mlpack-3.4.2:20210530-165340.log

 * Package:    sci-libs/mlpack-3.4.2
 * Repository: science
 * Maintainer: gentoo@aisha.cc sci@gentoo.org
 * USE:        R abi_x86_64 amd64 elibc_glibc julia kernel_linux openmp python_single_target_python3_8 userland_GNU
 * FEATURES:   fakeroot network-sandbox preserve-libs sandbox splitdebug userpriv usersandbox
Auto packing the repository in background for optimum performance.
See "git help gc" for manual housekeeping.
[master a622a938] saving uncommitted changes in /etc prior to emerge run
 Author: Alessandro-Barbieri <lssndrbarbieri@gmail.com>
 1 file changed, 1 insertion(+)
 * /etc/portage/package.cflags/cflags -> */*: NOFFLAGS=1
 * /etc/portage/package.cflags/cflags -> */*: LDFLAGS-="-Wl,-z,now -Wl,-z,relro"
 * /etc/portage/package.cflags/cflags -> */*: USE_NONGNU="" +fPIE +fstack-protector-all +D_FORTIFY_SOURCE=2 
 * /etc/portage/package.cflags/cflags -> */*: NOLDADD=1
 * FEATURES='assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg candy cgroup clean-logs config-protect-if-modified distlocks ebuild-locks fakeroot fixlafiles ipc-sandbox merge-sync metadata-transfer mount-sandbox multilib-strict network-sandbox news parallel-fetch parallel-install pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-elog split-log splitdebug strict strict-keepdir unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr'
 * CFLAGS='-Os -pipe -march=native -fdiagnostics-color=always -fexceptions -Wformat -fstack-clash-protection -Wimplicit-function-declaration -Wno-error=implicit-function-declaration'
 * CXXFLAGS='-Os -pipe -march=native -fdiagnostics-color=always -fexceptions -Wformat -fstack-clash-protection'
 * CPPFLAGS='-D_GLIBCXX_ASSERTIONS'
 * FFLAGS='-Os -pipe -march=native -fdiagnostics-color=always'
 * FCFLAGS='-Os -pipe -march=native -fdiagnostics-color=always'
 * F77FLAGS='-Os -pipe -march=native -fdiagnostics-color=always'
 * LDFLAGS='-Wl,-O1 -Wl,--as-needed -Wl,--sort-common'
 * MAKEOPTS='-j12 -l15'
 * gcc (Gentoo Hardened 10.2.0-r5 p6) 10.2.0
 * g++ (Gentoo Hardened 10.2.0-r5 p6) 10.2.0
 * LLD 12.0.0 (compatible with GNU linkers)
 * Linux ALESSAND-F1E8 5.10.4-rt-rt22-x86_64 #3 SMP PREEMPT_RT Sun Apr 18 16:12:36 CEST 2021 x86_64 AMD Ryzen 5 3600 6-Core Processor AuthenticAMD GNU/Linux
0;emerge 18:53:43 1|1 mlpack (root@ALESSAND-F1E8)
kemerge 18:53:43 1|1 mlpack (root@ALESSAND-F1E8)\ * If you want to build matlab bindings then you
 * need to make sure that matlab has been installed
 * prior to building this package and it is available
 * in the standard locations to be found by
 * CMake, library finders, header includes and other
 * trinkets that are used while compiling.
 * Matlab will not be entertained as a first class
 * citizen until we have enough personnel
 * Using python3.8 to build
>>> Unpacking source...
>>> Unpacking mlpack-3.4.2.tar.gz to /var/tmp/portage/sci-libs/mlpack-3.4.2/work
>>> Source unpacked in /var/tmp/portage/sci-libs/mlpack-3.4.2/work
>>> Preparing source in /var/tmp/portage/sci-libs/mlpack-3.4.2/work/mlpack-3.4.2 ...
 * Working in BUILD_DIR: "/var/tmp/portage/sci-libs/mlpack-3.4.2/work/mlpack-3.4.2_build"
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-libs/mlpack-3.4.2/work/mlpack-3.4.2 ...
 * Working in BUILD_DIR: "/var/tmp/portage/sci-libs/mlpack-3.4.2/work/mlpack-3.4.2_build"
cmake -C /var/tmp/portage/sci-libs/mlpack-3.4.2/work/mlpack-3.4.2_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DDISABLE_DOWNLOADS=ON -DDOWNLOAD_ENSMALLEN=OFF -DDOWNLOAD_STB_IMAGE=OFF -DBUILD_WITH_COVERAGE=OFF -DBUILD_PYTHON_BINDINGS=ON -DBUILD_SHARED_LIBS=ON -DBUILD_CLI_EXECUTABLES=ON -DTEST_VERBOSE=no -DBUILD_TESTS=no -DDEBUG=no -DPROFILE=no -DARMA_EXTRA_DEBUG=no -DUSE_OPENMP=yes -DMATLAB_BINDINGS=no -DBUILD_GO_SHLIB=no -DBUILD_JULIA_BINDINGS=yes -DBUILD_GO_BINDINGS=no -DBUILD_R_BINDINGS=yes -DBUILD_MARKDOWN_BINDINGS=no -DMATHJAX=no -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-libs/mlpack-3.4.2/work/mlpack-3.4.2_build/gentoo_toolchain.cmake  /var/tmp/portage/sci-libs/mlpack-3.4.2/work/mlpack-3.4.2
loading initial cache file /var/tmp/portage/sci-libs/mlpack-3.4.2/work/mlpack-3.4.2_build/gentoo_common_config.cmake
-- The C compiler identification is GNU 10.2.0
-- The CXX compiler identification is GNU 10.2.0
-- 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
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- cotire 1.7.10 loaded.
-- 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 Armadillo: /usr/lib64/libarmadillo.so (found suitable version "10.3.0", minimum required is "8.400.0") 
-- Found StbImage: /usr/include/stb/  
-- Found Ensmallen: /usr/include (found suitable version "2.16.2", minimum required is "2.10.0") 
-- Found Boost: /usr/include (found suitable version "1.76.0", minimum required is "1.58") found components: unit_test_framework serialization 
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Found Git: /usr/bin/git (found version "2.31.1") 
-- Regenerating arma_config.hpp.
-- Found Julia: /usr/bin/julia (found suitable version "1.6.0", minimum required is "0.7.0") 
-- Not building Markdown bindings.
-- Found PythonInterp: /var/tmp/portage/sci-libs/mlpack-3.4.2/temp/python3.8/bin/python (found version "3.8.10") 
-- Found PY_distutils: /usr/lib/python3.8/distutils  
-- Found PY_Cython: /usr/lib/python3.8/site-packages/Cython  
-- Found PY_numpy: /usr/lib/python3.8/site-packages/numpy  
-- Found PY_pandas: /usr/lib/python3.8/site-packages/pandas  
-- Not building Go bindings.
-- Found R: /usr/bin/R (found suitable version "4.0.5", minimum required is "4.0") 
-- Could NOT find R_roxygen2 (missing: R_ROXYGEN2) 
-- Found R_Rcpp: /usr/lib64/R/site-library/Rcpp (found suitable version "1.0.6", minimum required is "0.12.12")  
-- Could NOT find R_RcppArmadillo (missing: R_RCPPARMADILLO) 
-- Could NOT find R_RcppEnsmallen (missing: R_RCPPENSMALLEN) 
-- Could NOT find R_BH (missing: R_BH) 
-- Could NOT find R_testthat (missing: R_TESTTHAT) 
CMake Error at src/mlpack/bindings/R/CMakeLists.txt:64 (message):
  Could not Build R Bindings, Following modules are not available:

      - roxygen2
      - RcppArmadillo
      - RcppEnsmallen
      - BH
      - testthat


-- Configuring incomplete, errors occurred!
See also "/var/tmp/portage/sci-libs/mlpack-3.4.2/work/mlpack-3.4.2_build/CMakeFiles/CMakeOutput.log".
See also "/var/tmp/portage/sci-libs/mlpack-3.4.2/work/mlpack-3.4.2_build/CMakeFiles/CMakeError.log".
 * ERROR: sci-libs/mlpack-3.4.2::science failed (configure phase):
 *   cmake failed
 * 
 * Call stack:
 *     ebuild.sh, line  127:  Called src_configure
 *   environment, line 4288:  Called cmake_src_configure
 *   environment, line 2622:  Called die
 * The specific snippet of code:
 *       "${CMAKE_BINARY}" "${cmakeargs[@]}" "${CMAKE_USE_DIR}" || die "cmake failed";
 * 
 * If you need support, post the output of `emerge --info '=sci-libs/mlpack-3.4.2::science'`,
 * the complete build log and the output of `emerge -pqv '=sci-libs/mlpack-3.4.2::science'`.
 * The complete build log is located at '/var/log/portage/build/sci-libs/mlpack-3.4.2:20210530-165340.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/mlpack-3.4.2/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-libs/mlpack-3.4.2/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-libs/mlpack-3.4.2/work/mlpack-3.4.2_build'
 * S: '/var/tmp/portage/sci-libs/mlpack-3.4.2/work/mlpack-3.4.2'