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Gentoo's Bugzilla – Attachment 443658 Details for
Bug 591570
sci-biology/vienna-rna-2.1.8 : x86_64-pc-linux-gnu-gcc: error: libgomp.spec: No such file or directory
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sci-biology:vienna-rna-2.1.8:20160818-050917.log
sci-biology:vienna-rna-2.1.8:20160818-050917.log (text/plain), 104.31 KB, created by
Toralf Förster
on 2016-08-18 07:26:11 UTC
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Description:
sci-biology:vienna-rna-2.1.8:20160818-050917.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2016-08-18 07:26:11 UTC
Size:
104.31 KB
patch
obsolete
> * Package: sci-biology/vienna-rna-2.1.8 > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python python_targets_python2_7 userland_GNU > * FEATURES: preserve-libs sandbox userpriv usersandbox >>>> Unpacking source... >>>> Unpacking ViennaRNA-2.1.8.tar.gz to /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work >>>> Source unpacked in /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work >>>> Preparing source in /var/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 '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' ... > * Running aclocal ... > [ ok ] > * Running autoconf --force ... > [ ok ] > * Running autoheader ... > [ ok ] > * Running automake --add-missing --copy --force-missing ... > [ ok ] > * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70' ... > * Running aclocal ... > [ ok ] > * This package has a configure.in file which has long been deprecated. Please > * update it to use configure.ac instead as newer versions of autotools will die > * when it finds this file. See https://bugs.gentoo.org/426262 for details. > * Running autoconf --force ... > [ ok ] > * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' ... > * Running aclocal ... > [ ok ] > * Running autoconf --force ... > [ ok ] > * Running autoheader ... > [ ok ] > * Running automake --add-missing --copy --force-missing ... > [ ok ] > * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' ... > * Running aclocal ... > [ ok ] > * Running autoconf --force ... > [ ok ] > * Running autoheader ... > [ ok ] > * Running automake --add-missing --copy --force-missing ... > [ ok ] > * Running elibtoolize in: ViennaRNA-2.1.8/ > * Running elibtoolize in: ViennaRNA-2.1.8/Kinfold/ > * Running elibtoolize in: ViennaRNA-2.1.8/RNAforester/ > * Running elibtoolize in: ViennaRNA-2.1.8/RNAforester/g2-0.70/ >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ... >>>> Working in BUILD_DIR: "/var/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 >/var/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 --disable-openmp --without-doc-pdf --without-doc-html --without-doc >checking whether make supports nested variables... yes >checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/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 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 >configure: WARNING: You need Python >= 2.5 and < 3.0 to build the Python extension >configure: WARNING: You may set the PythonCmd environment variable to point to > a suitable python binary >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 >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 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 (/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold) >configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--disable-dependency-tracking' '--disable-silent-rules' '--libdir=/usr/lib64' '--docdir=/usr/share/doc/vienna-rna-2.1.8' '--enable-shared' '--disable-static' '--with-cluster' '--disable-openmp' '--without-doc-pdf' '--without-doc-html' '--without-doc' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-march=native -O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-march=native -O2 -pipe' --cache-file=/dev/null --srcdir=. >checking whether make supports nested variables... yes >checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/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 ViennaRNA package... headers in "../H" and library... "../lib" >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >checking for ANSI C header files... yes >checking for sys/types.h... yes >checking for sys/stat.h... yes >checking for stdlib.h... yes >checking for string.h... yes >checking for memory.h... yes >checking for strings.h... yes >checking for inttypes.h... yes >checking for stdint.h... yes >checking for unistd.h... yes >checking for stdlib.h... (cached) yes >checking for string.h... (cached) yes >checking for strings.h... (cached) yes >checking for unistd.h... (cached) yes >checking fold.h usability... yes >checking fold.h presence... yes >checking for fold.h... yes >checking for exp in -lm... yes >checking for stdlib.h... (cached) yes >checking for GNU libc compatible malloc... yes >checking for stdlib.h... (cached) yes >checking for GNU libc compatible realloc... yes >checking for an ANSI C-conforming const... yes >checking that generated files are newer than configure... done >configure: creating ./config.status >config.status: creating Example/Makefile >config.status: creating Makefile >config.status: creating config.h >config.status: executing depfiles commands >=== configuring in RNAforester (/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester) >configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--disable-dependency-tracking' '--disable-silent-rules' '--libdir=/usr/lib64' '--docdir=/usr/share/doc/vienna-rna-2.1.8' '--enable-shared' '--disable-static' '--with-cluster' '--disable-openmp' '--without-doc-pdf' '--without-doc-html' '--without-doc' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-march=native -O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-march=native -O2 -pipe' --cache-file=/dev/null --srcdir=. >checking whether make supports nested variables... yes >checking for a BSD-compatible install... /usr/lib/portage/python3.4/ebuild-helpers/xattr/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 >using (to be built) libRNA.a in ../lib >checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >checking for ANSI C header files... no >checking for sys/types.h... yes >checking for sys/stat.h... yes >checking for stdlib.h... yes >checking for string.h... yes >checking for memory.h... yes >checking for strings.h... yes >checking for inttypes.h... yes >checking for stdint.h... yes >checking for unistd.h... yes >checking g2.h usability... yes >checking g2.h presence... yes >checking for g2.h... yes >checking for an ANSI C-conforming const... yes >checking for inline... inline >checking for size_t... yes >checking that generated files are newer than configure... done >configure: creating ./config.status >config.status: creating Makefile >config.status: creating src/Makefile >config.status: creating man/Makefile >config.status: creating config.h >config.status: executing depfiles commands >=== configuring in g2-0.70 (/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70) >configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr' '--build=x86_64-pc-linux-gnu' '--host=x86_64-pc-linux-gnu' '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--datadir=/usr/share' '--sysconfdir=/etc' '--localstatedir=/var/lib' '--disable-dependency-tracking' '--disable-silent-rules' '--libdir=/usr/lib64' '--docdir=/usr/share/doc/vienna-rna-2.1.8' '--enable-shared' '--disable-static' '--with-cluster' '--disable-openmp' '--without-doc-pdf' '--without-doc-html' '--without-doc' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-march=native -O2 -pipe' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-march=native -O2 -pipe' --cache-file=/dev/null --srcdir=. >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/lib/portage/python3.4/ebuild-helpers/xattr/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: no > (HTML): no > (PDF): no >- >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 /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ... >>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8" >make -j1 >make all-recursive >make[1]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' >Making all in lib >make[2]: Entering directory '/var/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 -fpic -march=native -O2 -pipe -c -o libRNA_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c >treedist.c: In function âprint_postorder_listâ: >treedist.c:437:13: warning: type defaults to âintâ in declaration of âiâ [-Wimplicit-int] > register i; > ^ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-utils.o `test -f 'utils.c' || echo './'`utils.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-fold.o `test -f 'fold.c' || echo './'`fold.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-naview.o `test -f 'naview.c' || echo './'`naview.c >naview.c: In function âdump_loopsâ: >naview.c:341:10: warning: format â%dâ expects argument of type âintâ, but argument 2 has type âlong intâ [-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 -fpic -march=native -O2 -pipe -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 -fpic -march=native -O2 -pipe -c -o libRNA_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-params.o `test -f 'params.c' || echo './'`params.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -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 -fpic -march=native -O2 -pipe -c -o libRNA_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c >LPfold.c: In function âputoutpU_splitupâ: >LPfold.c:1012:14: warning: format â%sâ expects argument of type âchar *â, but argument 3 has type âintâ [-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 -fpic -march=native -O2 -pipe -c -o libRNA_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-ribo.o `test -f 'ribo.c' || echo './'`ribo.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-findpath.o `test -f 'findpath.c' || echo './'`findpath.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-convert_epars.o `test -f 'convert_epars.c' || echo './'`convert_epars.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-MEA.o `test -f 'MEA.c' || echo './'`MEA.c >MEA.c: In function âmea_backtrackâ: >MEA.c:223:9: warning: implicit declaration of function âget_gquad_pattern_pfâ [-Wimplicit-function-declaration] > get_gquad_pattern_pf(S, i, j, pf, &L, l); > ^ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-aliLfold.o `test -f 'aliLfold.c' || echo './'`aliLfold.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-mm.o `test -f 'mm.c' || echo './'`mm.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-2Dfold.o `test -f '2Dfold.c' || echo './'`2Dfold.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-2Dpfold.o `test -f '2Dpfold.c' || echo './'`2Dpfold.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-plex_functions.o `test -f 'plex_functions.c' || echo './'`plex_functions.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-plot_layouts.o `test -f 'plot_layouts.c' || echo './'`plot_layouts.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-ali_plex.o `test -f 'ali_plex.c' || echo './'`ali_plex.c >ali_plex.c: In function âalifind_maxâ: >ali_plex.c:595:27: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, > ^ >ali_plex.c: In function âaliplot_maxâ: >ali_plex.c:643:12: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", > ^ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-c_plex.o `test -f 'c_plex.c' || echo './'`c_plex.c >c_plex.c: In function âfind_max_Câ: >c_plex.c:1071:20: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, > ^ >c_plex.c: In function âplot_max_Câ: >c_plex.c:1112:14: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, > ^ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-plex.o `test -f 'plex.c' || echo './'`plex.c >plex.c: In function âfind_max_XSâ: >plex.c:1511:18: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf(" %s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f) [%5.2 > ^ >plex.c: In function âplot_max_XSâ: >plex.c:1607:12: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("%s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f) [%5.2f = %5. > ^ >plex.c: In function âfind_maxâ: >plex.c:2671:18: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("%s %3d,%-3d : %3d,%-3d (%5.2f) [%5.2f]\n", test.structure, > ^ >plex.c:2718:18: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, > ^ >plex.c: In function âplot_maxâ: >plex.c:2753:12: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("%s %3d,%-3d : %3d,%-3d (%5.2f) [%5.2f]\n", test.structure, > ^ >plex.c:2775:12: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, > ^ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-snofold.o `test -f 'snofold.c' || echo './'`snofold.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-snoop.o `test -f 'snoop.c' || echo './'`snoop.c >snoop.c: In function âfind_max_snoopâ: >snoop.c:1087:14: warning: format â%dâ expects argument of type âintâ, but argument 7 has type âlong intâ [-Wformat=] > printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f > ^ >snoop.c: In function âsnoop_subopt_XSâ: >snoop.c:1600:14: warning: format â%dâ expects argument of type âintâ, but argument 7 has type âlong intâ [-Wformat=] > printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f > ^ >snoop.c: In function âfind_max_snoop_XSâ: >snoop.c:2096:14: warning: format â%dâ expects argument of type âintâ, but argument 7 has type âlong intâ [-Wformat=] > printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f > ^ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -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 -fpic -march=native -O2 -pipe -c -o libRNA_a-gquad.o `test -f 'gquad.c' || echo './'`gquad.c >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -march=native -O2 -pipe -c -o svm.o `test -f '../libsvm-2.91/svm.cpp' || echo './'`../libsvm-2.91/svm.cpp >../libsvm-2.91/svm.cpp: In function âsvm_model* svm_load_model(const char*)â: >../libsvm-2.91/svm.cpp:2730:24: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%80s",cmd); > ^ >../libsvm-2.91/svm.cpp:2734:25: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%80s",cmd); > ^ >../libsvm-2.91/svm.cpp:2756:25: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%80s",cmd); > ^ >../libsvm-2.91/svm.cpp:2777:33: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%d",¶m.degree); > ^ >../libsvm-2.91/svm.cpp:2779:33: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%lf",¶m.gamma); > ^ >../libsvm-2.91/svm.cpp:2781:33: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%lf",¶m.coef0); > ^ >../libsvm-2.91/svm.cpp:2783:36: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â, 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 âint fscanf(FILE*, const char*, ...)â, 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 âint fscanf(FILE*, const char*, ...)â, 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 âint fscanf(FILE*, const char*, ...)â, 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 âint fscanf(FILE*, const char*, ...)â, 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 âint fscanf(FILE*, const char*, ...)â, 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 âint fscanf(FILE*, const char*, ...)â, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%d",&model->nSV[i]); > ^ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fpic -march=native -O2 -pipe -c -o libRNA_a-svm_utils.o `test -f 'svm_utils.c' || echo './'`svm_utils.c >rm -f libRNA.a >ar cru libRNA.a libRNA_a-dist_vars.o libRNA_a-fold_vars.o libRNA_a-part_func.o libRNA_a-read_epars.o libRNA_a-treedist.o libRNA_a-energy_par.o libRNA_a-inverse.o libRNA_a-ProfileDist.o libRNA_a-RNAstruct.o libRNA_a-utils.o libRNA_a-fold.o libRNA_a-naview.o libRNA_a-PS_dot.o libRNA_a-stringdist.o libRNA_a-params.o libRNA_a-subopt.o libRNA_a-list.o libRNA_a-Lfold.o libRNA_a-cofold.o libRNA_a-part_func_co.o libRNA_a-ProfileAln.o libRNA_a-duplex.o libRNA_a-alifold.o libRNA_a-alipfold.o libRNA_a-aln_util.o libRNA_a-LPfold.o libRNA_a-part_func_up.o libRNA_a-ribo.o libRNA_a-findpath.o libRNA_a-convert_epars.o libRNA_a-MEA.o libRNA_a-aliLfold.o libRNA_a-mm.o libRNA_a-2Dfold.o libRNA_a-2Dpfold.o libRNA_a-plex_functions.o libRNA_a-plot_layouts.o libRNA_a-ali_plex.o libRNA_a-c_plex.o libRNA_a-plex.o libRNA_a-snofold.o libRNA_a-snoop.o libRNA_a-move_set.o libRNA_a-gquad.o svm.o libRNA_a-svm_utils.o >x86_64-pc-linux-gnu-ranlib libRNA.a >make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib' >Making all in Progs >make[2]: Entering directory '/var/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 -march=native -O2 -pipe -c -o RNAfold_cmdl.o RNAfold_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAfold.o RNAfold.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAfold RNAfold_cmdl.o RNAfold.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAeval_cmdl.o RNAeval_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAeval.o RNAeval.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAeval RNAeval_cmdl.o RNAeval.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAheat_cmdl.o RNAheat_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAheat.o RNAheat.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAheat RNAheat_cmdl.o RNAheat.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNApdist_cmdl.o RNApdist_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNApdist.o RNApdist.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNApdist RNApdist_cmdl.o RNApdist.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAdistance_cmdl.o RNAdistance_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAdistance.o RNAdistance.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAdistance RNAdistance_cmdl.o RNAdistance.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAinverse_cmdl.o RNAinverse_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAinverse.o RNAinverse.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAinverse RNAinverse_cmdl.o RNAinverse.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAplot_cmdl.o RNAplot_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAplot.o RNAplot.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAplot RNAplot_cmdl.o RNAplot.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAsubopt_cmdl.o RNAsubopt_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAsubopt.o RNAsubopt.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAsubopt RNAsubopt_cmdl.o RNAsubopt.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNALfold_cmdl.o RNALfold_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNALfold.o RNALfold.c >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNALfold RNALfold_cmdl.o RNALfold.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAcofold_cmdl.o RNAcofold_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAcofold.o RNAcofold.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAcofold RNAcofold_cmdl.o RNAcofold.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNApaln_cmdl.o RNApaln_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNApaln.o RNApaln.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNApaln RNApaln_cmdl.o RNApaln.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAduplex_cmdl.o RNAduplex_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAduplex.o RNAduplex.c >RNAduplex.c: In function âmainâ: >RNAduplex.c:161:23: warning: format â%dâ expects argument of type âintâ, but argument 2 has type âsize_t {aka long unsigned int}â [-Wformat=] > if (istty) printf("lengths = %d,%d\n", strlen(s1), strlen(s2)); > ^ >RNAduplex.c:161:23: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âsize_t {aka long unsigned int}â [-Wformat=] >RNAduplex.c: In function âprint_strucâ: >RNAduplex.c:202:10: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", dup->structure, dup->i+1-l1, > ^ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAduplex RNAduplex_cmdl.o RNAduplex.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAalifold_cmdl.o RNAalifold_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAalifold.o RNAalifold.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAalifold RNAalifold_cmdl.o RNAalifold.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAplfold_cmdl.o RNAplfold_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAplfold.o RNAplfold.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAplfold RNAplfold_cmdl.o RNAplfold.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAup_cmdl.o RNAup_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAup.o RNAup.c >RNAup.c: In function âmainâ: >RNAup.c:346:5: warning: implicit declaration of function âread_parameter_fileâ [-Wimplicit-function-declaration] > read_parameter_file(ParamFile); > ^ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAup RNAup_cmdl.o RNAup.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAaliduplex_cmdl.o RNAaliduplex_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAaliduplex.o RNAaliduplex.c >RNAaliduplex.c: In function âprint_strucâ: >RNAaliduplex.c:170:10: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", dup->structure, dup->i+1-l1, > ^ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNALalifold_cmdl.o RNALalifold_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNALalifold.o RNALalifold.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNALalifold RNALalifold_cmdl.o RNALalifold.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNA2Dfold_cmdl.o RNA2Dfold_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNA2Dfold.o RNA2Dfold.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAparconv_cmdl.o RNAparconv_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAparconv.o RNAparconv.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAparconv RNAparconv_cmdl.o RNAparconv.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAPKplex_cmdl.o RNAPKplex_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAPKplex.o RNAPKplex.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAplex_cmdl.o RNAplex_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAplex.o RNAplex.c >RNAplex.c: In function âmainâ: >RNAplex.c:1100:16: warning: format â%dâ expects argument of type âintâ, but argument 2 has type âsize_t {aka long unsigned int}â [-Wformat=] > printf("lengths = %d,%d\n", strlen(s1), strlen(s2)); > ^ >RNAplex.c:1100:16: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âsize_t {aka long unsigned int}â [-Wformat=] >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAplex RNAplex_cmdl.o RNAplex.o ../lib/libRNA.a -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAsnoop_cmdl.o RNAsnoop_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -march=native -O2 -pipe -c -o RNAsnoop.o RNAsnoop.c >RNAsnoop.c: In function âprint_strucâ: >RNAsnoop.c:542:10: warning: format â%dâ expects argument of type âintâ, but argument 7 has type âlong intâ [-Wformat=] > printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f + 4 > ^ >RNAsnoop.c: In function âaliprint_strucâ: >RNAsnoop.c:623:10: warning: format â%dâ expects argument of type âintâ, but argument 7 has type âlong intâ [-Wformat=] > printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f + 4 > ^ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o RNAsnoop RNAsnoop_cmdl.o RNAsnoop.o ../lib/libRNA.a -lm -lm >make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs' >Making all in man >make[2]: Entering directory '/var/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 '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man' >Making all in Utils >make[2]: Entering directory '/var/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 -march=native -O2 -pipe -c -o b2ct.o b2ct.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o b2ct b2ct.o -L../lib -lRNA -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o popt.o popt.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o popt popt.o -L../lib -lRNA -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o ct2db_cmdl.o ct2db_cmdl.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o ct2db.o ct2db.c >ct2db.c: In function âmainâ: >ct2db.c:156:13: warning: implicit declaration of function âMEA_seqâ [-Wimplicit-function-declaration] > mea = MEA_seq(pairs, seq, structure, MEAgamma, params); > ^ >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o ct2db ct2db_cmdl.o ct2db.o -L../lib -lRNA -lm -lm >if test -n "/usr/bin/perl"; then \ > /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' b2mt.pl ; \ >fi >if test -n "/usr/bin/perl"; then \ > /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' ct2b.pl ; \ >fi >if test -n "/usr/bin/perl"; then \ > /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' dpzoom.pl ; \ >fi >if test -n "/usr/bin/perl"; then \ > /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' mountain.pl ; \ >fi >if test -n "/usr/bin/perl"; then \ > /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' relplot.pl ; \ >fi >if test -n "/usr/bin/perl"; then \ > /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' rotate_ss.pl ; \ >fi >if test -n "/usr/bin/perl"; then \ > /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' cmount.pl ; \ >fi >if test -n "/usr/bin/perl"; then \ > /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' colorrna.pl ; \ >fi >if test -n "/usr/bin/perl"; then \ > /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' coloraln.pl ; \ >fi >if test -n "/usr/bin/perl"; then \ > /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' refold.pl ; \ >fi >if test -n "/usr/bin/perl"; then \ > /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' switch.pl ; \ >fi >make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils' >Making all in H >make[2]: Entering directory '/var/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 '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H' >Making all in misc >make[2]: Entering directory '/var/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 '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc' >Making all in doc >make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc' >make[2]: Nothing to be done for 'all'. >make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc' >Making all in interfaces >make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces' >Making all in Perl >make[3]: Entering directory '/var/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 >Writing MYMETA.yml and MYMETA.json >make -f Makefile.perl >make[4]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' >cp RNA.pm blib/lib/RNA.pm >Running Mkbootstrap for RNA () >chmod 644 "RNA.bs" >x86_64-pc-linux-gnu-gcc -c -fwrapv -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -march=native -O2 -pipe -I../../H -O2 -pipe -DVERSION=\"2.1.8\" -DXS_VERSION=\"2.1.8\" -fPIC "-I/usr/lib64/perl5/5.24.0/x86_64-linux/CORE" RNA_wrap.c >RNA_wrap.c: In function âmy_alifoldâ: >RNA_wrap.c:2316:23: warning: passing argument 1 of âalifoldâ from incompatible pointer type [-Wincompatible-pointer-types] > *energy = alifold(strings, struc); > ^ >In file included from RNA_wrap.c:1578:0: >../../H/../H/alifold.h:86:8: note: expected âconst char **â but argument is of type âchar **â > float alifold( const char **strings, > ^ >RNA_wrap.c: In function â_wrap_LoopEnergyâ: >RNA_wrap.c:6632:5: warning: âLoopEnergyâ is deprecated [-Wdeprecated-declarations] > result = (int)LoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8); > ^ >In file included from RNA_wrap.c:1560:0: >../../H/../H/fold.h:523:16: note: declared here > DEPRECATED(int LoopEnergy(int n1, > ^ >../../H/../H/fold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_HairpinEâ: >RNA_wrap.c:6707:5: warning: âHairpinEâ is deprecated [-Wdeprecated-declarations] > result = (int)HairpinE(arg1,arg2,arg3,arg4,(char const *)arg5); > ^ >In file included from RNA_wrap.c:1560:0: >../../H/../H/fold.h:536:16: note: declared here > DEPRECATED(int HairpinE(int size, > ^ >../../H/../H/fold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_initialize_foldâ: >RNA_wrap.c:6742:5: warning: âinitialize_foldâ is deprecated [-Wdeprecated-declarations] > initialize_fold(arg1); > ^ >In file included from RNA_wrap.c:1560:0: >../../H/../H/fold.h:547:17: note: declared here > DEPRECATED(void initialize_fold(int length)); > ^ >../../H/../H/fold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_energy_of_structâ: >RNA_wrap.c:6780:5: warning: âenergy_of_structâ is deprecated [-Wdeprecated-declarations] > result = (float)energy_of_struct((char const *)arg1,(char const *)arg2); > ^ >In file included from RNA_wrap.c:1560:0: >../../H/../H/fold.h:563:18: note: declared here > DEPRECATED(float energy_of_struct(const char *string, > ^ >../../H/../H/fold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_energy_of_struct_ptâ: >RNA_wrap.c:6835:5: warning: âenergy_of_struct_ptâ is deprecated [-Wdeprecated-declarations] > result = (int)energy_of_struct_pt((char const *)arg1,arg2,arg3,arg4); > ^ >In file included from RNA_wrap.c:1560:0: >../../H/../H/fold.h:582:16: note: declared here > DEPRECATED(int energy_of_struct_pt( const char *string, > ^ >../../H/../H/fold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_energy_of_circ_structâ: >RNA_wrap.c:6879:5: warning: âenergy_of_circ_structâ is deprecated [-Wdeprecated-declarations] > result = (float)energy_of_circ_struct((char const *)arg1,(char const *)arg2 > ^ >In file included from RNA_wrap.c:1560:0: >../../H/../H/fold.h:601:18: note: declared here > DEPRECATED(float energy_of_circ_struct( const char *string, > ^ >../../H/../H/fold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_initialize_cofoldâ: >RNA_wrap.c:7403:5: warning: âinitialize_cofoldâ is deprecated [-Wdeprecated-declarations] > initialize_cofold(arg1); > ^ >In file included from RNA_wrap.c:1561:0: >../../H/../H/cofold.h:180:17: note: declared here > DEPRECATED(void initialize_cofold(int length)); > ^ >../../H/../H/cofold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_init_pf_foldâ: >RNA_wrap.c:8311:5: warning: âinit_pf_foldâ is deprecated [-Wdeprecated-declarations] > init_pf_fold(arg1); > ^ >In file included from RNA_wrap.c:1562:0: >../../H/../H/part_func.h:407:17: note: declared here > DEPRECATED(void init_pf_fold(int length)); > ^ >../../H/../H/part_func.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_centroidâ: >RNA_wrap.c:8347:5: warning: âcentroidâ is deprecated [-Wdeprecated-declarations] > result = (char *)centroid(arg1,arg2); > ^ >In file included from RNA_wrap.c:1562:0: >../../H/../H/part_func.h:413:18: note: declared here > DEPRECATED(char *centroid(int length, > ^ >../../H/../H/part_func.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_mean_bp_distâ: >RNA_wrap.c:8377:5: warning: âmean_bp_distâ is deprecated [-Wdeprecated-declarations] > result = (double)mean_bp_dist(arg1); > ^ >In file included from RNA_wrap.c:1562:0: >../../H/../H/part_func.h:421:19: note: declared here > DEPRECATED(double mean_bp_dist(int length)); > ^ >../../H/../H/part_func.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_expLoopEnergyâ: >RNA_wrap.c:8461:5: warning: âexpLoopEnergyâ is deprecated [-Wdeprecated-declarations] > result = (double)expLoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8); > ^ >In file included from RNA_wrap.c:1562:0: >../../H/../H/part_func.h:426:19: note: declared here > DEPRECATED(double expLoopEnergy(int u1, > ^ >../../H/../H/part_func.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_expHairpinEnergyâ: >RNA_wrap.c:8536:5: warning: âexpHairpinEnergyâ is deprecated [-Wdeprecated-declarations] > result = (double)expHairpinEnergy(arg1,arg2,arg3,arg4,(char const *)arg5); > ^ >In file included from RNA_wrap.c:1562:0: >../../H/../H/part_func.h:438:19: note: declared here > DEPRECATED(double expHairpinEnergy( int u, > ^ >../../H/../H/part_func.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_Make_bp_profileâ: >RNA_wrap.c:11742:5: warning: âMake_bp_profileâ is deprecated [-Wdeprecated-declarations] > result = (float *)Make_bp_profile(arg1); > ^ >In file included from RNA_wrap.c:1571:0: >../../H/../H/profiledist.h:56:19: note: declared here > DEPRECATED(float *Make_bp_profile(int length)); > ^ >../../H/../H/profiledist.h:5:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_copy_parametersâ: >RNA_wrap.c:13291:5: warning: âcopy_parametersâ is deprecated [-Wdeprecated-declarations] > result = (paramT *)copy_parameters(); > ^ >In file included from RNA_wrap.c:1576:0: >../../H/../H/params.h:126:24: note: declared here > DEPRECATED(paramT *copy_parameters(void)); > ^ >../../H/../H/params.h:8:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_set_parametersâ: >RNA_wrap.c:13317:5: warning: âset_parametersâ is deprecated [-Wdeprecated-declarations] > result = (paramT *)set_parameters(arg1); > ^ >In file included from RNA_wrap.c:1576:0: >../../H/../H/params.h:127:24: note: declared here > DEPRECATED(paramT *set_parameters(paramT *dest)); > ^ >../../H/../H/params.h:8:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_PS_dot_plotâ: >RNA_wrap.c:14984:5: warning: âPS_dot_plotâ is deprecated [-Wdeprecated-declarations] > result = (int)PS_dot_plot(arg1,arg2); > ^ >In file included from RNA_wrap.c:1566:0: >../../H/../H/PS_dot.h:195:16: note: declared here > DEPRECATED(int PS_dot_plot( char *string, > ^ >../../H/../H/PS_dot.h:8:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >rm -f blib/arch/auto/RNA/RNA.so >g++ -shared -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed RNA_wrap.o -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o blib/arch/auto/RNA/RNA.so ../../lib/libRNA.a \ > -lm \ > >chmod 755 blib/arch/auto/RNA/RNA.so >"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- RNA.bs blib/arch/auto/RNA/RNA.bs 644 >Manifying 1 pod document >make[4]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' >make[3]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl' >make[3]: Entering directory '/var/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 '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces' >make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces' >Making all in Cluster >make[2]: Entering directory '/var/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 -march=native -O2 -pipe -c -o split.o split.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o distance_matrix.o distance_matrix.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o cluster.o cluster.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o treeplot.o treeplot.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o AD_main.o AD_main.c >AD_main.c:16:1: warning: return type defaults to âintâ [-Wimplicit-int] > main(int argc, char *argv[]) > ^ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c ./../lib/utils.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o utils.o -lm -lm >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o statgeom.o statgeom.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o AS_main.o AS_main.c >AS_main.c:21:1: warning: return type defaults to âintâ [-Wimplicit-int] > main(int argc, char *argv[]) > ^ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -march=native -O2 -pipe -c -o PS3D.o PS3D.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -Wl,-O1 -Wl,--as-needed -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o utils.o -lm -lm >make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Cluster' >Making all in Kinfold >make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' >(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /var/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/sh ./config.status config.h >config.status: creating config.h >config.status: config.h is unchanged >make all-recursive >make[3]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' >Making all in Example >make[4]: Entering directory '/var/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 '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold/Example' >make[4]: Entering directory '/var/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 -march=native -O2 -pipe -c -o baum.o baum.c >baum.c: In function âini_or_reset_rlâ: >baum.c:206:7: warning: implicit declaration of function âinitialize_cofoldâ [-Wimplicit-function-declaration] > initialize_cofold(GSV.len); > ^ >baum.c:208:19: warning: implicit declaration of function âcofoldâ [-Wimplicit-function-declaration] > GAV.sE[0] = cofold(GAV.farbe_full, GAV.stopform[0]); > ^ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=native -O2 -pipe -c -o cache.o cache.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=native -O2 -pipe -c -o globals.o globals.c >globals.c: In function âprocess_options_ggâ: >globals.c:298:25: warning: passing argument 2 of âstrncpyâ makes pointer from integer without a cast [-Wint-conversion] > strncpy(GAV.ParamFile,255,args_info.Par_arg); > ^ >In file included from /usr/include/features.h:368:0, > from /usr/include/stdio.h:27, > from globals.c:9: >/usr/include/bits/string3.h:123:1: note: expected âconst char * restrictâ but argument is of type âintâ > __NTH (strncpy (char *__restrict __dest, const char *__restrict __src, > ^ >globals.c:298:29: warning: passing argument 3 of âstrncpyâ makes integer from pointer without a cast [-Wint-conversion] > strncpy(GAV.ParamFile,255,args_info.Par_arg); > ^ >In file included from /usr/include/features.h:368:0, > from /usr/include/stdio.h:27, > from globals.c:9: >/usr/include/bits/string3.h:123:1: note: expected âsize_t {aka long unsigned int}â but argument is of type âchar *â > __NTH (strncpy (char *__restrict __dest, const char *__restrict __src, > ^ >globals.c:331:39: warning: format â%gâ expects argument of type âfloat *â, but argument 3 has type âdouble *â [-Wformat=] > if (sscanf(args_info.pbounds_arg, "%g=%g=%g", > ^ >globals.c:331:39: warning: format â%gâ expects argument of type âfloat *â, but argument 4 has type âdouble *â [-Wformat=] >globals.c:331:39: warning: format â%gâ expects argument of type âfloat *â, but argument 5 has type âdouble *â [-Wformat=] >globals.c: In function âprocess_optionsâ: >globals.c:420:23: warning: format â%gâ expects argument of type âfloat *â, but argument 3 has type âdouble *â [-Wformat=] > if (sscanf(optarg, "%g=%g=%g", > ^ >globals.c:420:23: warning: format â%gâ expects argument of type âfloat *â, but argument 4 has type âdouble *â [-Wformat=] >globals.c:420:23: warning: format â%gâ expects argument of type âfloat *â, but argument 5 has type âdouble *â [-Wformat=] >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=native -O2 -pipe -c -o main.o main.c >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=native -O2 -pipe -c -o nachbar.o nachbar.c >nachbar.c: In function âsel_nbâ: >nachbar.c:302:18: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âsize_t {aka long unsigned int}â [-Wformat=] > sprintf(format, "%%-%ds %%6.2f %%10.3f", strlen(GAV.farbe_full)+1); > ^ >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -march=native -O2 -pipe -c -o cmdline.o cmdline.c >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -L../lib -Wl,-O1 -Wl,--as-needed -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o -lRNA -lm >make[4]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' >make[3]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' >make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' >Making all in RNAforester >make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' >(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /var/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/sh ./config.status config.h >config.status: creating config.h >config.status: config.h is unchanged >make all-recursive >make[3]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' >Making all in g2-0.70 >make[4]: Entering directory '/var/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 -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_device.c -o src/g2_device.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_control.c -o src/g2_ui_control.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_util.c -o src/g2_util.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_fif.c -o src/g2_fif.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_virtual_device.c -o src/g2_virtual_device.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_physical_device.c -o src/g2_physical_device.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_graphic_pd.c -o src/g2_graphic_pd.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_control_pd.c -o src/g2_control_pd.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_graphic.c -o src/g2_ui_graphic.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_virtual_device.c -o src/g2_ui_virtual_device.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_device.c -o src/g2_ui_device.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_splines.c -o src/g2_splines.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/PS/g2_PS.c -o src/PS/g2_PS.o >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/FIG/g2_FIG.c -o src/FIG/g2_FIG.o >src/FIG/g2_FIG.c: In function âg2_FIG_draw_stringâ: >src/FIG/g2_FIG.c:477:21: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_t {aka long unsigned int}â [-Wformat=] > fprintf(fig->fp,"4 0 %d 1 -1 0 %d 0 5 %d %d %d %d ", > ^ >x86_64-pc-linux-gnu-gcc -I./src -march=native -O2 -pipe -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/X11/g2_X11.c -o src/X11/g2_X11.o >ar -cr libg2.a ./src/g2_device.o ./src/g2_ui_control.o ./src/g2_util.o ./src/g2_fif.o ./src/g2_virtual_device.o ./src/g2_physical_device.o ./src/g2_graphic_pd.o ./src/g2_control_pd.o ./src/g2_ui_graphic.o ./src/g2_ui_virtual_device.o ./src/g2_ui_device.o ./src/g2_splines.o ./src/PS/g2_PS.o ./src/FIG/g2_FIG.o ./src/X11/g2_X11.o >test ! -n "x86_64-pc-linux-gnu-ranlib" || x86_64-pc-linux-gnu-ranlib libg2.a >test -d ./include || mkdir ./include >cp ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ./include/ >make[4]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70' >Making all in src >make[4]: Entering directory '/var/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/ -march=native -O2 -pipe -c -o Arguments.o Arguments.cpp >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o glib.o glib.c >glib.c: In function âReadGraphâ: >glib.c:161:2: warning: ignoring return value of âfscanfâ, 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 âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%d%d%d%d",°ree,&vlabel,&xcoord,&ycoord); > ^ >glib.c:176:4: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%d%d", &adj_node, &elabel); > ^ >glib.c: In function âReadEuclidâ: >glib.c:225:2: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%d %c",size,&c); > ^ >glib.c:234:3: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%d%d",&xcoord,&ycoord); > ^ >glib.c: In function âReadMatrixâ: >glib.c:272:2: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%d %c",size,&c); > ^ >glib.c:282:4: warning: ignoring return value of âfscanfâ, declared with attribute warn_unused_result [-Wunused-result] > fscanf(fp,"%d",&k); > ^ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o main.o main.cpp >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o ppforestbase.o ppforestbase.cpp >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o progressive_align.o progressive_align.cpp >progressive_align.cpp: In function ânode_entry* makePairsGraph(const RNAProfileAliMapType&, const DoubleScoreProfileAlgebraType*, const Matrix<double>*, double)â: >progressive_align.cpp:341:30: warning: deprecated conversion from string constant to âchar*â [-Wwrite-strings] > WriteGraph (graph,"test.out"); > ^ >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rna_profile_alignment.o rna_profile_alignment.cpp >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rna_alignment.o rna_alignment.cpp >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rna_algebra.o rna_algebra.cpp >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rna_alphabet.o rna_alphabet.cpp >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rnaforest.o rnaforest.cpp >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rnaforestsz.o rnaforestsz.cpp >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rnafuncs.o rnafuncs.cpp >x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o rnaforester_options.o rnaforester_options.cpp >x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -march=native -O2 -pipe -c -o wmatch.o wmatch.c >x86_64-pc-linux-gnu-g++ -march=native -O2 -pipe -L../g2-0.70 -L../../lib -L../../ViennaRNA -Wl,-O1 -Wl,--as-needed -o RNAforester Arguments.o glib.o main.o ppforestbase.o progressive_align.o rna_profile_alignment.o rna_alignment.o rna_algebra.o rna_alphabet.o rnaforest.o rnaforestsz.o rnafuncs.o rnaforester_options.o wmatch.o -lg2 -lRNA >make[4]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/src' >Making all in man >make[4]: Entering directory '/var/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 '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/man' >make[4]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' >make[4]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' >make[3]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' >make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' >make[2]: Entering directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' >make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' >make[1]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' >>>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8" >make -j1 -C Readseq build CC=x86_64-pc-linux-gnu-gcc >make: Entering directory '/var/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 -march=native -O2 -pipe -o readseq readseq.c ureadseq.c ureadasn.c >readseq.c: In function âformatstrâ: >readseq.c:257:34: warning: return discards âconstâ qualifier from pointer target type [-Wdiscarded-qualifiers] > case kASNseqset : return formats[kASN1-1]; > ^ >readseq.c:259:38: warning: return discards âconstâ qualifier from pointer target type [-Wdiscarded-qualifiers] > case kPhylipSequential: return formats[kPhylip-1]; > ^ >readseq.c:263:15: warning: return discards âconstâ qualifier from pointer target type [-Wdiscarded-qualifiers] > else return formats[format-1]; > ^ >readseq.c: In function âusageâ: >readseq.c:328:3: warning: format not a string literal and no format arguments [-Wformat-security] > fprintf(stderr,title); > ^ >readseq.c: In function âchooseFormatâ: >readseq.c:419:7: warning: implicit declaration of function âgetsâ [-Wimplicit-function-declaration] > gets(sform); > ^ >readseq.c: At top level: >readseq.c:712:1: warning: return type defaults to âintâ [-Wimplicit-int] > main( int argc, char *argv[]) > ^ >readseq.c: In function âmainâ: >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:910:28: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > sprintf( stemp,"%s_%d", oname, whichSeq); > ^ >readseq.c:912:29: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âlong intâ [-Wformat=] > fprintf( stderr,"Writing sequence %d to file %s\n", whichSeq, stemp > ^ >readseq.c:954:28: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âlong intâ [-Wformat=] > fprintf( stderr, "Sequence %d, length= %d, checksum= %X, format= %s, > ^ >readseq.c:954:28: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] >readseq.c:954:28: warning: format â%Xâ expects argument of type âunsigned intâ, but argument 5 has type âlong unsigned intâ [-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:972:50: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âlong intâ [-Wformat=] > if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen); > ^ >readseq.c:972:50: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] >readseq.c:973:36: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âlong intâ [-Wformat=] > else fprintf(foo," %d %d YF\n", i, seqlen); > ^ >readseq.c:973:36: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] >readseq.c:1075:17: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(foo,"\n %s MSF: %d Type: N January 01, 1776 12:00 Check: %d .. > ^ >readseq.c:1075:17: warning: format â%dâ expects argument of type âintâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >readseq.c:1087:36: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen); > ^ >readseq.c:1088:22: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > else fprintf(foo," %d %d YF\n", seqout, seqlen); > ^ >readseq.c:1112:21: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, seqlen); > ^ >readseq.c:757:5: warning: ignoring return value of âtmpnamâ, declared with attribute warn_unused_result [-Wunused-result] > tmpnam(tempname); > ^ >readseq.c:911:13: warning: ignoring return value of âfreopenâ, declared with attribute warn_unused_result [-Wunused-result] > freopen( stemp, "w", fout); > ^ >ureadseq.c: In function âseqFileFormatFpâ: >ureadseq.c:1346:17: warning: format â%dâ expects argument of type âint *â, but argument 3 has type âlong int *â [-Wformat=] > sscanf( sp, "%d%d", &nspp, &nlen); > ^ >ureadseq.c:1346:17: warning: format â%dâ expects argument of type âint *â, but argument 4 has type âlong int *â [-Wformat=] >ureadseq.c: In function âwriteSeqâ: >ureadseq.c:1595:20: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âlong intâ [-Wformat=] > sprintf(numform, "%d", seqlen); > ^ >ureadseq.c:1624:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen); > ^ >ureadseq.c:1625:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, > ^ >ureadseq.c:1625:20: warning: format â%Xâ expects argument of type âunsigned intâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >ureadseq.c:1639:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seq > ^ >ureadseq.c:1639:20: warning: format â%Xâ expects argument of type âunsigned intâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >ureadseq.c:1649:49: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âlong intâ [-Wformat=] > for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j); > ^ >ureadseq.c:1659:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); > ^ >ureadseq.c:1659:20: warning: format â%Xâ expects argument of type âunsigned intâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >ureadseq.c:1668:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checks > ^ >ureadseq.c:1668:20: warning: format â%Xâ expects argument of type âunsigned intâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >ureadseq.c:1669:20: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âlong intâ [-Wformat=] > fprintf(outf,"SQ %d BP\n", seqlen); > ^ >ureadseq.c:1680:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seql > ^ >ureadseq.c:1680:20: warning: format â%dâ expects argument of type âintâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >ureadseq.c:1689:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, > ^ >ureadseq.c:1689:20: warning: format â%Xâ expects argument of type âunsigned intâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >ureadseq.c:1695:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); > ^ >ureadseq.c:1695:20: warning: format â%Xâ expects argument of type âunsigned intâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >ureadseq.c:1726:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf," repr raw, mol %s, length %d, topology linear,\n", cp, > ^ >ureadseq.c:1748:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, chec > ^ >ureadseq.c:1748:20: warning: format â%Xâ expects argument of type âunsigned intâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >ureadseq.c:1765:22: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, chec > ^ >ureadseq.c:1765:22: warning: format â%Xâ expects argument of type âunsigned intâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >ureadseq.c:1771:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n", > ^ >ureadseq.c:1771:20: warning: format â%dâ expects argument of type âintâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >ureadseq.c:1783:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); > ^ >ureadseq.c:1783:20: warning: format â%Xâ expects argument of type âunsigned intâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >ureadseq.c:1792:20: warning: format â%dâ expects argument of type âintâ, but argument 4 has type âlong intâ [-Wformat=] > fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum); > ^ >ureadseq.c:1792:20: warning: format â%Xâ expects argument of type âunsigned intâ, but argument 5 has type âlong unsigned intâ [-Wformat=] >ureadseq.c:1833:38: warning: format â%dâ expects argument of type âintâ, but argument 3 has type âlong intâ [-Wformat=] > if (numline==1) fprintf(outf,"%-9d ",i+1); > ^ >/var/tmp/portage/sci-biology/vienna-rna-2.1.8/temp/ccfjE92g.o: In function `main': >readseq.c:(.text.startup+0x5ec): warning: the use of `tmpnam' is dangerous, better use `mkstemp' >/var/tmp/portage/sci-biology/vienna-rna-2.1.8/temp/ccfjE92g.o: In function `chooseFormat.part.1': >readseq.c:(.text+0x36d): warning: the `gets' function is dangerous and should not be used. >make: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq' >make -j1 RNA_wrap.c >make: Nothing to be done for 'RNA_wrap.c'. > * python2_7: running distutils-r1_run_phase distutils-r1_python_compile >/usr/bin/python2.7 setup.py build >running build >running build_py >creating /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/lib/RNA >copying ./version_test.py -> /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/lib/RNA >copying ./__init__.py -> /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/lib/RNA >warning: build_py: byte-compiling is disabled, skipping. > >running build_ext >building '_RNA' extension >creating /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/temp.linux-x86_64-2.7 >x86_64-pc-linux-gnu-gcc -march=native -O2 -pipe -fPIC -I../../H -I/usr/include/python2.7 -c RNA_wrap.c -o /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/temp.linux-x86_64-2.7/RNA_wrap.o -fopenmp >RNA_wrap.c: In function âmy_alifoldâ: >RNA_wrap.c:3803:23: warning: passing argument 1 of âalifoldâ from incompatible pointer type [-Wincompatible-pointer-types] > *energy = alifold(strings, struc); > ^ >In file included from RNA_wrap.c:3023:0: >../../H/../H/alifold.h:86:8: note: expected âconst char **â but argument is of type âchar **â > float alifold( const char **strings, > ^ >RNA_wrap.c: In function â_wrap_LoopEnergyâ: >RNA_wrap.c:6691:3: warning: âLoopEnergyâ is deprecated [-Wdeprecated-declarations] > result = (int)LoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8); > ^ >In file included from RNA_wrap.c:3005:0: >../../H/../H/fold.h:523:16: note: declared here > DEPRECATED(int LoopEnergy(int n1, > ^ >../../H/../H/fold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_HairpinEâ: >RNA_wrap.c:6750:3: warning: âHairpinEâ is deprecated [-Wdeprecated-declarations] > result = (int)HairpinE(arg1,arg2,arg3,arg4,(char const *)arg5); > ^ >In file included from RNA_wrap.c:3005:0: >../../H/../H/fold.h:536:16: note: declared here > DEPRECATED(int HairpinE(int size, > ^ >../../H/../H/fold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_initialize_foldâ: >RNA_wrap.c:6773:3: warning: âinitialize_foldâ is deprecated [-Wdeprecated-declarations] > initialize_fold(arg1); > ^ >In file included from RNA_wrap.c:3005:0: >../../H/../H/fold.h:547:17: note: declared here > DEPRECATED(void initialize_fold(int length)); > ^ >../../H/../H/fold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_energy_of_structâ: >RNA_wrap.c:6806:3: warning: âenergy_of_structâ is deprecated [-Wdeprecated-declarations] > result = (float)energy_of_struct((char const *)arg1,(char const *)arg2); > ^ >In file included from RNA_wrap.c:3005:0: >../../H/../H/fold.h:563:18: note: declared here > DEPRECATED(float energy_of_struct(const char *string, > ^ >../../H/../H/fold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_energy_of_struct_ptâ: >RNA_wrap.c:6860:3: warning: âenergy_of_struct_ptâ is deprecated [-Wdeprecated-declarations] > result = (int)energy_of_struct_pt((char const *)arg1,arg2,arg3,arg4); > ^ >In file included from RNA_wrap.c:3005:0: >../../H/../H/fold.h:582:16: note: declared here > DEPRECATED(int energy_of_struct_pt( const char *string, > ^ >../../H/../H/fold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_energy_of_circ_structâ: >RNA_wrap.c:6895:3: warning: âenergy_of_circ_structâ is deprecated [-Wdeprecated-declarations] > result = (float)energy_of_circ_struct((char const *)arg1,(char const *)arg2); > ^ >In file included from RNA_wrap.c:3005:0: >../../H/../H/fold.h:601:18: note: declared here > DEPRECATED(float energy_of_circ_struct( const char *string, > ^ >../../H/../H/fold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_initialize_cofoldâ: >RNA_wrap.c:7360:3: warning: âinitialize_cofoldâ is deprecated [-Wdeprecated-declarations] > initialize_cofold(arg1); > ^ >In file included from RNA_wrap.c:3006:0: >../../H/../H/cofold.h:180:17: note: declared here > DEPRECATED(void initialize_cofold(int length)); > ^ >../../H/../H/cofold.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_init_pf_foldâ: >RNA_wrap.c:8155:3: warning: âinit_pf_foldâ is deprecated [-Wdeprecated-declarations] > init_pf_fold(arg1); > ^ >In file included from RNA_wrap.c:3007:0: >../../H/../H/part_func.h:407:17: note: declared here > DEPRECATED(void init_pf_fold(int length)); > ^ >../../H/../H/part_func.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_centroidâ: >RNA_wrap.c:8186:3: warning: âcentroidâ is deprecated [-Wdeprecated-declarations] > result = (char *)centroid(arg1,arg2); > ^ >In file included from RNA_wrap.c:3007:0: >../../H/../H/part_func.h:413:18: note: declared here > DEPRECATED(char *centroid(int length, > ^ >../../H/../H/part_func.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_mean_bp_distâ: >RNA_wrap.c:8208:3: warning: âmean_bp_distâ is deprecated [-Wdeprecated-declarations] > result = (double)mean_bp_dist(arg1); > ^ >In file included from RNA_wrap.c:3007:0: >../../H/../H/part_func.h:421:19: note: declared here > DEPRECATED(double mean_bp_dist(int length)); > ^ >../../H/../H/part_func.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_expLoopEnergyâ: >RNA_wrap.c:8293:3: warning: âexpLoopEnergyâ is deprecated [-Wdeprecated-declarations] > result = (double)expLoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8); > ^ >In file included from RNA_wrap.c:3007:0: >../../H/../H/part_func.h:426:19: note: declared here > DEPRECATED(double expLoopEnergy(int u1, > ^ >../../H/../H/part_func.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_expHairpinEnergyâ: >RNA_wrap.c:8352:3: warning: âexpHairpinEnergyâ is deprecated [-Wdeprecated-declarations] > result = (double)expHairpinEnergy(arg1,arg2,arg3,arg4,(char const *)arg5); > ^ >In file included from RNA_wrap.c:3007:0: >../../H/../H/part_func.h:438:19: note: declared here > DEPRECATED(double expHairpinEnergy( int u, > ^ >../../H/../H/part_func.h:7:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_Make_bp_profileâ: >RNA_wrap.c:12008:3: warning: âMake_bp_profileâ is deprecated [-Wdeprecated-declarations] > result = (float *)Make_bp_profile(arg1); > ^ >In file included from RNA_wrap.c:3016:0: >../../H/../H/profiledist.h:56:19: note: declared here > DEPRECATED(float *Make_bp_profile(int length)); > ^ >../../H/../H/profiledist.h:5:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_copy_parametersâ: >RNA_wrap.c:13464:3: warning: âcopy_parametersâ is deprecated [-Wdeprecated-declarations] > result = (paramT *)copy_parameters(); > ^ >In file included from RNA_wrap.c:3021:0: >../../H/../H/params.h:126:24: note: declared here > DEPRECATED(paramT *copy_parameters(void)); > ^ >../../H/../H/params.h:8:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_set_parametersâ: >RNA_wrap.c:13486:3: warning: âset_parametersâ is deprecated [-Wdeprecated-declarations] > result = (paramT *)set_parameters(arg1); > ^ >In file included from RNA_wrap.c:3021:0: >../../H/../H/params.h:127:24: note: declared here > DEPRECATED(paramT *set_parameters(paramT *dest)); > ^ >../../H/../H/params.h:8:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >RNA_wrap.c: In function â_wrap_PS_dot_plotâ: >RNA_wrap.c:15036:3: warning: âPS_dot_plotâ is deprecated [-Wdeprecated-declarations] > result = (int)PS_dot_plot(arg1,arg2); > ^ >In file included from RNA_wrap.c:3011:0: >../../H/../H/PS_dot.h:195:16: note: declared here > DEPRECATED(int PS_dot_plot( char *string, > ^ >../../H/../H/PS_dot.h:8:26: note: in definition of macro âDEPRECATEDâ > #define DEPRECATED(func) func __attribute__ ((deprecated)) > ^ >x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -march=native -O2 -pipe /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/temp.linux-x86_64-2.7/RNA_wrap.o -L../../lib -L/usr/lib64 -lRNA -lpython2.7 -o /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8-python2_7/lib/_RNA.so -fopenmp -lstdc++ -s >x86_64-pc-linux-gnu-gcc: error: libgomp.spec: No such file or directory >error: command 'x86_64-pc-linux-gnu-gcc' failed with exit status 1 > * ERROR: sci-biology/vienna-rna-2.1.8::gentoo failed (compile phase): > * (no error message) > * > * Call stack: > * ebuild.sh, line 115: Called src_compile > * environment, line 5044: Called distutils-r1_src_compile > * environment, line 1522: Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile' > * environment, line 604: Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile' > * environment, line 4578: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile' > * environment, line 3308: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile' > * environment, line 3306: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile' > * environment, line 881: Called distutils-r1_run_phase 'distutils-r1_python_compile' > * environment, line 1513: Called distutils-r1_python_compile > * environment, line 1388: Called esetup.py 'build' > * environment, line 2419: Called die > * The specific snippet of code: > * "${@}" || die "${die_args[@]}"; > * > * 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-2.1.8:20160818-050917.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Python' > * S: '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8'
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