* 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 userpriv usersandbox >>> Unpacking source... >>> Unpacking ViennaRNA-2.1.8.tar.gz to /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work >>> Source unpacked in /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work >>> Preparing source in /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ... * Applying vienna-rna-2.1.8-bindir.patch ... [ ok ] * Applying vienna-rna-2.1.1-prll.patch ... [ ok ] * Applying vienna-rna-2.1.1-impl-decl.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' ... * Running aclocal ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70' ... * Running aclocal ... [ ok ] * This package has a configure.in file which has long been deprecated. Please * update it to use configure.ac instead as newer versions of autotools will die * when it finds this file. See https://bugs.gentoo.org/426262 for details. * Running autoconf --force ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' ... * Running aclocal ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' ... * Running aclocal ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] * Running elibtoolize in: ViennaRNA-2.1.8/ * Running elibtoolize in: ViennaRNA-2.1.8/Kinfold/ * Running elibtoolize in: ViennaRNA-2.1.8/RNAforester/ * Running elibtoolize in: ViennaRNA-2.1.8/RNAforester/g2-0.70/ >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8" * econf: updating ViennaRNA-2.1.8/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-2.1.8/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-2.1.8/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-2.1.8/config/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-2.1.8/RNAforester/g2-0.70/config.sub with /usr/share/gnuconfig/config.sub * econf: updating ViennaRNA-2.1.8/RNAforester/g2-0.70/config.guess with /usr/share/gnuconfig/config.guess * econf: updating ViennaRNA-2.1.8/RNAforester/config.guess with /usr/share/gnuconfig/config.guess /var/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64 --docdir=/usr/share/doc/vienna-rna-2.1.8 --enable-shared --disable-static --with-cluster --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/python3.6/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking if malloc debugging is wanted... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking 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... /usr/bin/pdflatex checking for latex... /usr/bin/latex checking for makeindex... /usr/bin/makeindex 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' 'CXXFLAGS=-O2 -pipe -march=native -fno-common -falign-functions=32:25:16' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-O2 -pipe -march=native -fno-common -falign-functions=32:25:16' --cache-file=/dev/null --srcdir=. checking whether make supports nested variables... yes checking for a BSD-compatible install... /usr/lib/portage/python3.6/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' 'CXXFLAGS=-O2 -pipe -march=native -fno-common -falign-functions=32:25:16' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-O2 -pipe -march=native -fno-common -falign-functions=32:25:16' --cache-file=/dev/null --srcdir=. checking whether make supports nested variables... yes checking for a BSD-compatible install... /usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking 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' 'CXXFLAGS=-O2 -pipe -march=native -fno-common -falign-functions=32:25:16' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-O2 -pipe -march=native -fno-common -falign-functions=32:25:16' --cache-file=/dev/null --srcdir=. checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking for a BSD-compatible install... /usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c checking for find... find checking for makedepend... makedepend checking for dlopen in -ldl... yes checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for main in -lm... yes checking for main in -lX11... yes checking for main in -lgd... yes checking for gdImagePng... no checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes configure: creating ./config.status config.status: creating Makefile config.status: creating demo/Makefile config.status: creating g2_perl/Makefile.PL Supported devices: PostScript FIG X11 Unsupported devices: Win32 GD Run 'make depend' to create dependencies. configure: Configure successful with the following options: RNAlib Interfaces: Perl Interface: yes Python Interface: no Ruby Interface: no Extra Programs: Analyse{Dists,Seqs}: yes Kinfold: yes RNAforester: yes Other Options: SVM: yes Documentation: no (HTML): no (PDF): no - Files will be installed in the following directories: Executables: /usr/bin Libraries: /usr/lib64 Header files: /usr/include Extra Data: /usr/share Man pages: /usr/share/man Documentation: /usr/share/doc/vienna-rna-2.1.8 (HTML): /usr/share/doc/vienna-rna-2.1.8/html (PDF): /usr/share/doc/vienna-rna-2.1.8 sed: -e expression #2, char 78: unknown option to `s' * ERROR: sci-biology/vienna-rna-2.1.8::gentoo failed (configure phase): * (no error message) * * Call stack: * ebuild.sh, line 125: Called src_configure * environment, line 4785: Called die * The specific snippet of code: * sed -e "s:CC=gcc:CC=$(tc-getCC):" -e "s:^CFLAGS=:CFLAGS=${CFLAGS}:" -i Readseq/Makefile || die; * * If you need support, post the output of `emerge --info '=sci-biology/vienna-rna-2.1.8::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/vienna-rna-2.1.8::gentoo'`. * The complete build log is located at '/var/log/portage/sci-biology:vienna-rna-2.1.8:20200223-014038.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'