starting phase `separate-from-pid1' build process now running as PID 18 phase `separate-from-pid1' succeeded after 0.0 seconds starting phase `set-SOURCE-DATE-EPOCH' phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds starting phase `set-paths' environment variable `PATH' set to `/gnu/store/fxagzk10plg9cj26vk1i599xml0pzrb8-cmake-minimal-3.24.2/bin:/gnu/store/9qcvl6rg6idqns39ra2jbm2kdz1rwicx-tar-1.34/bin:/gnu/store/5yv24flz74w2bjbpl4fy9n8brcnhhg0m-gzip-1.13/bin:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/bin:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/bin:/gnu/store/nq9418ayx64v9ahnwldvihlv4mddg64c-diffutils-3.10/bin:/gnu/store/drgzs1dic48b1rz090b39yw09wvjs0qa-patch-2.7.6/bin:/gnu/store/r4r6zdsgqc1wmxmy3lasxj1z1bg9ciqc-findutils-4.9.0/bin:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/bin:/gnu/store/swsr50qcmki242ka78gwvqyw821463rv-zstd-1.5.2/bin:/gnu/store/rjjzvnkk4cv57859wvjchgdsd0zrjnim-sed-4.8/bin:/gnu/store/iy4f97nh5mrn7q7miw2ypxnz4fp19k6k-grep-3.11/bin:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/bin:/gnu/store/3bg5qfsmjw6p7bh1xadarbaq246zis0d-coreutils-9.1/bin:/gnu/store/m3fxyhpqp774hi0kx8vmxibsqz99lqa7-make-4.4.1/bin:/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin:/gnu/store/mg6dkhs9w5a46b4nvdx1nmmdgbp0cfcd-ld-wrapper-0/bin:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/bin:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/bin:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/bin:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/sbin' environment variable `CMAKE_PREFIX_PATH' set to `/gnu/store/fxagzk10plg9cj26vk1i599xml0pzrb8-cmake-minimal-3.24.2/:/gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/:/gnu/store/9qcvl6rg6idqns39ra2jbm2kdz1rwicx-tar-1.34/:/gnu/store/5yv24flz74w2bjbpl4fy9n8brcnhhg0m-gzip-1.13/:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/:/gnu/store/nq9418ayx64v9ahnwldvihlv4mddg64c-diffutils-3.10/:/gnu/store/drgzs1dic48b1rz090b39yw09wvjs0qa-patch-2.7.6/:/gnu/store/r4r6zdsgqc1wmxmy3lasxj1z1bg9ciqc-findutils-4.9.0/:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/:/gnu/store/swsr50qcmki242ka78gwvqyw821463rv-zstd-1.5.2/:/gnu/store/rjjzvnkk4cv57859wvjchgdsd0zrjnim-sed-4.8/:/gnu/store/iy4f97nh5mrn7q7miw2ypxnz4fp19k6k-grep-3.11/:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/:/gnu/store/3bg5qfsmjw6p7bh1xadarbaq246zis0d-coreutils-9.1/:/gnu/store/m3fxyhpqp774hi0kx8vmxibsqz99lqa7-make-4.4.1/:/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/:/gnu/store/mg6dkhs9w5a46b4nvdx1nmmdgbp0cfcd-ld-wrapper-0/:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/:/gnu/store/hwzlxqp51gl75fni0vzyshsfbn062bhz-glibc-2.39-static/:/gnu/store/j0w4q2cbzjbg7s4yf9lip8dcbslbw3hi-linux-libre-headers-5.15.49/' environment variable `SSL_CERT_DIR' unset environment variable `SSL_CERT_FILE' unset environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/include:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/include:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/include:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/include:/gnu/store/m3fxyhpqp774hi0kx8vmxibsqz99lqa7-make-4.4.1/include:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/include:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/include:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/include:/gnu/store/j0w4q2cbzjbg7s4yf9lip8dcbslbw3hi-linux-libre-headers-5.15.49/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/include:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/include:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/include:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/include:/gnu/store/m3fxyhpqp774hi0kx8vmxibsqz99lqa7-make-4.4.1/include:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/include:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/include/c++:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/include:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/include:/gnu/store/j0w4q2cbzjbg7s4yf9lip8dcbslbw3hi-linux-libre-headers-5.15.49/include' environment variable `OBJC_INCLUDE_PATH' set to `/gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/include:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/include:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/include:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/include:/gnu/store/m3fxyhpqp774hi0kx8vmxibsqz99lqa7-make-4.4.1/include:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/include:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/include:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/include:/gnu/store/j0w4q2cbzjbg7s4yf9lip8dcbslbw3hi-linux-libre-headers-5.15.49/include' environment variable `OBJCPLUS_INCLUDE_PATH' set to `/gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/include:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/include:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/include:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/include:/gnu/store/m3fxyhpqp774hi0kx8vmxibsqz99lqa7-make-4.4.1/include:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/include:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/include/c++:/gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/include:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/include:/gnu/store/j0w4q2cbzjbg7s4yf9lip8dcbslbw3hi-linux-libre-headers-5.15.49/include' environment variable `LIBRARY_PATH' set to `/gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/lib:/gnu/store/pdsn19r59s8mbac1z7qj17738b0yng92-bzip2-1.0.8/lib:/gnu/store/z7r7qf08p6qgaw27qy86d8fgbknz8c0s-file-5.45/lib:/gnu/store/5wsbh52qwg83h2zap0pgic5fn985cq2z-gawk-5.3.0/lib:/gnu/store/ylddhkxf92aq06m28nzz671jbcmdw48j-xz-5.4.5/lib:/gnu/store/byb1pwq6pw3j8mmx3p7491jx7a6a03c5-binutils-2.41/lib:/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/lib:/gnu/store/hwzlxqp51gl75fni0vzyshsfbn062bhz-glibc-2.39-static/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/6w2vw5ms0i6l3yn7aqxlcv9g3sccl6qz-glibc-2.39/lib/locale' environment variable `TZDIR' unset phase `set-paths' succeeded after 0.0 seconds starting phase `install-locale' using 'C.UTF-8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' ngshmmalign-0.1.1/ ngshmmalign-0.1.1/aclocal.m4 ngshmmalign-0.1.1/._CMakeLists.txt ngshmmalign-0.1.1/CMakeLists.txt ngshmmalign-0.1.1/compile ngshmmalign-0.1.1/config.guess ngshmmalign-0.1.1/config.sub ngshmmalign-0.1.1/configure ngshmmalign-0.1.1/._configure.ac ngshmmalign-0.1.1/configure.ac ngshmmalign-0.1.1/depcomp ngshmmalign-0.1.1/install-sh ngshmmalign-0.1.1/._Makefile.am ngshmmalign-0.1.1/Makefile.am ngshmmalign-0.1.1/Makefile.in ngshmmalign-0.1.1/missing ngshmmalign-0.1.1/._README.md ngshmmalign-0.1.1/README.md ngshmmalign-0.1.1/src/ ngshmmalign-0.1.1/test-driver ngshmmalign-0.1.1/testsuite/ ngshmmalign-0.1.1/testsuite/._dna_array_compile_test.cpp ngshmmalign-0.1.1/testsuite/dna_array_compile_test.cpp ngshmmalign-0.1.1/testsuite/._hmmalign_forward_compile_test.cpp ngshmmalign-0.1.1/testsuite/hmmalign_forward_compile_test.cpp ngshmmalign-0.1.1/testsuite/._reference_compile_test.cpp ngshmmalign-0.1.1/testsuite/reference_compile_test.cpp ngshmmalign-0.1.1/testsuite/._type_caster_compile_test.cpp ngshmmalign-0.1.1/testsuite/type_caster_compile_test.cpp ngshmmalign-0.1.1/src/._aligner.hpp ngshmmalign-0.1.1/src/aligner.hpp ngshmmalign-0.1.1/src/._aligner_impl.hpp ngshmmalign-0.1.1/src/aligner_impl.hpp ngshmmalign-0.1.1/src/._debug.hpp ngshmmalign-0.1.1/src/debug.hpp ngshmmalign-0.1.1/src/._dna_array.hpp ngshmmalign-0.1.1/src/dna_array.hpp ngshmmalign-0.1.1/src/._fasta.hpp ngshmmalign-0.1.1/src/fasta.hpp ngshmmalign-0.1.1/src/._fastq.hpp ngshmmalign-0.1.1/src/fastq.hpp ngshmmalign-0.1.1/src/._hmmalign.hpp ngshmmalign-0.1.1/src/hmmalign.hpp ngshmmalign-0.1.1/src/._hmmalign_impl.hpp ngshmmalign-0.1.1/src/hmmalign_impl.hpp ngshmmalign-0.1.1/src/._index_impl.hpp ngshmmalign-0.1.1/src/index_impl.hpp ngshmmalign-0.1.1/src/main.cpp ngshmmalign-0.1.1/src/._reference.hpp ngshmmalign-0.1.1/src/reference.hpp ngshmmalign-0.1.1/src/._reference_impl.hpp ngshmmalign-0.1.1/src/reference_impl.hpp ngshmmalign-0.1.1/src/._utility_functions.hpp ngshmmalign-0.1.1/src/utility_functions.hpp phase `unpack' succeeded after 0.0 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.2 seconds starting phase `patch-source-shebangs' patch-shebang: ./compile: changing `/bin/sh' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/sh' patch-shebang: ./config.guess: changing `/bin/sh' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/sh' patch-shebang: ./config.sub: changing `/bin/sh' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/sh' patch-shebang: ./configure: changing `/bin/sh' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/sh' patch-shebang: ./depcomp: changing `/bin/sh' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/sh' patch-shebang: ./install-sh: changing `/bin/sh' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/sh' patch-shebang: ./missing: changing `/bin/sh' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/sh' patch-shebang: ./test-driver: changing `/bin/sh' to `/gnu/store/yxlaq640a0fn912h5pr74m5b8iz85rw1-bash-minimal-5.1.16/bin/sh' phase `patch-source-shebangs' succeeded after 0.0 seconds starting phase `configure' source directory: "/tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1" (relative from build: "../ngshmmalign-0.1.1") build directory: "/tmp/guix-build-ngshmmalign-0.1.1.drv-0/build" running 'cmake' with arguments ("../ngshmmalign-0.1.1" "-DCMAKE_BUILD_TYPE=RelWithDebInfo" "-DCMAKE_INSTALL_PREFIX=/gnu/store/ayfxd2d6k1hd0k7fq4m1k845f34x9vc2-ngshmmalign-0.1.1" "-DCMAKE_INSTALL_LIBDIR=lib" "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" "-DCMAKE_INSTALL_RPATH=/gnu/store/ayfxd2d6k1hd0k7fq4m1k845f34x9vc2-ngshmmalign-0.1.1/lib" "-DCMAKE_VERBOSE_MAKEFILE=ON") -- The CXX compiler identification is GNU 11.4.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at CMakeLists.txt:15 (cmake_policy): The OLD behavior for policy CMP0042 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found Boost: /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/lib/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.59.0") found components: filesystem iostreams program_options system -- The following OPTIONAL packages have been found: * OpenMP -- The following REQUIRED packages have been found: * boost_atomic (required version == 1.83.0) * boost_filesystem (required version == 1.83.0) * boost_iostreams (required version == 1.83.0) * boost_program_options (required version == 1.83.0) * boost_headers (required version == 1.83.0) * boost_system (required version == 1.83.0) * Boost (required version >= 1.59.0) -- Configuring done -- Generating done -- Build files have been written to: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/build phase `configure' succeeded after 1.1 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `build' /gnu/store/fxagzk10plg9cj26vk1i599xml0pzrb8-cmake-minimal-3.24.2/bin/cmake -S/tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1 -B/tmp/guix-build-ngshmmalign-0.1.1.drv-0/build --check-build-system CMakeFiles/Makefile.cmake 0 /gnu/store/fxagzk10plg9cj26vk1i599xml0pzrb8-cmake-minimal-3.24.2/bin/cmake -E cmake_progress_start /tmp/guix-build-ngshmmalign-0.1.1.drv-0/build/CMakeFiles /tmp/guix-build-ngshmmalign-0.1.1.drv-0/build//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/tmp/guix-build-ngshmmalign-0.1.1.drv-0/build' make -f CMakeFiles/ngshmmalign.dir/build.make CMakeFiles/ngshmmalign.dir/depend make[2]: Entering directory '/tmp/guix-build-ngshmmalign-0.1.1.drv-0/build' cd /tmp/guix-build-ngshmmalign-0.1.1.drv-0/build && /gnu/store/fxagzk10plg9cj26vk1i599xml0pzrb8-cmake-minimal-3.24.2/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1 /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1 /tmp/guix-build-ngshmmalign-0.1.1.drv-0/build /tmp/guix-build-ngshmmalign-0.1.1.drv-0/build /tmp/guix-build-ngshmmalign-0.1.1.drv-0/build/CMakeFiles/ngshmmalign.dir/DependInfo.cmake --color= make[2]: Leaving directory '/tmp/guix-build-ngshmmalign-0.1.1.drv-0/build' make -f CMakeFiles/ngshmmalign.dir/build.make CMakeFiles/ngshmmalign.dir/build make[2]: Entering directory '/tmp/guix-build-ngshmmalign-0.1.1.drv-0/build' [ 50%] Building CXX object CMakeFiles/ngshmmalign.dir/src/main.cpp.o /gnu/store/bqxrv6awpk0y1k67c040qm28imk7xds1-gcc-11.4.0/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPACKAGE_NAME=\"ngshmmalign\" -DPACKAGE_VERSION=\"0.1.1\" -fopenmp -O2 -g -DNDEBUG -std=c++11 -MD -MT CMakeFiles/ngshmmalign.dir/src/main.cpp.o -MF CMakeFiles/ngshmmalign.dir/src/main.cpp.o.d -o CMakeFiles/ngshmmalign.dir/src/main.cpp.o -c /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp In file included from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:41, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner.hpp:236, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:33: /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/progress.hpp:23:3: error: #error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.) 23 | # error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.) | ^~~~~ In file included from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/progress.hpp:29, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:41, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner.hpp:236, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:33: /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/timer.hpp:21:3: error: #error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.) 21 | # error This header is deprecated and will be removed. (You can define BOOST_TIMER_ENABLE_DEPRECATED to suppress this error.) | ^~~~~ In file included from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/reference.hpp:43, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/hmmalign.hpp:36, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner.hpp:32, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:33: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/utility_functions.hpp: In function ‘char {anonymous}::rev_comp_char(char)’: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/utility_functions.hpp:95:25: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 95 | throw std::invalid_argument(std::string(1, c) + std::string(" is an unknown base! Exiting...\n")); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/system/detail/requires_cxx11.hpp:9, from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/system/detail/config.hpp:11, from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/system/detail/error_category.hpp:13, from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/system/error_category.hpp:10, from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem/detail/path_traits.hpp:25, from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem/path.hpp:21, from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem.hpp:16, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:30: /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/progress.hpp: At global scope: /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/progress.hpp:27:1: note: ‘#pragma message: This header is deprecated. Use the facilities in or instead.’ 27 | BOOST_HEADER_DEPRECATED( "the facilities in or " ) | ^~~~~~~~~~~~~~~~~~~~~~~ /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/timer.hpp:25:1: note: ‘#pragma message: This header is deprecated. Use the facilities in instead.’ 25 | BOOST_HEADER_DEPRECATED( "the facilities in " ) | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner.hpp:236, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:33: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp: In member function ‘void {anonymous}::single_end_aligner::load_parameters(const string&, {anonymous}::background_rates&, bool)’: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:334:48: warning: ‘std::string boost::filesystem::extension(const boost::filesystem::path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 334 | std::string ref_ext(boost::filesystem::extension(input_file)); | ^~~~~~~~~ In file included from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem.hpp:21, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:30: /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner.hpp:236, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:33: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:334:57: warning: ‘std::string boost::filesystem::extension(const boost::filesystem::path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 334 | std::string ref_ext(boost::filesystem::extension(input_file)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem.hpp:21, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:30: /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner.hpp:236, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:33: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp: In instantiation of ‘void {anonymous}::single_end_aligner::load_parameters(const string&, {anonymous}::background_rates&, bool) [with T = int; std::string = std::__cxx11::basic_string]’: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:255:30: required from here /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:334:57: warning: ‘std::string boost::filesystem::extension(const boost::filesystem::path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 334 | std::string ref_ext(boost::filesystem::extension(input_file)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem.hpp:21, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:30: /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner.hpp:236, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:33: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:334:57: warning: ‘std::string boost::filesystem::extension(const boost::filesystem::path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 334 | std::string ref_ext(boost::filesystem::extension(input_file)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem.hpp:21, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:30: /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner.hpp:236, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:33: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:334:57: warning: ‘std::string boost::filesystem::extension(const boost::filesystem::path&)’ is deprecated: Use path::extension() instead [-Wdeprecated-declarations] 334 | std::string ref_ext(boost::filesystem::extension(input_file)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem.hpp:21, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:30: /gnu/store/brk9q1fakasvrwqb8lkipwhhm96s36bx-boost-1.83.0/include/boost/filesystem/convenience.hpp:29:20: note: declared here 29 | inline std::string extension(const path& p) | ^~~~~~~~~ In file included from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/hmmalign.hpp:35, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner.hpp:32, from /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:33: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp: In instantiation of ‘const value_type& {anonymous}::dna_array::operator[](char) const [with T = double; long unsigned int N = 5; {anonymous}::dna_array::const_reference = const double&]’: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp:182:73: required from ‘{anonymous}::dna_array::value_type& {anonymous}::dna_array::operator[](char) [with T = double; long unsigned int N = 5; {anonymous}::dna_array::reference = double&]’ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:618:36: required from here /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp:152:41: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 152 | throw std::invalid_argument(std::string(1, base) + std::string(" is an unknown base! Exiting...\n")); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp:170:41: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 170 | throw std::invalid_argument(std::string(1, base) + std::string(" is an unknown base! Exiting...\n")); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp: In instantiation of ‘const value_type& {anonymous}::dna_array::operator[](char) const [with T = bool; long unsigned int N = 5; {anonymous}::dna_array::const_reference = const bool&]’: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:1259:71: required from ‘void {anonymous}::single_end_aligner::post_alignment_processing(bool, uint64_t, double, double, bool) [with T = int; uint64_t = long unsigned int]’ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:267:40: required from here /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp:152:41: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 152 | throw std::invalid_argument(std::string(1, base) + std::string(" is an unknown base! Exiting...\n")); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp:170:41: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 170 | throw std::invalid_argument(std::string(1, base) + std::string(" is an unknown base! Exiting...\n")); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp: In instantiation of ‘const value_type& {anonymous}::dna_array::operator[](char) const [with T = int; long unsigned int N = 2; {anonymous}::dna_array::const_reference = const int&]’: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/hmmalign_impl.hpp:292:58: required from ‘static T {anonymous}::hmmalign::viterbi(const {anonymous}::reference_genome&, const string_ref&, uint32_t, uint32_t, std::vector<{anonymous}::minimal_alignment>&) [with T = int; boost::string_ref = boost::basic_string_ref >; uint32_t = unsigned int]’ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:987:33: required from ‘void {anonymous}::single_end_aligner::perform_alignment_impl(bool, bool) [with T = int]’ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:790:2: required from ‘void {anonymous}::single_end_aligner::estimate_parameters(const string&, const string&, const {anonymous}::background_rates&, uint64_t, bool, bool, bool) [with T = int; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]’ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:260:35: required from here /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp:152:41: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 152 | throw std::invalid_argument(std::string(1, base) + std::string(" is an unknown base! Exiting...\n")); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp:170:41: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 170 | throw std::invalid_argument(std::string(1, base) + std::string(" is an unknown base! Exiting...\n")); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp: In instantiation of ‘const value_type& {anonymous}::dna_array::operator[](char) const [with T = int; long unsigned int N = 5; {anonymous}::dna_array::const_reference = const int&]’: /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/hmmalign_impl.hpp:309:75: required from ‘static T {anonymous}::hmmalign::viterbi(const {anonymous}::reference_genome&, const string_ref&, uint32_t, uint32_t, std::vector<{anonymous}::minimal_alignment>&) [with T = int; boost::string_ref = boost::basic_string_ref >; uint32_t = unsigned int]’ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:987:33: required from ‘void {anonymous}::single_end_aligner::perform_alignment_impl(bool, bool) [with T = int]’ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/aligner_impl.hpp:790:2: required from ‘void {anonymous}::single_end_aligner::estimate_parameters(const string&, const string&, const {anonymous}::background_rates&, uint64_t, bool, bool, bool) [with T = int; std::string = std::__cxx11::basic_string; uint64_t = long unsigned int]’ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/main.cpp:260:35: required from here /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp:152:41: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 152 | throw std::invalid_argument(std::string(1, base) + std::string(" is an unknown base! Exiting...\n")); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /tmp/guix-build-ngshmmalign-0.1.1.drv-0/ngshmmalign-0.1.1/src/dna_array.hpp:170:41: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 170 | throw std::invalid_argument(std::string(1, base) + std::string(" is an unknown base! Exiting...\n")); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [CMakeFiles/ngshmmalign.dir/build.make:79: CMakeFiles/ngshmmalign.dir/src/main.cpp.o] Error 1 make[2]: Leaving directory '/tmp/guix-build-ngshmmalign-0.1.1.drv-0/build' make[1]: *** [CMakeFiles/Makefile2:86: CMakeFiles/ngshmmalign.dir/all] Error 2 make[1]: Leaving directory '/tmp/guix-build-ngshmmalign-0.1.1.drv-0/build' make: *** [Makefile:139: all] Error 2 error: in phase 'build': uncaught exception: %exception #<&invoke-error program: "make" arguments: ("-j" "64") exit-status: 2 term-signal: #f stop-signal: #f> phase `build' failed after 7.4 seconds command "make" "-j" "64" failed with status 2 build process 18 exited with status 256