* Package: sci-biology/fasttree-2.1.11 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * 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'