sci-biology:fasttree-2.1.11:20210608-033818.log

sci-biology:fasttree-2.1.11:20210608-033818.log (text/plain), 7.48 KB, created by Toralf Förster on 2021-06-08 07:09:50 UTC

 * Package:    sci-biology/fasttree-2.1.11
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 cpu_flags_x86_sse3 elibc_glibc kernel_linux openmp userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox splitdebug userpriv usersandbox

>>> Unpacking source...
>>> Unpacking FastTree-2.1.11.c to /var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11
unpack FastTree-2.1.11.c: file format not recognized. Ignoring.
>>> Unpacking FastTreeUPGMA-2.1.11.c to /var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11
unpack FastTreeUPGMA-2.1.11.c: file format not recognized. Ignoring.
>>> Unpacking MOTreeComparison-2.1.11.tar.gz to /var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11
>>> Source unpacked in /var/tmp/portage/sci-biology/fasttree-2.1.11/work
>>> Preparing source in /var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11 ...
 * Applying fasttree-2.1.11-format-security.patch ...
 [ ok ]
 * Working in BUILD_DIR: "/var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11_build"
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11 ...
 * Working in BUILD_DIR: "/var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11_build"
cmake -C /var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DVERSION=2.1.11 -DHAS_SSE3=yes -DUSE_OPENMP=yes -DUSE_DOUBLE=no -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11_build/gentoo_toolchain.cmake  /var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11
loading initial cache file /var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11_build/gentoo_common_config.cmake
-- The C compiler identification is GNU 11.1.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -pipe -march=native -fno-diagnostics-color -DOPENMP -fopenmp
C++             
Linker flags:
Executable      -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DOPENMP -fopenmp
Module          -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0
Shared          -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0

-- Configuring done
-- Generating done
-- Build files have been written to: /var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11_build
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11 ...
 * Working in BUILD_DIR: "/var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11_build"
ninja -v -j3 -l0
[1/4] /usr/bin/x86_64-pc-linux-gnu-gcc    -pipe -march=native -fno-diagnostics-color -DOPENMP -fopenmp -MD -MT CMakeFiles/FastTreeUPGMA.dir/FastTreeUPGMA-2.1.11.c.o -MF CMakeFiles/FastTreeUPGMA.dir/FastTreeUPGMA-2.1.11.c.o.d -o CMakeFiles/FastTreeUPGMA.dir/FastTreeUPGMA-2.1.11.c.o -c /var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11/FastTreeUPGMA-2.1.11.c
[2/4] : && /usr/bin/x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -DOPENMP -fopenmp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DOPENMP -fopenmp    -rdynamic CMakeFiles/FastTreeUPGMA.dir/FastTreeUPGMA-2.1.11.c.o -o FastTreeUPGMA  -lm && :
[3/4] /usr/bin/x86_64-pc-linux-gnu-gcc    -pipe -march=native -fno-diagnostics-color -DOPENMP -fopenmp -MD -MT CMakeFiles/FastTree.dir/FastTree-2.1.11.c.o -MF CMakeFiles/FastTree.dir/FastTree-2.1.11.c.o.d -o CMakeFiles/FastTree.dir/FastTree-2.1.11.c.o -c /var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11/FastTree-2.1.11.c
/var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11/FastTree-2.1.11.c: In function ‘CreateGTR’:
/var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11/FastTree-2.1.11.c:9554:10: warning: ‘CreateTransitionMatrix’ accessing 3200 bytes in a region of size 640 [-Wstringop-overflow=]
 9554 |   return(CreateTransitionMatrix(matrix,f));
      |         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11/FastTree-2.1.11.c:9554:10: note: referencing argument 1 of type ‘double (*)[20]’
/var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11/FastTree-2.1.11.c:9557:22: note: in a call to function ‘CreateTransitionMatrix’
 9557 | transition_matrix_t *CreateTransitionMatrix(/*IN*/double matrix[MAXCODES][MAXCODES],
      |                      ^~~~~~~~~~~~~~~~~~~~~~
[4/4] : && /usr/bin/x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -DOPENMP -fopenmp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DOPENMP -fopenmp    -rdynamic CMakeFiles/FastTree.dir/FastTree-2.1.11.c.o -o FastTree  -lm && :
FAILED: FastTree 
: && /usr/bin/x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -DOPENMP -fopenmp -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -DOPENMP -fopenmp    -rdynamic CMakeFiles/FastTree.dir/FastTree-2.1.11.c.o -o FastTree  -lm && :
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: CMakeFiles/FastTree.dir/FastTree-2.1.11.c.o: in function `vector_multiply_sum':
FastTree-2.1.11.c:(.text+0x2a5e0): undefined reference to `mm_sum'
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: CMakeFiles/FastTree.dir/FastTree-2.1.11.c.o: in function `vector_multiply3_sum':
FastTree-2.1.11.c:(.text+0x2a745): undefined reference to `mm_sum'
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: CMakeFiles/FastTree.dir/FastTree-2.1.11.c.o: in function `vector_dot_product_rot':
FastTree-2.1.11.c:(.text+0x2a8f5): undefined reference to `mm_sum'
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: FastTree-2.1.11.c:(.text+0x2a906): undefined reference to `mm_sum'
/usr/lib/gcc/x86_64-pc-linux-gnu/11.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: CMakeFiles/FastTree.dir/FastTree-2.1.11.c.o: in function `vector_sum':
FastTree-2.1.11.c:(.text+0x2a9df): undefined reference to `mm_sum'
collect2: error: ld returned 1 exit status
ninja: build stopped: subcommand failed.
 * ERROR: sci-biology/fasttree-2.1.11::gentoo failed (compile phase):
 *   ninja -v -j3 -l0 failed
 * 
 * Call stack:
 *     ebuild.sh, line  127:  Called src_compile
 *   environment, line 2085:  Called cmake_src_compile
 *   environment, line  781:  Called cmake_build
 *   environment, line  750:  Called eninja
 *   environment, line 1202:  Called die
 * The specific snippet of code:
 *       "$@" || die "${nonfatal_args[@]}" "${*} failed"
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/fasttree-2.1.11::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/fasttree-2.1.11::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:fasttree-2.1.11:20210608-033818.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/fasttree-2.1.11/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/fasttree-2.1.11/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11_build'
 * S: '/var/tmp/portage/sci-biology/fasttree-2.1.11/work/fasttree-2.1.11'