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Gentoo's Bugzilla – Attachment 641724 Details for
Bug 725318
sci-biology/vienna-rna calls ar directly
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build.log
build.log (text/plain), 55.67 KB, created by
Agostino Sarubbo
on 2020-05-25 13:11:48 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2020-05-25 13:11:48 UTC
Size:
55.67 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 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 âprint_postorder_listâ: >treedist.c:437:13: warning: type defaults to âintâ in declaration of âiâ []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 âdump_loopsâ: >naview.c:341:28: warning: format â%dâ expects argument of type âintâ, but argument 2 has type âlong intâ []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 âstrncpyâ, > inlined from âPS_color_alnâ at PS_dot.c:1818:11: >/usr/include/bits/string_fortified.h:106:10: warning: â__builtin_strncpyâ 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 âPS_color_alnâ: >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 âstrncpyâ, > inlined from âaliPS_color_alnâ at PS_dot.c:2090:11: >/usr/include/bits/string_fortified.h:106:10: warning: â__builtin_strncpyâ 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 âaliPS_color_alnâ: >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 âputoutpU_splitupâ: >LPfold.c:1012:18: warning: format â%sâ expects argument of type âchar *â, but argument 3 has type âintâ []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 âmea_backtrackâ: >MEA.c:223:9: warning: implicit declaration of function âget_gquad_pattern_pfâ []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 âfind_max_Câ: >c_plex.c:1071:42: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_tâ {aka âlong unsigned intâ} []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 âplot_max_Câ: >c_plex.c:1112:36: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_tâ {aka âlong unsigned intâ} []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 âalifind_maxâ: >ali_plex.c:595:49: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_tâ {aka âlong unsigned intâ} []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 âaliplot_maxâ: >ali_plex.c:643:34: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_tâ {aka âlong unsigned intâ} []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 âfind_max_XSâ: >plex.c:1511:41: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_tâ {aka âlong unsigned intâ} []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 âplot_max_XSâ: >plex.c:1607:34: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_tâ {aka âlong unsigned intâ} []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 âfind_maxâ: >plex.c:2671:40: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_tâ {aka âlong unsigned intâ} []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 â%dâ expects argument of type âintâ, but argument 6 has type âsize_tâ {aka âlong unsigned intâ} []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 âplot_maxâ: >plex.c:2753:34: warning: format â%dâ expects argument of type âintâ, but argument 6 has type âsize_tâ {aka âlong unsigned intâ} []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 â%dâ expects argument of type âintâ, but argument 6 has type âsize_tâ {aka âlong unsigned intâ} []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 âfind_max_snoopâ: >snoop.c:1087:40: warning: format â%dâ expects argument of type âintâ, but argument 7 has type âlong intâ []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 âsnoop_subopt_XSâ: >snoop.c:1600:40: warning: format â%dâ expects argument of type âintâ, but argument 7 has type âlong intâ []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 âfind_max_snoop_XSâ: >snoop.c:2096:40: warning: format â%dâ expects argument of type âintâ, but argument 7 has type âlong intâ []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 âsvm_model* svm_load_model(const char*)â: >../libsvm-2.91/svm.cpp:2730:9: warning: ignoring return value of âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 âint fscanf(FILE*, const char*, ...)â declared with attribute âwarn_unused_resultâ []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 >
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bug 725318
: 641724