sci-biology:eugene-4.1d-r1:20240421-221839.log

sci-biology:eugene-4.1d-r1:20240421-221839.log (text/plain), 10.92 KB, created by Toralf Förster on 2024-04-22 17:48:09 UTC

 * Package:    sci-biology/eugene-4.1d-r1:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking eugene-4.1d.tar.gz to /var/tmp/portage/sci-biology/eugene-4.1d-r1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/eugene-4.1d-r1/work
>>> Preparing source in /var/tmp/portage/sci-biology/eugene-4.1d-r1/work/eugene-4.1d ...
 * Applying eugene-3.6-overflow.patch ...
 [ ok ]
 * Applying eugene-3.6-plugins.patch ...
 [ ok ]
 * Applying eugene-4.1-format-security.patch ...
 [ ok ]
 * Applying eugene-4.1d-fix-c++14.patch ...
 [ ok ]
 * Applying eugene-4.1d-Wformat.patch ...
 [ ok ]
 * Applying eugene-4.1d-portable-getopt.patch ...
 [ ok ]
 * Applying eugene-4.1d-clang16.patch ...
 [ ok ]
 * Running eautoreconf in '/var/tmp/portage/sci-biology/eugene-4.1d-r1/work/eugene-4.1d' ...
 * Running 'aclocal --system-acdir=/var/tmp/portage/sci-biology/eugene-4.1d-r1/temp/aclocal' ...
 [ ok ]
 * Running 'autoconf --force' ...
 [ ok ]
 * Running 'autoheader' ...
 [ ok ]
 * Running 'automake --add-missing --copy --force-missing' ...
 [ ok ]
 * Running elibtoolize in: eugene-4.1d/
>>> Source prepared.
 * Modern C testing: this build is using a /etc/portage/bashrc hook (2023-11-30T22:24)!
 * Modern C testing: see https://wiki.gentoo.org/wiki/Modern_C_porting for more info.
>>> Configuring source in /var/tmp/portage/sci-biology/eugene-4.1d-r1/work/eugene-4.1d ...
 * econf: updating eugene-4.1d/config/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating eugene-4.1d/config/config.sub with /usr/share/gnuconfig/config.sub
 * econf: updating eugene-4.1d/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating eugene-4.1d/config.sub with /usr/share/gnuconfig/config.sub
./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 --datarootdir=/usr/share --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/eugene-4.1d-r1 --htmldir=/usr/share/doc/eugene-4.1d-r1/html --libdir=/usr/lib64
checking for a BSD-compatible install... /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... 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 the compiler supports GNU C++... yes
checking whether clang++ accepts -g... yes
checking for clang++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of clang++... none
checking for x86_64-pc-linux-gnu-gcc... clang
checking whether the compiler supports GNU C... yes
checking whether clang accepts -g... yes
checking for clang option to enable C11 features... none needed
checking whether clang understands -c and -o together... yes
checking dependency style of clang... none
checking for gawk... (cached) gawk
checking whether ln -s works... yes
checking for x86_64-pc-linux-gnu-ar... llvm-ar
checking the archiver (llvm-ar) interface... ar
checking for x86_64-pc-linux-gnu-ranlib... llvm-ranlib
checking for main in -lc... yes
checking for main in -ldl... yes
checking for main in -lgcc... yes
checking for main in -lgd... yes
checking for main in -lm... yes
checking for main in -lpng... yes
checking for main in -lz... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for netdb.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 values.h... yes
checking for getopt.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking whether struct tm is in sys/time.h or time.h... time.h
checking for size_t... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for GNU libc compatible malloc... yes
checking whether lstat correctly handles trailing slash... yes
checking whether stat accepts an empty string... no
checking for floor... yes
checking for pow... yes
checking for sqrt... yes
checking for strchr... yes
checking for strspn... yes
checking for uname... yes
checking for getopt... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating README
config.status: creating src/Makefile
config.status: creating src/GDIF/Makefile
config.status: creating src/Parametrization/Makefile
config.status: creating src/SensorPlugins/Makefile
config.status: creating src/SensorPlugins/0_SensorTk/Makefile
config.status: creating src/SensorPlugins/0_SensorTk/GetData/Makefile
config.status: creating src/SensorPlugins/AnnotaStruct/Makefile
config.status: creating src/SensorPlugins/BlastX/Makefile
config.status: creating src/SensorPlugins/Est/Makefile
config.status: creating src/SensorPlugins/EuStop/Makefile
config.status: creating src/SensorPlugins/FrameShift/Makefile
config.status: creating src/SensorPlugins/GCPlot/Makefile
config.status: creating src/SensorPlugins/GFF/Makefile
config.status: creating src/SensorPlugins/GSplicer/Makefile
config.status: creating src/SensorPlugins/Homology/Makefile
config.status: creating src/SensorPlugins/IfElse/Makefile
config.status: creating src/SensorPlugins/MarkovConst/Makefile
config.status: creating src/SensorPlugins/MarkovIMM/Makefile
config.status: creating src/SensorPlugins/MarkovIMM/GetData/Makefile
config.status: creating src/SensorPlugins/MarkovProt/Makefile
config.status: creating src/SensorPlugins/MarkovProt/GetData/Makefile
config.status: creating src/SensorPlugins/NcRNA/Makefile
config.status: creating src/SensorPlugins/NG2/Makefile
config.status: creating src/SensorPlugins/NStart/Makefile
config.status: creating src/SensorPlugins/NStretch/Makefile
config.status: creating src/SensorPlugins/PatConst/Makefile
config.status: creating src/SensorPlugins/PepSignal/Makefile
config.status: creating src/SensorPlugins/ProStart/Makefile
config.status: creating src/SensorPlugins/Plotter/Makefile
config.status: creating src/SensorPlugins/QualData/Makefile
config.status: creating src/SensorPlugins/Repeat/Makefile
config.status: creating src/SensorPlugins/RibosomalFrameShift/Makefile
config.status: creating src/SensorPlugins/Riken/Makefile
config.status: creating src/SensorPlugins/SMachine/Makefile
config.status: creating src/SensorPlugins/SPred/Makefile
config.status: creating src/SensorPlugins/SpliceWAM/Makefile
config.status: creating src/SensorPlugins/StartWAM/Makefile
config.status: creating src/SensorPlugins/Tester/Makefile
config.status: creating src/SensorPlugins/Transcript/Makefile
config.status: creating plugins/Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
>>> Source configured.
'/var/tmp/portage/sci-biology/eugene-4.1d-r1/temp/clang16-errors.log' -> '/var/tmp/clang/sci-biology/eugene-4.1d-r1/clang16-errors.log'
'/var/tmp/portage/sci-biology/eugene-4.1d-r1/temp/clang16-safe.log' -> '/var/tmp/clang/sci-biology/eugene-4.1d-r1/clang16-safe.log'
>>> Compiling source in /var/tmp/portage/sci-biology/eugene-4.1d-r1/work/eugene-4.1d ...
make -j4 
make  all-recursive
make[1]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d-r1/work/eugene-4.1d'
Making all in src
make[2]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d-r1/work/eugene-4.1d/src'
Making all in Parametrization
make[3]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d-r1/work/eugene-4.1d/src/Parametrization'
clang++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -O2 -pipe -march=native -fno-diagnostics-color -c -o ParaOptimization.o ParaOptimization.cc
clang++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -O2 -pipe -march=native -fno-diagnostics-color -c -o OptiAlgorithm.o OptiAlgorithm.cc
clang++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -O2 -pipe -march=native -fno-diagnostics-color -c -o Random.o Random.cc
clang++ -DHAVE_CONFIG_H -I. -I../..    -rdynamic -fPIC -O2 -pipe -march=native -fno-diagnostics-color -c -o LineSearch.o LineSearch.cc
clang++: clang++warning: : argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument]
warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument]
clang++: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument]
clang++: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument]
OptiAlgorithm.cc:84:16: error: use of undeclared identifier 'setiosflags'; did
      you mean 'std::setiosflags'?
   84 |   std::cout << setiosflags (std::ios::fixed);
      |                ^~~~~~~~~~~
      |                std::setiosflags
/usr/include/c++/v1/iomanip:104:39: note: 'std::setiosflags' declared here
  104 | inline _LIBCPP_HIDE_FROM_ABI __iom_t2 setiosflags(ios_base::fmtflags __m...
      |                                       ^
1 error generated.
make[3]: *** [Makefile:403: OptiAlgorithm.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d-r1/work/eugene-4.1d/src/Parametrization'
make[2]: *** [Makefile:511: all-recursive] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d-r1/work/eugene-4.1d/src'
make[1]: *** [Makefile:479: all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d-r1/work/eugene-4.1d'
make: *** [Makefile:418: all] Error 2
 * ERROR: sci-biology/eugene-4.1d-r1::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/eugene-4.1d-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/eugene-4.1d-r1::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:eugene-4.1d-r1:20240421-221839.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/eugene-4.1d-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/eugene-4.1d-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/eugene-4.1d-r1/work/eugene-4.1d'
 * S: '/var/tmp/portage/sci-biology/eugene-4.1d-r1/work/eugene-4.1d'