=> Bootstrap dependency digest>=20211023: found digest-20211023 => Checksum BLAKE2s OK for kallisto-0.46.1.tar.gz => Checksum SHA512 OK for kallisto-0.46.1.tar.gz ===> Installing dependencies for kallisto-0.46.1 => Tool dependency autoconf>=2.50: found autoconf-2.71nb1 => Tool dependency cmake>=2.8.1nb1: found cmake-3.21.4 => Tool dependency gmake>=3.81: found gmake-4.3nb2 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Build dependency cwrappers>=20150314: found cwrappers-20180325 => Full dependency hdf5>=1.8.11: found hdf5-1.10.7 => Full dependency libaec>=1.0.4: found libaec-1.0.4 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Overriding tools for kallisto-0.46.1 ===> Extracting for kallisto-0.46.1 /bin/cp /amd/pkgsrc/CHROOT/P/pkgsrc/biology/kallisto/files/kallisto-test /tmp/biology/kallisto/work/kallisto-0.46.1 ===> Patching for kallisto-0.46.1 ===> Creating toolchain wrappers for kallisto-0.46.1 ===> Configuring for kallisto-0.46.1 => Substituting "test" in kallisto-test => Fixing CMAKE_MODULE_PATH in CMakeLists.txt INFO: [subst.mk:cmake] Nothing changed in "CMakeLists.txt". => Checking for portability problems in extracted files -- The C compiler identification is GNU 7.4.0 -- The CXX compiler identification is GNU 7.4.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /tmp/biology/kallisto/work/.cwrapper/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: /tmp/biology/kallisto/work/.cwrapper/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done shared build -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found HDF5: /usr/pkg/lib/libhdf5.so;/usr/pkg/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libm.so (found version "1.10.7") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.10") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: USE_HDF5 -- Build files have been written to: /tmp/biology/kallisto/work/kallisto-0.46.1 => Rewrite cmake Dependencies files