* Package: sci-biology/vienna-rna-2.1.8 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux openmp python_targets_python2_7 userland_GNU * FEATURES: network-sandbox preserve-libs sandbox test 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/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 * 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 /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 --enable-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/python3.7/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 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 whether make supports the include directive... yes (GNU style) checking dependency style of x86_64-pc-linux-gnu-g++... none checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-pc-linux-gnu-gcc... none checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking whether x86_64-pc-linux-gnu-gcc accepts -fpic... yes checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking whether make sets $(MAKE)... (cached) yes checking for grep that handles long lines and -e... /bin/grep checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp checking for exp in -lm... yes checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for unistd.h... (cached) yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strtod... yes checking for floor... yes checking for strdup... yes checking for strstr... yes checking for strchr... yes checking for strrchr... yes checking for strstr... (cached) yes checking for strtol... yes checking for strtoul... yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for erand48... yes checking for memset... yes checking for memmove... yes checking for erand48... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for interfaces/Perl/Makefile.am... yes checking for Kinfold/Makefile.am... yes checking for RNAforester/Makefile.am... yes checking for Cluster/Makefile.am... yes checking for libsvm-2.91/svm.cpp... yes checking for libsvm-2.91/svm.h... yes checking whether float precision is used for partition function arrays instead of double precision... no checking for perl... /usr/bin/perl checking for python... /usr/bin/python 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... no checking for pdflatex... no checking for latex... no checking for makeindex... no checking for dot... no 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' '--enable-openmp' '--without-doc-pdf' '--without-doc-html' '--without-doc' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXX=x86_64-pc-linux-gnu-g++' 'CXXFLAGS=-O2 -pipe -march=native -frecord-gcc-switches' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0' 'CC=x86_64-pc-linux-gnu-gcc' 'CFLAGS=-O2 -pipe -march=native -frecord-gcc-switches' 'CPP=x86_64-pc-linux-gnu-gcc -E' --cache-file=/dev/null --srcdir=. checking whether make supports nested variables... yes checking for a BSD-compatible install... /usr/lib/portage/python3.7/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 whether make supports the include directive... yes (GNU style) checking dependency style of x86_64-pc-linux-gnu-gcc... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for strdup... yes checking for memset... yes checking for strchr... yes checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp checking for ViennaRNA package... headers in "../H" and library... "../lib" checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking fold.h usability... yes checking fold.h presence... yes checking for fold.h... yes checking for exp in -lm... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for an ANSI C-conforming const... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Example/Makefile config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in RNAforester (/var/tmp/portage/sci-biology/vienna-rna-2.1.8/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' '--enable-openmp' '--without-doc-pdf' '--without-doc-html' '--without-doc' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXX=x86_64-pc-linux-gnu-g++' 'CXXFLAGS=-O2 -pipe -march=native -frecord-gcc-switches' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0' 'CC=x86_64-pc-linux-gnu-gcc' 'CFLAGS=-O2 -pipe -march=native -frecord-gcc-switches' 'CPP=x86_64-pc-linux-gnu-gcc -E' --cache-file=/dev/null --srcdir=. checking whether make supports nested variables... yes checking for a BSD-compatible install... /usr/lib/portage/python3.7/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 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 whether make supports the include directive... yes (GNU style) checking dependency style of x86_64-pc-linux-gnu-g++... none checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking dependency style of x86_64-pc-linux-gnu-gcc... none checking for x86_64-pc-linux-gnu-g++ option to support OpenMP... -fopenmp using (to be built) libRNA.a in ../lib checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking g2.h usability... yes checking g2.h presence... yes checking for g2.h... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in g2-0.70 (/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' '--enable-openmp' '--without-doc-pdf' '--without-doc-html' '--without-doc' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXX=x86_64-pc-linux-gnu-g++' 'CXXFLAGS=-O2 -pipe -march=native -frecord-gcc-switches' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0' 'CC=x86_64-pc-linux-gnu-gcc' 'CFLAGS=-O2 -pipe -march=native -frecord-gcc-switches' 'CPP=x86_64-pc-linux-gnu-gcc -E' --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 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/python3.7/ebuild-helpers/xattr/install -c checking for find... find checking for makedepend... : checking for dlopen in -ldl... yes checking for X... no checking for main in -lm... yes checking for main in -lX11... no 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 Unsupported devices: X11 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 -j4 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 -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c treedist.c: In function ‘print_postorder_list’: treedist.c:437:13: warning: type defaults to ‘int’ in declaration of ‘i’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wimplicit-int-Wimplicit-int]8;;] 437 | register i; | ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-utils.o `test -f 'utils.c' || echo './'`utils.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-fold.o `test -f 'fold.c' || echo './'`fold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-naview.o `test -f 'naview.c' || echo './'`naview.c naview.c: In function ‘dump_loops’: naview.c:341:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 341 | printf("\nRoot loop is #%d\n",(root-loops)+1); | ~^ ~~~~~~~~~~~~~~ | | | | int long int | %ld x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-params.o `test -f 'params.c' || echo './'`params.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c In file included from /usr/include/string.h:495, from PS_dot.c:12: In function ‘strncpy’, inlined from ‘PS_color_aln’ at PS_dot.c:1818:11: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-overflow=-Wstringop-overflow=]8;;] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PS_dot.c: In function ‘PS_color_aln’: PS_dot.c:1818:11: note: length computed here 1818 | strncpy(ruler+i,tmpBuffer,strlen(tmpBuffer)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from PS_dot.c:12: In function ‘strncpy’, inlined from ‘aliPS_color_aln’ at PS_dot.c:2090:11: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wstringop-overflow=-Wstringop-overflow=]8;;] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PS_dot.c: In function ‘aliPS_color_aln’: PS_dot.c:2090:11: note: length computed here 2090 | strncpy(ruler+i,tmpBuffer,strlen(tmpBuffer)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c LPfold.c: In function ‘putoutpU_splitup’: LPfold.c:1012:18: warning: format ‘%s’ expects argument of type ‘char *’, but argument 3 has type ‘int’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 1012 | fprintf(fp,"\t%s\n",ident); | ~^ ~~~~~ | | | | | int | char * | %d x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-ribo.o `test -f 'ribo.c' || echo './'`ribo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-findpath.o `test -f 'findpath.c' || echo './'`findpath.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-convert_epars.o `test -f 'convert_epars.c' || echo './'`convert_epars.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-MEA.o `test -f 'MEA.c' || echo './'`MEA.c MEA.c: In function ‘mea_backtrack’: MEA.c:223:9: warning: implicit declaration of function ‘get_gquad_pattern_pf’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wimplicit-function-declaration-Wimplicit-function-declaration]8;;] 223 | 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 -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-aliLfold.o `test -f 'aliLfold.c' || echo './'`aliLfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-mm.o `test -f 'mm.c' || echo './'`mm.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-2Dfold.o `test -f '2Dfold.c' || echo './'`2Dfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-2Dpfold.o `test -f '2Dpfold.c' || echo './'`2Dpfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-plex_functions.o `test -f 'plex_functions.c' || echo './'`plex_functions.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-plot_layouts.o `test -f 'plot_layouts.c' || echo './'`plot_layouts.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-ali_plex.o `test -f 'ali_plex.c' || echo './'`ali_plex.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-c_plex.o `test -f 'c_plex.c' || echo './'`c_plex.c c_plex.c: In function ‘find_max_C’: c_plex.c:1071:42: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 1071 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, | ~~~^ | | | int | %-3ld ...... 1075 | (begin_q -11) + test.j + strlen(test.structure)-l1-2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} c_plex.c: In function ‘plot_max_C’: c_plex.c:1112:36: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 1112 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, | ~~~^ | | | int | %-3ld 1113 | begin_t-10+test.i-l1, begin_t-10+test.i-1, begin_q-10 +test.j-1 , 1114 | (begin_q -11) + test.j + strlen(test.structure)-l1-2 , test.energy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} ali_plex.c: In function ‘alifind_max’: ali_plex.c:595:49: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 595 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, | ~~~^ | | | int | %-3ld ...... 599 | begin_q-11 + test.j +strlen(test.structure) -l1 -2 , test.energy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} ali_plex.c: In function ‘aliplot_max’: ali_plex.c:643:34: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 643 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", | ~~~^ | | | int | %-3ld ...... 648 | begin_q -11 + test.j +strlen(test.structure) - l1 - 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-plex.o `test -f 'plex.c' || echo './'`plex.c plex.c: In function ‘find_max_XS’: plex.c:1511:41: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 1511 | printf(" %s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f) [%5.2f = %5.2f + %5.2f + %5.2f] %d \n", test.structure, | ~~~^ | | | int | %-3ld ...... 1515 | (begin_q -11) + test.j + strlen(test.structure)-l1-2-10, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} plex.c: In function ‘plot_max_XS’: plex.c:1607:34: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 1607 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f) [%5.2f = %5.2f + %5.2f + %5.2f] \n", test.structure, | ~~~^ | | | int | %-3ld ...... 1611 | (begin_q -11) + test.j + strlen(test.structure)-l1-2-10, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} plex.c: In function ‘find_max’: plex.c:2671:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 2671 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f) [%5.2f]\n", test.structure, | ~~~^ | | | int | %-3ld ...... 2675 | (begin_q -11) + test.j + strlen(test.structure)-l1-2-10, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} plex.c:2718:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 2718 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, | ~~~^ | | | int | %-3ld ...... 2722 | (begin_q -11) + test.j + strlen(test.structure)-l1-2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} plex.c: In function ‘plot_max’: plex.c:2753:34: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 2753 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f) [%5.2f]\n", test.structure, | ~~~^ | | | int | %-3ld ...... 2757 | (begin_q -11) + test.j + strlen(test.structure)-l1-2-10, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} plex.c:2775:34: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 2775 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, | ~~~^ | | | int | %-3ld ...... 2779 | (begin_q -11) + test.j + strlen(test.structure)-l1-2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-snofold.o `test -f 'snofold.c' || echo './'`snofold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-snoop.o `test -f 'snoop.c' || echo './'`snoop.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -c -o libRNA_a-move_set.o `test -f 'move_set.c' || echo './'`move_set.c snoop.c: In function ‘find_max_snoop’: snoop.c:1087:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 1087 | printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f + 4.1 ) (%5.2f) \n%s&%s\n", | ~~~^ | | | int | %-3ld 1088 | target_struct,begin + test.i-5-l1,begin + test.i -6 , begin + test.u -6, 1089 | test.j+1, test.j + (strrchr(test.structure,'>') - strchr(test.structure,'>'))+1 , | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long int snoop.c: In function ‘snoop_subopt_XS’: snoop.c:1600:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 1600 | printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f + %5.2f + 4.10) (%5.2f)\n%s&%s\n" , | ~~~^ | | | int | %-3ld 1601 | test.structure, i - (n5 - test.i) ,i - 5, i - (n5 - test.u ), 1602 | j-5, j-5 + (strrchr(test.structure,'>') - strchr(test.structure,'>')), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long int snoop.c: In function ‘find_max_snoop_XS’: snoop.c:2096:40: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘long int’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 2096 | printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f + %5.2f + 4.10) (%5.2f)\n%s&%s\n" , | ~~~^ | | | int | %-3ld 2097 | test.structure, pos - (n5 - test.i) ,pos - 5, pos - (n5 - test.u ), 2098 | max_pos_j-5, max_pos_j-5 + (strrchr(test.structure,'>') - strchr(test.structure,'>')), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long int x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -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 -O2 -pipe -march=native -frecord-gcc-switches -c -o svm.o `test -f '../libsvm-2.91/svm.cpp' || echo './'`../libsvm-2.91/svm.cpp ../libsvm-2.91/svm.cpp: In function ‘svm_model* svm_load_model(const char*)’: ../libsvm-2.91/svm.cpp:2730:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2730 | fscanf(fp,"%80s",cmd); | ~~~~~~^~~~~~~~~~~~~~~ ../libsvm-2.91/svm.cpp:2734:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2734 | fscanf(fp,"%80s",cmd); | ~~~~~~^~~~~~~~~~~~~~~ ../libsvm-2.91/svm.cpp:2756:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2756 | fscanf(fp,"%80s",cmd); | ~~~~~~^~~~~~~~~~~~~~~ ../libsvm-2.91/svm.cpp:2777:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2777 | fscanf(fp,"%d",¶m.degree); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../libsvm-2.91/svm.cpp:2779:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2779 | fscanf(fp,"%lf",¶m.gamma); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../libsvm-2.91/svm.cpp:2781:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2781 | fscanf(fp,"%lf",¶m.coef0); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ ../libsvm-2.91/svm.cpp:2783:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2783 | fscanf(fp,"%d",&model->nr_class); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ ../libsvm-2.91/svm.cpp:2785:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2785 | fscanf(fp,"%d",&model->l); | ~~~~~~^~~~~~~~~~~~~~~~~~~ ../libsvm-2.91/svm.cpp:2791:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2791 | fscanf(fp,"%lf",&model->rho[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ ../libsvm-2.91/svm.cpp:2798:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2798 | fscanf(fp,"%d",&model->label[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ ../libsvm-2.91/svm.cpp:2805:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2805 | fscanf(fp,"%lf",&model->probA[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../libsvm-2.91/svm.cpp:2812:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2812 | fscanf(fp,"%lf",&model->probB[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../libsvm-2.91/svm.cpp:2819:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-result-Wunused-result]8;;] 2819 | fscanf(fp,"%d",&model->nSV[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -march=native -frecord-gcc-switches -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 make[2]: ar: No such file or directory make[2]: *** [Makefile:512: libRNA.a] Error 127 make[2]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib' make[1]: *** [Makefile:467: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' make: *** [Makefile:383: all] Error 2 * ERROR: sci-biology/vienna-rna-2.1.8::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/vienna-rna-2.1.8::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/vienna-rna-2.1.8::gentoo'`. * The complete build log is located at '/var/log/emerge-log/build/sci-biology/vienna-rna-2.1.8:20200525-124145.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' * S: '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' emerge --info: Portage 2.3.100 (python 3.7.7-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r3, 5.4.0-1009-aws x86_64) ================================================================= System uname: Linux-5.4.0-1009-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7 KiB Mem: 16011344 total, 1832892 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Mon, 25 May 2020 12:35:49 +0000 sh bash 5.0_p17 ld GNU ld (Gentoo 2.34 p4) 2.34.0 app-shells/bash: 5.0_p17::gentoo dev-lang/perl: 5.30.2-r2::gentoo dev-lang/python: 2.7.18::gentoo, 3.7.7-r2::gentoo, 3.8.3::gentoo sys-apps/baselayout: 2.7::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.18::gentoo sys-devel/autoconf: 2.69-r5::gentoo sys-devel/automake: 1.16.2::gentoo sys-devel/binutils: 2.34-r1::gentoo sys-devel/gcc: 10.1.0::gentoo sys-devel/gcc-config: 2.3::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.6::gentoo (virtual/os-headers) sys-libs/glibc: 2.31-r3::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: yes sync-rsync-verify-jobs: 1 sync-rsync-verify-max-age: 24 sync-rsync-extra-opts: ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXX="x86_64-pc-linux-gnu-g++" CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--with-bdeps=y --binpkg-respect-use=y -1 -b -k" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="C.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" MAKEOPTS="-j4" PKGDIR="/root/.packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="acl amd64 berkdb bzip2 cli crypt dri fortran gdbm iconv ipv6 libtirpc multilib ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS