Running phase: unpackPhase unpacking source archive /nix/store/bkdv6ksy8f85ik8d4b623qvdza6v3ang-source source root is source Running phase: patchPhase Running phase: updateAutotoolsGnuConfigScriptsPhase Running phase: configurePhase fixing cmake files... cmake flags: -DCMAKE_FIND_USE_SYSTEM_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=OFF -DCMAKE_INSTALL_LOCALEDIR=/nix/store/rkcdaclvb6h5vnd3ivi2pi438mh206b7-mni_autoreg-unstable-2022-05-20/share/locale -DCMAKE_INSTALL_LIBEXECDIR=/nix/store/rkcdaclvb6h5vnd3ivi2pi438mh206b7-mni_autoreg-unstable-2022-05-20/libexec -DCMAKE_INSTALL_LIBDIR=/nix/store/rkcdaclvb6h5vnd3ivi2pi438mh206b7-mni_autoreg-unstable-2022-05-20/lib -DCMAKE_INSTALL_DOCDIR=/nix/store/rkcdaclvb6h5vnd3ivi2pi438mh206b7-mni_autoreg-unstable-2022-05-20/share/doc/mni_autoreg -DCMAKE_INSTALL_INFODIR=/nix/store/rkcdaclvb6h5vnd3ivi2pi438mh206b7-mni_autoreg-unstable-2022-05-20/share/info -DCMAKE_INSTALL_MANDIR=/nix/store/rkcdaclvb6h5vnd3ivi2pi438mh206b7-mni_autoreg-unstable-2022-05-20/share/man -DCMAKE_INSTALL_INCLUDEDIR=/nix/store/rkcdaclvb6h5vnd3ivi2pi438mh206b7-mni_autoreg-unstable-2022-05-20/include -DCMAKE_INSTALL_SBINDIR=/nix/store/rkcdaclvb6h5vnd3ivi2pi438mh206b7-mni_autoreg-unstable-2022-05-20/sbin -DCMAKE_INSTALL_BINDIR=/nix/store/rkcdaclvb6h5vnd3ivi2pi438mh206b7-mni_autoreg-unstable-2022-05-20/bin -DCMAKE_INSTALL_NAME_DIR=/nix/store/rkcdaclvb6h5vnd3ivi2pi438mh206b7-mni_autoreg-unstable-2022-05-20/lib -DCMAKE_POLICY_DEFAULT_CMP0025=NEW -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_STRIP=/nix/store/ii75mhh7sxl11167m1b86p0qrjsjyjmd-gcc-wrapper-14-20241116/bin/strip -DCMAKE_RANLIB=/nix/store/ii75mhh7sxl11167m1b86p0qrjsjyjmd-gcc-wrapper-14-20241116/bin/ranlib -DCMAKE_AR=/nix/store/ii75mhh7sxl11167m1b86p0qrjsjyjmd-gcc-wrapper-14-20241116/bin/ar -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_INSTALL_PREFIX=/nix/store/rkcdaclvb6h5vnd3ivi2pi438mh206b7-mni_autoreg-unstable-2022-05-20 -DLIBMINC_DIR=/nix/store/9fq6khrmsv8waizzawmm80l564ngyp4p-libminc-2.4.06/lib/cmake CMake Deprecation Warning at CMakeLists.txt:5 (CMAKE_MINIMUM_REQUIRED): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.1 -- The CXX compiler identification is GNU 14.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /nix/store/ii75mhh7sxl11167m1b86p0qrjsjyjmd-gcc-wrapper-14-20241116/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /nix/store/ii75mhh7sxl11167m1b86p0qrjsjyjmd-gcc-wrapper-14-20241116/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Perl: /nix/store/l4x3hcysvp19pxv9fsy7k8gwqzr9mln0-perl-5.40.0/bin/perl (found version "5.40.0") CMake Deprecation Warning at CMakeLists.txt:40 (CMAKE_POLICY): The OLD behavior for policy CMP0026 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. -- Looking for include file float.h -- Looking for include file float.h - found -- Looking for include file limits.h -- Looking for include file limits.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file sys/types.h -- Looking for include file sys/types.h - found -- Looking for include file values.h -- Looking for include file values.h - found -- Looking for include file unistd.h -- Looking for include file unistd.h - found -- Looking for include file memory.h -- Looking for include file memory.h - found -- Looking for include file math.h -- Looking for include file math.h - found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file stdlib.h -- Looking for include file stdlib.h - found -- Looking for include file inttypes.h -- Looking for include file inttypes.h - found -- Looking for include file string.h -- Looking for include file string.h - found -- Looking for include file strings.h -- Looking for include file strings.h - found -- Configuring done (2.3s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_BINDIR CMAKE_INSTALL_DOCDIR CMAKE_INSTALL_INCLUDEDIR CMAKE_INSTALL_INFODIR CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LIBEXECDIR CMAKE_INSTALL_LOCALEDIR CMAKE_INSTALL_MANDIR CMAKE_INSTALL_SBINDIR -- Build files have been written to: /build/source/build cmake: enabled parallel building cmake: enabled parallel installing Running phase: buildPhase build flags: -j2 SHELL=/nix/store/11ciq72n4fdv8rw6wgjgasfv4mjs1jrw-bash-5.2p37/bin/bash [ 1%] Building C object minctracc/CMakeFiles/_minctracc.dir/Files/read_data_files.c.o [ 2%] Building C object Proglib/CMakeFiles/Proglib.dir/print_error.c.o [ 4%] Building C object Proglib/CMakeFiles/Proglib.dir/print_version.c.o [ 5%] Building C object Proglib/CMakeFiles/Proglib.dir/get_history.c.o [ 7%] Building C object minctracc/CMakeFiles/_minctracc.dir/Optimize/def_obj_functions.c.o [ 8%] Linking C static library libProglib.a [ 8%] Built target Proglib [ 10%] Building C object minctracc/CMakeFiles/crispify.dir/Extra_progs/crispify.c.o [ 11%] Building C object minctracc/CMakeFiles/_minctracc.dir/Optimize/extras.c.o /build/source/minctracc/Extra_progs/crispify.c: In function 'load_volume': /build/source/minctracc/Extra_progs/crispify.c:295:34: error: implicit declaration of function 'volume_size_is_ok' [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wimplicit-function-declaration-Wimplicit-function-declaration8;;] 295 | if ( fuzzy_vol_index >= 1 && !volume_size_is_ok( *volume )){ | ^~~~~~~~~~~~~~~~~ /build/source/minctracc/Extra_progs/crispify.c: In function 'scan_fuzzy_volumes': /build/source/minctracc/Extra_progs/crispify.c:340:7: error: implicit declaration of function 'write'; did you mean 'fwrite'? [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wimplicit-function-declaration-Wimplicit-function-declaration8;;] 340 | write(2,"*",1); | ^~~~~ | fwrite make[2]: *** [minctracc/CMakeFiles/crispify.dir/build.make:79: minctracc/CMakeFiles/crispify.dir/Extra_progs/crispify.c.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:663: minctracc/CMakeFiles/crispify.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... [ 13%] Building C object minctracc/CMakeFiles/_minctracc.dir/Optimize/sub_lattice.c.o [ 14%] Building C object minctracc/CMakeFiles/_minctracc.dir/Optimize/amoeba.c.o [ 16%] Building C object minctracc/CMakeFiles/_minctracc.dir/Optimize/vox_space.c.o [ 17%] Building C object minctracc/CMakeFiles/_minctracc.dir/Optimize/objectives.c.o [ 19%] Building C object minctracc/CMakeFiles/_minctracc.dir/Optimize/optimize.c.o /build/source/minctracc/Optimize/optimize.c: In function 'replace_volume_data_with_ubyte': /build/source/minctracc/Optimize/optimize.c:1130:3: error: implicit declaration of function 'get_volume_minimum_maximum_real_value' [8;;https://gcc.gnu.org/onlinedocs/gcc-14.2.0/gcc/Warning-Options.html#index-Wimplicit-function-declaration-Wimplicit-function-declaration8;;] 1130 | get_volume_minimum_maximum_real_value(data, &min, &max); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [minctracc/CMakeFiles/_minctracc.dir/build.make:177: minctracc/CMakeFiles/_minctracc.dir/Optimize/optimize.c.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[1]: *** [CMakeFiles/Makefile2:471: minctracc/CMakeFiles/_minctracc.dir/all] Error 2 make: *** [Makefile:166: all] Error 2