sci-biology:vienna-rna-2.1.8:20200223-014038.log

sci-biology:vienna-rna-2.1.8:20200223-014038.log (text/plain), 20.16 KB, created by Toralf Förster on 2020-02-23 10:07:17 UTC

 * Package:    sci-biology/vienna-rna-2.1.8
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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'