to `mp_ref' for \ref command /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc/mainpage.h:139: warning: unable to resolve reference to `mp_ref' for \ref command cd latex; \ make; \ mv refman.pdf ../RNAlib-2.1.8.pdf make[3]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/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 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2014/05/01> Babel <3.9l> and hyphenation patterns for 30 languages loaded. /usr/bin/makeindex refman.idx This is makeindex, version 2.15 [TeX Live 2014] (kpathsea + Thai support). Scanning input file refman.idx....done (574 entries accepted, 73 rejected). Sorting entries.......done (5876 comparisons). Generating output file refman.ind....done (1326 lines written, 0 warnings). Output written in refman.ind. Transcript written in refman.ilg. bibtex refman This is BibTeX, Version 0.99d (TeX Live 2014) 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 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2014/05/01> Babel <3.9l> and hyphenation patterns for 30 languages loaded. pdflatex refman This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2014/05/01> Babel <3.9l> and hyphenation patterns for 30 languages 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 /usr/bin/makeindex refman.idx This is makeindex, version 2.15 [TeX Live 2014] (kpathsea + Thai support). Scanning input file refman.idx....done (574 entries accepted, 73 rejected). Sorting entries.......done (5876 comparisons). Generating output file refman.ind....done (1326 lines written, 0 warnings). Output written in refman.ind. Transcript written in refman.ilg. pdflatex refman This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2014/05/01> Babel <3.9l> and hyphenation patterns for 30 languages loaded. make[3]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc/latex' make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc' Making all in interfaces make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces' Making all in Perl make[3]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' /usr/bin/perl Makefile.PL INSTALLDIRS=vendor PREFIX=/usr INSTALL_BASE= Generating a Unix-style Makefile.perl Writing Makefile.perl for RNA make -f Makefile.perl make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' x86_64-pc-linux-gnu-gcc -c -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I../../H -O2 -pipe -ggdb -ftracer -frecord-gcc-switches -DVERSION=\"2.1.8\" -DXS_VERSION=\"2.1.8\" -fPIC "-I/usr/lib64/perl5/5.20.1/x86_64-linux-thread-multi/CORE" RNA_wrap.c Running Mkbootstrap for RNA () cp RNA.pm blib/lib/RNA.pm chmod 644 RNA.bs RNA_wrap.c: In function 'my_alifold': RNA_wrap.c:2316:23: warning: passing argument 1 of 'alifold' from incompatible pointer type *energy = alifold(strings, struc); ^ In file included from RNA_wrap.c:1578:0: ../../H/../H/alifold.h:86:8: note: expected 'const char **' but argument is of type 'char **' float alifold( const char **strings, ^ RNA_wrap.c: In function '_wrap_LoopEnergy': RNA_wrap.c:6632:5: warning: 'LoopEnergy' is deprecated (declared at ../../H/../H/fold.h:523) [-Wdeprecated-declarations] result = (int)LoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8); ^ RNA_wrap.c: In function '_wrap_HairpinE': RNA_wrap.c:6707:5: warning: 'HairpinE' is deprecated (declared at ../../H/../H/fold.h:536) [-Wdeprecated-declarations] result = (int)HairpinE(arg1,arg2,arg3,arg4,(char const *)arg5); ^ RNA_wrap.c: In function '_wrap_initialize_fold': RNA_wrap.c:6742:5: warning: 'initialize_fold' is deprecated (declared at ../../H/../H/fold.h:547) [-Wdeprecated-declarations] initialize_fold(arg1); ^ RNA_wrap.c: In function '_wrap_energy_of_struct': RNA_wrap.c:6780:5: warning: 'energy_of_struct' is deprecated (declared at ../../H/../H/fold.h:563) [-Wdeprecated-declarations] result = (float)energy_of_struct((char const *)arg1,(char const *)arg2); ^ RNA_wrap.c: In function '_wrap_energy_of_struct_pt': RNA_wrap.c:6835:5: warning: 'energy_of_struct_pt' is deprecated (declared at ../../H/../H/fold.h:582) [-Wdeprecated-declarations] result = (int)energy_of_struct_pt((char const *)arg1,arg2,arg3,arg4); ^ RNA_wrap.c: In function '_wrap_energy_of_circ_struct': RNA_wrap.c:6879:5: warning: 'energy_of_circ_struct' is deprecated (declared at ../../H/../H/fold.h:601) [-Wdeprecated-declarations] result = (float)energy_of_circ_struct((char const *)arg1,(char const *)arg2); ^ RNA_wrap.c: In function '_wrap_initialize_cofold': RNA_wrap.c:7403:5: warning: 'initialize_cofold' is deprecated (declared at ../../H/../H/cofold.h:180) [-Wdeprecated-declarations] initialize_cofold(arg1); ^ RNA_wrap.c: In function '_wrap_init_pf_fold': RNA_wrap.c:8311:5: warning: 'init_pf_fold' is deprecated (declared at ../../H/../H/part_func.h:407) [-Wdeprecated-declarations] init_pf_fold(arg1); ^ RNA_wrap.c: In function '_wrap_centroid': RNA_wrap.c:8347:5: warning: 'centroid' is deprecated (declared at ../../H/../H/part_func.h:413) [-Wdeprecated-declarations] result = (char *)centroid(arg1,arg2); ^ RNA_wrap.c: In function '_wrap_mean_bp_dist': RNA_wrap.c:8377:5: warning: 'mean_bp_dist' is deprecated (declared at ../../H/../H/part_func.h:421) [-Wdeprecated-declarations] result = (double)mean_bp_dist(arg1); ^ RNA_wrap.c: In function '_wrap_expLoopEnergy': RNA_wrap.c:8461:5: warning: 'expLoopEnergy' is deprecated (declared at ../../H/../H/part_func.h:426) [-Wdeprecated-declarations] result = (double)expLoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8); ^ RNA_wrap.c: In function '_wrap_expHairpinEnergy': RNA_wrap.c:8536:5: warning: 'expHairpinEnergy' is deprecated (declared at ../../H/../H/part_func.h:438) [-Wdeprecated-declarations] result = (double)expHairpinEnergy(arg1,arg2,arg3,arg4,(char const *)arg5); ^ RNA_wrap.c: In function '_wrap_Make_bp_profile': RNA_wrap.c:11742:5: warning: 'Make_bp_profile' is deprecated (declared at ../../H/../H/profiledist.h:56) [-Wdeprecated-declarations] result = (float *)Make_bp_profile(arg1); ^ RNA_wrap.c: In function '_wrap_copy_parameters': RNA_wrap.c:13291:5: warning: 'copy_parameters' is deprecated (declared at ../../H/../H/params.h:126) [-Wdeprecated-declarations] result = (paramT *)copy_parameters(); ^ RNA_wrap.c: In function '_wrap_set_parameters': RNA_wrap.c:13317:5: warning: 'set_parameters' is deprecated (declared at ../../H/../H/params.h:127) [-Wdeprecated-declarations] result = (paramT *)set_parameters(arg1); ^ RNA_wrap.c: In function '_wrap_PS_dot_plot': RNA_wrap.c:14984:5: warning: 'PS_dot_plot' is deprecated (declared at ../../H/../H/PS_dot.h:195) [-Wdeprecated-declarations] result = (int)PS_dot_plot(arg1,arg2); ^ rm -f blib/arch/auto/RNA/RNA.so g++ -shared -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed RNA_wrap.o -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 /usr/bin/perl5.20.1 -MExtUtils::Command::MM -e 'cp_nonempty' -- RNA.bs blib/arch/auto/RNA/RNA.bs 644 Manifying blib/man3/RNA.3pm make[4]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' make[3]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' make[3]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces' make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces' Making all in Cluster make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Cluster' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o split.o split.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o distance_matrix.o distance_matrix.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o cluster.o cluster.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o treeplot.o treeplot.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o AD_main.o AD_main.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c ./../lib/utils.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o statgeom.o statgeom.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o AS_main.o AS_main.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o PS3D.o PS3D.c x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Cluster' Making all in Kinfold make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/missing autoheader) rm -f stamp-h1 touch config.h.in cd . && /bin/bash ./config.status config.h config.status: creating config.h config.status: config.h is unchanged make all-recursive make[3]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' Making all in Example make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold/Example' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold/Example' make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o baum.o baum.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o cache.o cache.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o globals.o globals.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o main.o main.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o nachbar.o nachbar.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o cmdline.o cmdline.c globals.c: In function 'process_options_gg': globals.c:298:25: warning: passing argument 2 of 'strncpy' makes pointer from integer without a cast strncpy(GAV.ParamFile,255,args_info.Par_arg); ^ In file included from /usr/include/features.h:366:0, from /usr/include/stdio.h:27, from globals.c:9: /usr/include/bits/string3.h:117:1: note: expected 'const char * __restrict__' but argument is of type 'int' __NTH (strncpy (char *__restrict __dest, const char *__restrict __src, ^ globals.c:298:29: warning: passing argument 3 of 'strncpy' makes integer from pointer without a cast strncpy(GAV.ParamFile,255,args_info.Par_arg); ^ In file included from /usr/include/features.h:366:0, from /usr/include/stdio.h:27, from globals.c:9: /usr/include/bits/string3.h:117:1: note: expected 'size_t' but argument is of type 'char *' __NTH (strncpy (char *__restrict __dest, const char *__restrict __src, ^ globals.c:334:9: warning: format '%g' expects argument of type 'float *', but argument 3 has type 'double *' [-Wformat=] &GAV.phi_bounds[2]) == 0) ^ 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=] &GAV.phi_bounds[2]) == 0) ^ 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=] sprintf(format, "%%-%ds %%6.2f %%10.3f", strlen(GAV.farbe_full)+1); ^ x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' make[3]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' Making all in RNAforester make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/missing autoheader) rm -f stamp-h1 touch config.h.in cd . && /bin/bash ./config.status config.h config.status: creating config.h config.status: config.h is unchanged make all-recursive make[3]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' Making all in g2-0.70 make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70' x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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=] fig->pen_color, fig->font_size, fig->font_size, fig->font_size*strlen(text), x, y); ^ 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 '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70' Making all in src make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/src' x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o Arguments.o Arguments.cpp x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o glib.o glib.c x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o main.o main.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o ppforestbase.o ppforestbase.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o progressive_align.o progressive_align.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rna_alignment.o rna_alignment.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rna_algebra.o rna_algebra.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rna_alphabet.o rna_alphabet.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rnaforest.o rnaforest.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rnaforestsz.o rnaforestsz.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rnafuncs.o rnafuncs.cpp x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rnaforester_options.o rnaforester_options.cpp x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o wmatch.o wmatch.c glib.c: In function 'ReadGraph': glib.c:161:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d%d %c",size,&edges,&c); ^ glib.c:170:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d%d%d%d",&degree,&vlabel,&xcoord,&ycoord); ^ glib.c:176:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d%d", &adj_node, &elabel); ^ glib.c: In function 'ReadEuclid': glib.c:225:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d %c",size,&c); ^ glib.c:234:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d%d",&xcoord,&ycoord); ^ glib.c: In function 'ReadMatrix': glib.c:272:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d %c",size,&c); ^ glib.c:282:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp,"%d",&k); ^ progressive_align.cpp: In function 'node_entry* makePairsGraph(const RNAProfileAliMapType&, const DoubleScoreProfileAlgebraType*, const Matrix*, double)': progressive_align.cpp:341:30: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] WriteGraph (graph,"test.out"); ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/src' Making all in man make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/man' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/man' make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' make[4]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' make[3]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' >>> Working in BUILD_DIR: "/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8" make -j24 -C Readseq build CC=x86_64-pc-linux-gnu-gcc make: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq' Compiling readseq... x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -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 case kASNseqset : return formats[kASN1-1]; ^ readseq.c:259:31: warning: return discards 'const' qualifier from pointer target type case kPhylipSequential: return formats[kPhylip-1]; ^ readseq.c:263:8: warning: return discards 'const' qualifier from pointer target type else return formats[format-1]; ^ readseq.c: In function 'usage': readseq.c:328:3: warning: format not a string literal and no format arguments [-Wformat-security] fprintf(stderr,title); ^ readseq.c: In function 'chooseFormat': readseq.c:419:7: warning: 'gets' is deprecated (declared at /usr/include/bits/stdio2.h:233) [-Wdeprecated-declarations] gets(sform); ^ readseq.c: In function 'main': readseq.c:768:3: warning: format not a string literal and no format arguments [-Wformat-security] if (verbose || (!quietly && !gotinputfile)) fprintf( stderr, title); ^ readseq.c:775:5: warning: 'gets' is deprecated (declared at /usr/include/bits/stdio2.h:233) [-Wdeprecated-declarations] gets(oname= onamestore); ^ readseq.c:839:7: warning: 'gets' is deprecated (declared at /usr/include/bits/stdio2.h:233) [-Wdeprecated-declarations] gets(stemp= stempstore); ^ readseq.c:885:9: warning: 'gets' is deprecated (declared at /usr/include/bits/stdio2.h:233) [-Wdeprecated-declarations] gets(stemp= stempstore); ^ readseq.c:910:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] sprintf( stemp,"%s_%d", oname, whichSeq); ^ readseq.c:912:13: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf( stderr,"Writing sequence %d to file %s\n", whichSeq, stemp); ^ readseq.c:955:17: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] whichSeq, seqlen, checksum, formatstr(format), seqidptr); ^ 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] if (seqout == 0) fprintf( foo, kASN1headline); ^ readseq.c:972:19: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); ^ 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=] else fprintf(foo," %d %d YF\n", i, seqlen); ^ 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=] cp, seqlen, checkall); ^ 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=] if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen); ^ readseq.c:1088:5: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] else fprintf(foo," %d %d YF\n", seqout, seqlen); ^ readseq.c:1112:9: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, seqlen); ^ readseq.c: In function 'chooseFormat': readseq.c:419:7: warning: ignoring return value of 'gets', declared with attribute warn_unused_result [-Wunused-result] gets(sform); ^ readseq.c: In function 'main': readseq.c:757:5: warning: ignoring return value of 'tmpnam', declared with attribute warn_unused_result [-Wunused-result] tmpnam(tempname); ^ readseq.c:775:5: warning: ignoring return value of 'gets', declared with attribute warn_unused_result [-Wunused-result] gets(oname= onamestore); ^ readseq.c:839:7: warning: ignoring return value of 'gets', declared with attribute warn_unused_result [-Wunused-result] gets(stemp= stempstore); ^ readseq.c:885:9: warning: ignoring return value of 'gets', declared with attribute warn_unused_result [-Wunused-result] gets(stemp= stempstore); ^ readseq.c:911:13: warning: ignoring return value of 'freopen', declared with attribute warn_unused_result [-Wunused-result] freopen( stemp, "w", fout); ^ 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=] sscanf( sp, "%d%d", &nspp, &nlen); ^ 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=] sprintf(numform, "%d", seqlen); ^ ureadseq.c:1624:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen); ^ ureadseq.c:1625:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ^ 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=] fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ^ 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=] for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j); ^ ureadseq.c:1659:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ^ 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=] fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ^ 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=] fprintf(outf,"SQ %d BP\n", seqlen); ^ ureadseq.c:1680:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum); ^ 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=] fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum); ^ 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=] fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ^ 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=] fprintf(outf," repr raw, mol %s, length %d, topology linear,\n", cp, seqlen); ^ ureadseq.c:1748:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum); ^ 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=] fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum); ^ 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=] idword, seqlen, checksum); ^ 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=] fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ^ 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=] fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); ^ 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=] if (numline==1) fprintf(outf,"%-9d ",i+1); ^ /tmp/portage/sci-biology/vienna-rna-2.1.8/temp/ccoGj8lo.o: In function `main': /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq/readseq.c:757: warning: the use of `tmpnam' is dangerous, better use `mkstemp' /tmp/portage/sci-biology/vienna-rna-2.1.8/temp/ccoGj8lo.o: In function `gets': /usr/include/bits/stdio2.h:236: warning: the `gets' function is dangerous and should not be used. make: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq' >>> Source compiled. >>> Test phase: sci-biology/vienna-rna-2.1.8 >>> Working in BUILD_DIR: "/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8" make -j24 -C interfaces/Perl check make: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' make -f Makefile.perl make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' Running Mkbootstrap for RNA () chmod 644 RNA.bs make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' make check-local make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' make -f Makefile.perl make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' make -f Makefile.perl test make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' PERL_DL_NONLAZY=1 /usr/bin/perl5.20.1 "-Iblib/lib" "-Iblib/arch" test.pl 1..24 # Running under perl version 5.020001 for linux # Current time local: Wed Nov 12 08:52:24 2014 # Current time GMT: Wed Nov 12 08:52:24 2014 # Using Test.pm version 1.26 ok 1 ok 2 ok 3 not ok 4 # Failed test 4 in test.pl at line 42 # test.pl line 42 is: ok($struct eq $struc1); WARNING: bases 1 and 16 (()) can't pair! WARNING: bases 2 and 15 (()) can't pair! WARNING: bases 3 and 14 (()) can't pair! WARNING: bases 5 and 13 (()) can't pair! WARNING: bases 6 and 12 (()) can't pair! WARNING: bases 7 and 11 (()) can't pair! not ok 5 # Test 5 got: "16.7000007629395" (test.pl at line 44) # Expected: "0" # test.pl line 44 is: ok(RNA::energy_of_struct($seq1,$struc1), $mfe); not ok 6 # Test 6 got: "................" (test.pl at line 49) # Expected: "(((..........)))" # test.pl line 49 is: ok($struct3, '(((..........)))'); ok 7 not ok 8 # Test 8 got: "................((((((...))).)))" (test.pl at line 56) # Expected: "(((.(((...))))))((((((...))).)))" # test.pl line 56 is: ok($costruct, '(((.(((...))))))((((((...))).)))'); ok 9 ok 10 not ok 11 # Failed test 11 in test.pl at line 74 # test.pl line 74 is: ok((abs($AB-0.0)+abs($AA-0.00578)+abs($BB-0.01100)+abs($A-0.48843)+abs($B-0.47801))<0.0001); not ok 12 # Failed test 12 in test.pl at line 79 # test.pl line 79 is: ok(($f<$mfe)&&($mfe-$f<0.8)); ok 13 ok 14 ok 15 not ok 16 # Failed test 16 in test.pl at line 107 # test.pl line 107 is: ok(($p1<0.999) && ($p1>0.99) && (abs($p1-$p2)<1.2e-7)); ok 17 ok 18 ok 19 please check the two postscript files test_ss.ps and test_dp.ps ok 20 1 suboptimals ................ 0.00 ok 21 not ok 22 # Test 22 got: ".&." (test.pl at line 159) # Expected: "(.(.(((.....(((.&))))))...).)." # test.pl line 159 is: ok($duplex->{structure}, "(.(.(((.....(((.&))))))...).)."); ok 23 ok 24 make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' make: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' >>> Working in BUILD_DIR: "/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8" make -j24 -C Readseq test make: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq' Test for general read/write of all chars: ./readseq -p alphabet.std -otest.alpha diff test.alpha alphabet.std 1c1 < >alphabet['!'..'~'], 83 bases, E14ECBE2 checksum. --- > >alphabet['!'..'~'], 83 bases, 9429 checksum. Makefile:51: recipe for target 'test' failed make: [test] Error 1 (ignored) Test for valid format conversions: ./readseq -v -p -f=ig nucleic.std -otest.ig readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino test ./readseq -v -p -f=gb test.ig -otest.gb readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 1. IG/Stanford, id= nucleic/amino ./readseq -v -p -f=nbrf test.gb -otest.nbrf readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 2. GenBank/GB, id= nucleic/amino 228 bp ./readseq -v -p -f=embl test.nbrf -otest.embl readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 3. NBRF, id= nucleic/amino ./readseq -v -p -f=gcg test.embl -otest.gcg readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 4. EMBL, id= nucleic/amino ./readseq -v -p -f=strider test.gcg -otest.strider readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 5. GCG, id= nucleic/amino ./readseq -v -p -f=fitch test.strider -otest.fitch readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 6. DNAStrider, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=fasta test.fitch -otest.fasta readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 7. Fitch, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=pir test.fasta -otest.pir readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino, 228 bases, 1B5655D0 checksum. ./readseq -v -p -f=ig test.pir -otest.ig-b readSeq (1Feb93), multi-format molbio sequence reader. Sequence 1, length= 228, checksum= 1B5655D0, format= 14. PIR/CODATA, id= nucleic/amino, diff test.ig test.ig-b 1,2c1,2 < ;nucleic/amino test, 228 bases, 1B5655D0 checksum. < nucleic/amino --- > ;nucleic/amino, , 228 bases, 1B5655D0 checksum. > nucleic/amino, Makefile:51: recipe for target 'test' failed make: [test] Error 1 (ignored) Test for multiple-sequence format conversions: ./readseq -p -f=ig multi.std -otest.m-ig ./readseq -p -f=gb test.m-ig -otest.m-gb ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf ./readseq -p -f=embl test.m-nbrf -otest.m-embl ./readseq -p -f=fasta test.m-embl -otest.m-fasta ./readseq -p -f=pir test.m-fasta -otest.m-pir ./readseq -p -f=msf test.m-pir -otest.m-msf ./readseq -p -f=paup test.m-msf -otest.m-paup ./readseq -p -f=ig test.m-paup -otest.m-ig-b diff test.m-ig test.m-ig-b 1,2c1,2 < ;acarr58sst , 183 bases, 64754A4D checksum. < acarr58sst --- > ;acarr58ss, 183 bases, 64754A4D checksum. > acarr58ss 7c7 < ;amgrrbst , 183 bases, C886D2FB checksum. --- > ;amgrrbst, 183 bases, C886D2FB checksum. 13c13 < ;bmorrbst , 183 bases, 3E9C23D6 checksum. --- > ;bmorrbst, 183 bases, 3E9C23D6 checksum. 19c19 < ;crerrbst , 183 bases, AC88A337 checksum. --- > ;crerrbst, 183 bases, AC88A337 checksum. 25,26c25,26 < ;ddirr58sst , 183 bases, 1E3D23B8 checksum. < ddirr58sst --- > ;ddirr58ss, 183 bases, 1E3D23B8 checksum. > ddirr58ss Makefile:51: recipe for target 'test' failed make: [test] Error 1 (ignored) Expect differences in the header lines due to different format headers. If any sequence lines differ, or if the checksums differ, there is a problem. ---------------------- To clean up test files, command me: make clean make: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq' >>> Completed testing sci-biology/vienna-rna-2.1.8 >>> Install vienna-rna-2.1.8 into /tmp/portage/sci-biology/vienna-rna-2.1.8/image/ category sci-biology >>> Working in BUILD_DIR: "/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8" make -j24 DESTDIR=/tmp/portage/sci-biology/vienna-rna-2.1.8/image/ install Making install in lib make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib' make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/lib64' /usr/bin/install -c -m 644 libRNA.a '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/lib64' ( cd '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/lib64' && x86_64-pc-linux-gnu-ranlib libRNA.a ) make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib' make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib' Making install in Progs make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs' make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/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 '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/bin' make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs' make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs' Making install in man make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man' make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man' make[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/man/man1' /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/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 '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/man/man1' /usr/bin/install -c -m 644 ./RNAlib.info '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/info' install-info --info-dir='/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/info' '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/info/RNAlib.info' make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man' make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man' Making install in Utils make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils' make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils' make[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/bin' /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/bin' /usr/bin/install -c b2ct popt ct2db '/tmp/portage/sci-biology/vienna-rna-2.1.8/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 '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/bin' make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils' make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils' Making install in H make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H' make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H' make[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/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 '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/include/ViennaRNA' /usr/bin/install -c -m 644 plex.h snofold.h snoop.h move_set.h gquad.h svm_utils.h '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/include/ViennaRNA' make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H' make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H' Making install in misc make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc' make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc' make[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/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 '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/ViennaRNA' make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc' make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc' Making install in doc make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc' make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc' make[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8' /usr/bin/install -c -m 644 RNAlib-2.1.8.tag RNAlib-2.1.8.pdf '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8' /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8' /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/ViennaRNA' /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 RNAlib-2.1.8.tag RNAlib-2.1.8.pdf '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8' /usr/bin/install -c -m 644 viennarna.bib '/tmp/portage/sci-biology/vienna-rna-2.1.8/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.js html/2Dfold_8h__incl.map html/2Dfold_8h__incl.md5 html/2Dfold_8h__incl.png html/2Dfold_8h_source.html html/2Dpfold_8h.html html/2Dpfold_8h.js html/2Dpfold_8h__incl.map html/2Dpfold_8h__incl.md5 html/2Dpfold_8h__incl.png html/2Dpfold_8h_source.html html/LPfold_8h.html html/LPfold_8h.js html/LPfold_8h__incl.map html/LPfold_8h__incl.md5 html/LPfold_8h__incl.png html/LPfold_8h_source.html html/Lfold_8h.html html/Lfold_8h.js html/Lfold_8h_source.html html/MEA_8h.html html/MEA_8h.js html/MEA_8h__incl.map html/MEA_8h__incl.md5 html/MEA_8h__incl.png html/MEA_8h_source.html html/PKplex_8h_source.html html/PS__dot_8h.html html/PS__dot_8h.js html/PS__dot_8h__incl.map html/PS__dot_8h__incl.md5 html/PS__dot_8h__incl.png html/PS__dot_8h_source.html '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/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.js html/2Dfold_8h__incl.map html/2Dfold_8h__incl.md5 html/2Dfold_8h__incl.png html/2Dfold_8h_source.html html/2Dpfold_8h.html html/2Dpfold_8h.js html/2Dpfold_8h__incl.map html/2Dpfold_8h__incl.md5 html/2Dpfold_8h__incl.png html/2Dpfold_8h_source.html html/LPfold_8h.html html/LPfold_8h.js html/LPfold_8h__incl.map html/LPfold_8h__incl.md5 html/LPfold_8h__incl.png html/LPfold_8h_source.html html/Lfold_8h.html html/Lfold_8h.js html/Lfold_8h_source.html html/MEA_8h.html html/MEA_8h.js html/MEA_8h__incl.map html/MEA_8h__incl.md5 html/MEA_8h__incl.png html/MEA_8h_source.html html/PKplex_8h_source.html html/PS__dot_8h.html html/PS__dot_8h.js html/PS__dot_8h__incl.map html/PS__dot_8h__incl.md5 html/PS__dot_8h__incl.png html/PS__dot_8h_source.html '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install: cannot create regular file '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html/1_88_84__epars_8h.html': File exists /usr/bin/install -c -m 644 html/ProfileAln_8h_source.html html/RNAstruct_8h.html html/RNAstruct_8h.js html/RNAstruct_8h_source.html html/ali__plex_8h_source.html html/alifold_8h.html html/alifold_8h.js html/alifold_8h__incl.map html/alifold_8h__incl.md5 html/alifold_8h__incl.png html/alifold_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.js html/cofold_8h__incl.map html/cofold_8h__incl.md5 html/cofold_8h__incl.png html/cofold_8h_source.html html/convert__epars_8h.html html/convert__epars_8h.js html/convert__epars_8h_source.html html/data__structures_8h.html html/data__structures_8h.js html/data__structures_8h__dep__incl.map html/data__structures_8h__dep__incl.md5 html/data__structures_8h__dep__incl.png html/data__structures_8h__incl.map html/data__structures_8h__incl.md5 html/data__structures_8h__incl.png html/data__structures_8h_source.html html/deprecated.html html/dir_97aefd0d527b934f1d99a682da8fe6a9.html html/dir_97aefd0d527b934f1d99a682da8fe6a9.js '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' Makefile:349: recipe for target 'install-dist_docdir_htmlDATA' failed make[2]: *** [install-dist_docdir_htmlDATA] Error 1 make[2]: *** Waiting for unfinished jobs.... /usr/bin/install -c -m 644 html/dir_97aefd0d527b934f1d99a682da8fe6a9_dep.map html/dir_97aefd0d527b934f1d99a682da8fe6a9_dep.md5 html/dir_97aefd0d527b934f1d99a682da8fe6a9_dep.png html/dir_d72344b28b4f2089ce25682c4e6eba22.html html/dir_d72344b28b4f2089ce25682c4e6eba22.js html/dir_d72344b28b4f2089ce25682c4e6eba22_dep.map html/dir_d72344b28b4f2089ce25682c4e6eba22_dep.md5 html/dir_d72344b28b4f2089ce25682c4e6eba22_dep.png html/dist__vars_8h.html html/dist__vars_8h.js html/dist__vars_8h__dep__incl.map html/dist__vars_8h__dep__incl.md5 html/dist__vars_8h__dep__incl.png html/dist__vars_8h_source.html html/doxygen.css html/doxygen.png html/duplex_8h.html html/duplex_8h.js html/duplex_8h__incl.map html/duplex_8h__incl.md5 html/duplex_8h__incl.png html/duplex_8h_source.html html/dynsections.js html/edit__cost_8h.html html/edit__cost_8h.js html/edit__cost_8h_source.html html/energy__const_8h.html html/energy__const_8h.js html/energy__const_8h__dep__incl.map html/energy__const_8h__dep__incl.md5 html/energy__const_8h__dep__incl.png html/energy__const_8h__incl.map html/energy__const_8h__incl.md5 html/energy__const_8h__incl.png html/energy__const_8h_source.html html/energy__par_8h_source.html html/files.html html/files.js html/findpath_8h.html html/findpath_8h.js '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/findpath_8h__incl.map html/findpath_8h__incl.md5 html/findpath_8h__incl.png html/findpath_8h_source.html html/fold_8h.html html/fold_8h.js html/fold_8h__incl.map html/fold_8h__incl.md5 html/fold_8h__incl.png html/fold_8h_source.html html/fold__vars_8h.html html/fold__vars_8h.js html/fold__vars_8h__dep__incl.map html/fold__vars_8h__dep__incl.md5 html/fold__vars_8h__dep__incl.png html/fold__vars_8h__incl.map html/fold__vars_8h__incl.md5 html/fold__vars_8h__incl.png html/fold__vars_8h_source.html html/form_0.png html/form_1.png html/form_10.png html/form_11.png html/form_12.png html/form_13.png html/form_14.png html/form_15.png html/form_16.png html/form_17.png html/form_18.png html/form_19.png html/form_2.png html/form_20.png html/form_21.png html/form_22.png html/form_23.png html/form_24.png html/form_25.png html/form_26.png html/form_27.png '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/form_28.png html/form_29.png html/form_3.png html/form_4.png html/form_5.png html/form_6.png html/form_7.png html/form_8.png html/form_9.png html/formula.repository html/ftv2blank.png html/ftv2cl.png html/ftv2doc.png html/ftv2folderclosed.png html/ftv2folderopen.png html/ftv2lastnode.png html/ftv2link.png html/ftv2mlastnode.png html/ftv2mnode.png html/ftv2mo.png html/ftv2node.png html/ftv2ns.png html/ftv2plastnode.png html/ftv2pnode.png html/ftv2splitbar.png html/ftv2vertline.png html/functions.html html/functions_vars.html html/globals.html html/globals_0x62.html html/globals_0x63.html html/globals_0x64.html html/globals_0x65.html html/globals_0x66.html html/globals_0x67.html html/globals_0x68.html html/globals_0x69.html html/globals_0x6a.html html/globals_0x6b.html html/globals_0x6c.html '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/globals_0x6d.html html/globals_0x6e.html html/globals_0x6f.html html/globals_0x70.html html/globals_0x72.html html/globals_0x73.html html/globals_0x74.html html/globals_0x75.html html/globals_0x76.html html/globals_0x77.html html/globals_0x78.html html/globals_0x7a.html html/globals_defs.html html/globals_dup.js html/globals_func.html html/globals_vars.html html/gquad_8h.html html/gquad_8h.js html/gquad_8h__incl.map html/gquad_8h__incl.md5 html/gquad_8h__incl.png html/gquad_8h_source.html html/graph_legend.html html/graph_legend.md5 html/graph_legend.png html/group__centroid__fold.html html/group__centroid__fold.js html/group__centroid__fold.map html/group__centroid__fold.md5 html/group__centroid__fold.png html/group__class__fold.html html/group__class__fold.js html/group__class__fold.map html/group__class__fold.md5 html/group__class__fold.png html/group__cofold.html html/group__cofold.js html/group__cofold.map html/group__cofold.md5 html/group__cofold.png '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/group__consensus__fold.html html/group__consensus__fold.js html/group__consensus__fold.map html/group__consensus__fold.md5 html/group__consensus__fold.png html/group__consensus__mfe__fold.html html/group__consensus__mfe__fold.js html/group__consensus__mfe__fold.map html/group__consensus__mfe__fold.md5 html/group__consensus__mfe__fold.png html/group__consensus__pf__fold.html html/group__consensus__pf__fold.js html/group__consensus__pf__fold.map html/group__consensus__pf__fold.md5 html/group__consensus__pf__fold.png html/group__consensus__stochbt.html html/group__consensus__stochbt.js html/group__consensus__stochbt.map html/group__consensus__stochbt.md5 html/group__consensus__stochbt.png html/group__dos.html html/group__dos.js html/group__dos.map html/group__dos.md5 html/group__dos.png html/group__energy__parameters.html html/group__energy__parameters.js html/group__energy__parameters.map html/group__energy__parameters.md5 html/group__energy__parameters.png html/group__energy__parameters__convert.html html/group__energy__parameters__convert.js html/group__energy__parameters__convert.map html/group__energy__parameters__convert.md5 html/group__energy__parameters__convert.png html/group__energy__parameters__rw.html html/group__energy__parameters__rw.js html/group__energy__parameters__rw.map html/group__energy__parameters__rw.md5 html/group__energy__parameters__rw.png '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/group__eval.html html/group__eval.js html/group__eval.map html/group__eval.md5 html/group__eval.png html/group__folding__routines.html html/group__folding__routines.js html/group__folding__routines.map html/group__folding__routines.md5 html/group__folding__routines.png html/group__inverse__fold.html html/group__inverse__fold.js html/group__inverse__fold.map html/group__inverse__fold.md5 html/group__inverse__fold.png html/group__kl__neighborhood.html html/group__kl__neighborhood.js html/group__kl__neighborhood.map html/group__kl__neighborhood.md5 html/group__kl__neighborhood.png html/group__kl__neighborhood__mfe.html html/group__kl__neighborhood__mfe.js html/group__kl__neighborhood__mfe.map html/group__kl__neighborhood__mfe.md5 html/group__kl__neighborhood__mfe.png html/group__kl__neighborhood__pf.html html/group__kl__neighborhood__pf.js html/group__kl__neighborhood__pf.map html/group__kl__neighborhood__pf.md5 html/group__kl__neighborhood__pf.png html/group__kl__neighborhood__stochbt.html html/group__kl__neighborhood__stochbt.js html/group__kl__neighborhood__stochbt.map html/group__kl__neighborhood__stochbt.md5 html/group__kl__neighborhood__stochbt.png html/group__local__consensus__fold.html html/group__local__consensus__fold.js html/group__local__consensus__fold.map html/group__local__consensus__fold.md5 html/group__local__consensus__fold.png '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/group__local__fold.html html/group__local__fold.js html/group__local__fold.map html/group__local__fold.md5 html/group__local__fold.png html/group__local__mfe__fold.html html/group__local__mfe__fold.js html/group__local__mfe__fold.map html/group__local__mfe__fold.md5 html/group__local__mfe__fold.png html/group__local__pf__fold.html html/group__local__pf__fold.js html/group__local__pf__fold.map html/group__local__pf__fold.md5 html/group__local__pf__fold.png html/group__mea__fold.html html/group__mea__fold.map html/group__mea__fold.md5 html/group__mea__fold.png html/group__mfe__cofold.html html/group__mfe__cofold.js html/group__mfe__cofold.map html/group__mfe__cofold.md5 html/group__mfe__cofold.png html/group__mfe__fold.html html/group__mfe__fold.js html/group__mfe__fold.map html/group__mfe__fold.md5 html/group__mfe__fold.png html/group__parse.html html/group__pf__cofold.html html/group__pf__cofold.js html/group__pf__cofold.map html/group__pf__cofold.md5 html/group__pf__cofold.png html/group__pf__fold.html html/group__pf__fold.js html/group__pf__fold.map html/group__pf__fold.md5 html/group__pf__fold.png '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/group__subopt__fold.html html/group__subopt__fold.js html/group__subopt__fold.map html/group__subopt__fold.md5 html/group__subopt__fold.png html/group__subopt__stochbt.html html/group__subopt__stochbt.js html/group__subopt__stochbt.map html/group__subopt__stochbt.md5 html/group__subopt__stochbt.png html/group__subopt__wuchty.html html/group__subopt__wuchty.js html/group__subopt__wuchty.map html/group__subopt__wuchty.md5 html/group__subopt__wuchty.png html/group__subopt__zuker.html html/group__subopt__zuker.js html/group__subopt__zuker.map html/group__subopt__zuker.md5 html/group__subopt__zuker.png html/group__up__cofold.html html/group__up__cofold.js html/group__up__cofold.map html/group__up__cofold.md5 html/group__up__cofold.png html/index.html html/intl11_8h_source.html html/intl11dH_8h_source.html html/intl21_8h_source.html html/intl21dH_8h_source.html html/intl22_8h_source.html html/intl22dH_8h_source.html html/inverse_8h.html html/inverse_8h.js html/inverse_8h_source.html html/jquery.js html/list_8h_source.html html/loop__energies_8h.html html/loop__energies_8h.js html/loop__energies_8h__incl.map '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/loop__energies_8h__incl.md5 html/loop__energies_8h__incl.png html/loop__energies_8h_source.html html/mainpage_8h_source.html html/mm_8h.html html/mm_8h.js html/mm_8h_source.html html/modules.html html/modules.js html/move__set_8h_source.html html/mp_example.html html/mp_parse.html html/mp_utils.html html/nav_f.png html/nav_g.png html/nav_h.png html/naview_8h.html html/naview_8h.js html/naview_8h__dep__incl.map html/naview_8h__dep__incl.md5 html/naview_8h__dep__incl.png html/naview_8h_source.html html/navtree.css html/navtree.js html/navtreeindex0.js html/navtreeindex1.js html/navtreeindex2.js html/navtreeindex3.js html/navtreeindex4.js html/navtreeindex5.js html/open.png html/pages.html html/pair__mat_8h_source.html html/params_8h.html html/params_8h.js html/params_8h__dep__incl.map html/params_8h__dep__incl.md5 html/params_8h__dep__incl.png html/params_8h__incl.map html/params_8h__incl.md5 '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/params_8h__incl.png html/params_8h_source.html html/part__func_8h.html html/part__func_8h.js html/part__func_8h__incl.map html/part__func_8h__incl.md5 html/part__func_8h__incl.png html/part__func_8h_source.html html/part__func__co_8h.html html/part__func__co_8h.js html/part__func__co_8h__incl.map html/part__func__co_8h__incl.md5 html/part__func__co_8h__incl.png html/part__func__co_8h_source.html html/part__func__up_8h.html html/part__func__up_8h.js html/part__func__up_8h__incl.map html/part__func__up_8h__incl.md5 html/part__func__up_8h__incl.png html/part__func__up_8h_source.html html/plex_8h_source.html html/plot__layouts_8h.html html/plot__layouts_8h.js html/plot__layouts_8h__dep__incl.map html/plot__layouts_8h__dep__incl.md5 html/plot__layouts_8h__dep__incl.png html/plot__layouts_8h__incl.map html/plot__layouts_8h__incl.md5 html/plot__layouts_8h__incl.png html/plot__layouts_8h_source.html html/profiledist_8h.html html/profiledist_8h.js html/profiledist_8h__incl.map html/profiledist_8h__incl.md5 html/profiledist_8h__incl.png html/profiledist_8h_source.html html/read__epars_8h.html html/read__epars_8h.js html/read__epars_8h_source.html html/resize.js '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/ribo_8h_source.html html/snofold_8h_source.html html/snoop_8h_source.html html/stringdist_8h.html html/stringdist_8h.js html/stringdist_8h__incl.map html/stringdist_8h__incl.md5 html/stringdist_8h__incl.png html/stringdist_8h_source.html html/structCOORDINATE.html html/structCOORDINATE.js html/structConcEnt.html html/structConcEnt.js html/structINTERVAL.html html/structINTERVAL.js html/structLIST.html html/structLIST.js html/structLIST__coll__graph.map html/structLIST__coll__graph.md5 html/structLIST__coll__graph.png html/structLST__BUCKET.html html/structLST__BUCKET.js html/structLST__BUCKET__coll__graph.map html/structLST__BUCKET__coll__graph.md5 html/structLST__BUCKET__coll__graph.png html/structPAIR.html html/structPAIR.js html/structPostorder__list.html html/structPostorder__list.js html/structSOLUTION.html html/structSOLUTION.js html/structTree.html html/structTree.js html/structTree__coll__graph.map html/structTree__coll__graph.md5 html/structTree__coll__graph.png html/structTwoDfold__solution.html html/structTwoDfold__solution.js html/structTwoDfold__vars.html html/structTwoDfold__vars.js '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/structTwoDfold__vars__coll__graph.map html/structTwoDfold__vars__coll__graph.md5 html/structTwoDfold__vars__coll__graph.png html/structTwoDpfold__solution.html html/structTwoDpfold__solution.js html/structTwoDpfold__vars.html html/structTwoDpfold__vars.js html/structTwoDpfold__vars__coll__graph.map html/structTwoDpfold__vars__coll__graph.md5 html/structTwoDpfold__vars__coll__graph.png html/structbondT.html html/structbondT.js html/structbondTEn.html html/structbondTEn.js html/structcofoldF.html html/structcofoldF.js html/structconstrain.html html/structconstrain.js html/structcpair.html html/structcpair.js html/structdupVar.html html/structdupVar.js html/structduplexT.html html/structduplexT.js html/structfolden.html html/structfolden.js html/structinteract.html html/structinteract.js html/structintermediate__t.html html/structintermediate__t.js html/structintermediate__t__coll__graph.map html/structintermediate__t__coll__graph.md5 html/structintermediate__t__coll__graph.png html/structmodel__detailsT.html html/structmodel__detailsT.js html/structmove__t.html html/structmove__t.js html/structpair__info.html html/structpair__info.js html/structpairpro.html '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/structpairpro.js html/structpairpro__coll__graph.map html/structpairpro__coll__graph.md5 html/structpairpro__coll__graph.png html/structparamT.html html/structparamT.js html/structparamT__coll__graph.map html/structparamT__coll__graph.md5 html/structparamT__coll__graph.png html/structpath__t.html html/structpath__t.js html/structpf__paramT.html html/structpf__paramT.js html/structpf__paramT__coll__graph.map html/structpf__paramT__coll__graph.md5 html/structpf__paramT__coll__graph.png html/structplist.html html/structplist.js html/structpu__contrib.html html/structpu__contrib.js html/structpu__out.html html/structpu__out.js html/structsect.html html/structsect.js html/structsnoopT.html html/structsnoopT.js html/structstruct__en.html html/structstruct__en.js html/structsvm__model.html html/structsvm__model.js html/structswString.html html/structswString.js html/subopt_8h.html html/subopt_8h.js html/subopt_8h__incl.map html/subopt_8h__incl.md5 html/subopt_8h__incl.png html/subopt_8h_source.html html/svgpan.js html/svm__utils_8h_source.html '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' /usr/bin/install -c -m 644 html/sync_off.png html/sync_on.png html/tab_a.png html/tab_b.png html/tab_h.png html/tab_s.png html/tabs.css html/treedist_8h.html html/treedist_8h.js html/treedist_8h__incl.map html/treedist_8h__incl.md5 html/treedist_8h__incl.png html/treedist_8h_source.html html/utils_8h.html html/utils_8h.js html/utils_8h__dep__incl.map html/utils_8h__dep__incl.md5 html/utils_8h__dep__incl.png html/utils_8h_source.html '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html' make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc' Makefile:482: recipe for target 'install-am' failed make[1]: *** [install-am] Error 2 make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc' Makefile:457: recipe for target 'install-recursive' failed make: *** [install-recursive] Error 1 * ERROR: sci-biology/vienna-rna-2.1.8::gentoo failed (install phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/vienna-rna-2.1.8::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/vienna-rna-2.1.8::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:vienna-rna-2.1.8:20141112-085103.log'. * The ebuild environment file is located at '/tmp/portage/sci-biology/vienna-rna-2.1.8/temp/environment'. * Working directory: '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' * S: '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' * QA Notice: make jobserver unavailable: * * make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.