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Gentoo's Bugzilla – Attachment 390002 Details for
Bug 529752
sci-biology/vienna-rna-2.1.8[doc] fails to build
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build.log
build.log (text/plain), 138.05 KB, created by
Ian Stakenvicius (RETIRED)
on 2014-11-21 16:48:06 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Ian Stakenvicius (RETIRED)
Created:
2014-11-21 16:48:06 UTC
Size:
138.05 KB
patch
obsolete
> * 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>*, 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.
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