build.log

build.log (text/plain), 9.90 KB, created by Martin Mokrejš on 2020-09-07 11:32:17 UTC

[32;01m * [39;49;00mPackage:    sci-biology/kallisto-0.46.1
[32;01m * [39;49;00mRepository: gentoo
[32;01m * [39;49;00mMaintainer: [e-mail]
[32;01m * [39;49;00mUSE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU
[32;01m * [39;49;00mFEATURES:   network-sandbox nostrip preserve-libs sandbox splitdebug userpriv usersandbox
>>> Unpacking source...
>>> Unpacking kallisto-0.46.1.tar.gz to /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work
>>> Source unpacked in /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work
>>> Preparing source in /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 ...
 [32;01m*[0m Hardcoded definition(s) removed in CMakeLists.txt:
 [32;01m*[0m      set(CMAKE_BUILD_TYPE "Release")
>>> Source prepared.
>>> Configuring source in /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 ...
>>> Working in BUILD_DIR: "/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build"
cmake -C /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_TOOLCHAIN_FILE=/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/gentoo_toolchain.cmake  /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1
loading initial cache file /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_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
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/lib64/libhdf5.so;/usr/lib64/libz.so;/usr/lib64/libdl.so;/usr/lib64/libm.so (found version "1.10.5")  
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") 
-- <<< Gentoo configuration >>>
Build type      Gentoo
Install path    /usr
Compiler flags:
C               -O2 -pipe -march=native -ftree-vectorize
C++             -O2 -pipe -march=native -ftree-vectorize
Linker flags:
Executable      -Wl,-O1 -Wl,--as-needed
Module          -Wl,-O1 -Wl,--as-needed
Shared          -Wl,-O1 -Wl,--as-needed

-- Configuring done
-- Generating done
-- Build files have been written to: /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build
>>> Source configured.
>>> Compiling source in /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 ...
>>> Working in BUILD_DIR: "/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build"
make -j1 VERBOSE=1 
/usr/bin/cmake -S/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 -B/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/CMakeFiles /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build//CMakeFiles/progress.marks
make  -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build'
make  -f CMakeFiles/htslib.dir/build.make CMakeFiles/htslib.dir/depend
make[2]: Entering directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build'
cd /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1 /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/CMakeFiles/htslib.dir/DependInfo.cmake --color=
Dependee "/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/CMakeFiles/htslib.dir/DependInfo.cmake" is newer than depender "/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/CMakeFiles/htslib.dir/depend.internal".
Dependee "/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build/CMakeFiles/htslib.dir/depend.internal".
[35m[1mScanning dependencies of target htslib[0m
make[2]: Leaving directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build'
make  -f CMakeFiles/htslib.dir/build.make CMakeFiles/htslib.dir/build
make[2]: Entering directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build'
[  3%] [34m[1mCreating directories for 'htslib'[0m
/usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib
/usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib
/usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib
/usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/tmp
/usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp
/usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src
/usr/bin/cmake -E make_directory /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp
/usr/bin/cmake -E touch /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-mkdir
[  6%] [34m[1mNo download step for 'htslib'[0m
/usr/bin/cmake -E echo_append
/usr/bin/cmake -E touch /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-download
[ 10%] [34m[1mNo update step for 'htslib'[0m
/usr/bin/cmake -E echo_append
/usr/bin/cmake -E touch /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-update
[ 13%] [34m[1mNo patch step for 'htslib'[0m
/usr/bin/cmake -E echo_append
/usr/bin/cmake -E touch /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-patch
[ 17%] [34m[1mPerforming configure step for 'htslib'[0m
cd /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib && autoheader && autoconf && /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/configure --prefix= --disable-bz2 --disable-lzma --disable-libcurl
configure.ac:26: warning: AC_INIT: not a literal: make3: Entering directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib'
configure.ac:26: 1.4.1
configure.ac:26: make3: Leaving directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib'
configure.ac:26: warning: AC_INIT: not a literal: make3: Entering directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib'
configure.ac:26: 1.4.1
configure.ac:26: make3: Leaving directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib'
/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/configure: line 4: 1.4.1: command not found
/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/configure: line 5: make3:: command not found
checking for gcc... gcc
checking whether the C compiler works... no
configure: error: in `/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib':
configure: error: C compiler cannot create executables
See `config.log' for more details
make[2]: *** [CMakeFiles/htslib.dir/build.make:127: /scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1/ext/htslib/src/htslib-stamp/htslib-configure] Error 77
make[2]: Leaving directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build'
make[1]: *** [CMakeFiles/Makefile2:117: CMakeFiles/htslib.dir/all] Error 2
make[1]: Leaving directory '/data/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build'
make: *** [Makefile:149: all] Error 2
 [31;01m*[0m ERROR: sci-biology/kallisto-0.46.1::gentoo failed (compile phase):
 [31;01m*[0m   emake failed
 [31;01m*[0m 
 [31;01m*[0m If you need support, post the output of `emerge --info '=sci-biology/kallisto-0.46.1::gentoo'`,
 [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-biology/kallisto-0.46.1::gentoo'`.
 [31;01m*[0m The complete build log is located at '/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/temp/build.log'.
 [31;01m*[0m The ebuild environment file is located at '/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/temp/environment'.
 [31;01m*[0m Working directory: '/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1_build'
 [31;01m*[0m S: '/scratch/var/tmp/portage/sci-biology/kallisto-0.46.1/work/kallisto-0.46.1'