sci-chemistry:dssp-4.4.0:20230720-093426.log

sci-chemistry:dssp-4.4.0:20230720-093426.log (text/plain), 6.77 KB, created by Toralf Förster on 2023-07-20 11:39:01 UTC

 * Package:    sci-chemistry/dssp-4.4.0:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking dssp-4.4.0.tar.gz to /var/tmp/portage/sci-chemistry/dssp-4.4.0/work
>>> Source unpacked in /var/tmp/portage/sci-chemistry/dssp-4.4.0/work
>>> Preparing source in /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0 ...
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0_build"
 * Hardcoded definition(s) removed in CMakeLists.txt:
 *  		set(CMAKE_INSTALL_PREFIX "$ENV{CCP4}")
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0 ...
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0_build"
cmake -C /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0_build/gentoo_common_config.cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr -DBUILD_WEBSERVER=OFF -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_TOOLCHAIN_FILE=/var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0_build/gentoo_toolchain.cmake /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0
loading initial cache file /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0_build/gentoo_common_config.cmake
-- The CXX compiler identification is GNU 13.1.1
-- 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
CMake Warning (dev) at CMakeLists.txt:37 (include):
  Policy CMP0145 is not set: The Dart and FindDart modules are removed.  Run
  "cmake --help-policy CMP0145" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at /usr/share/cmake/Modules/Dart.cmake:47 (message):
  Policy CMP0145 is not set: The Dart and FindDart modules are removed.  Run
  "cmake --help-policy CMP0145" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.
Call Stack (most recent call first):
  CMakeLists.txt:37 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Looking for C++ include filesystem
-- Looking for C++ include filesystem - found
-- Performing Test CXX_FILESYSTEM_NO_LINK_NEEDED
-- Performing Test CXX_FILESYSTEM_NO_LINK_NEEDED - Success
-- Not using resources since mrc was not found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.13")  
-- <<< Gentoo configuration >>>
Build type      RelWithDebInfo
Install path    /usr
Compiler flags:
C               
C++             -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers
Linker flags:
Executable      -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0
Module          -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0
Shared          -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0

-- Configuring done (1.9s)
-- Generating done (0.0s)
-- Build files have been written to: /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0_build
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0 ...
 * Source directory (CMAKE_USE_DIR): "/var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0"
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0_build"
ninja -v -j5 -l0
[1/9] cd /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0/doc && /usr/bin/pandoc -o mkdssp.html mkdssp.1
[2/9] cd /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0/doc && /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0_build/pandoc-md.sh
[3/9] cd /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0/doc && /usr/bin/pandoc -o mkdssp.pdf mkdssp.1 -t html
FAILED: /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0/doc/mkdssp.pdf 
cd /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0/doc && /usr/bin/pandoc -o mkdssp.pdf mkdssp.1 -t html
wkhtmltopdf not found. Please select a different --pdf-engine or install wkhtmltopdf
[4/9] /usr/bin/x86_64-pc-linux-gnu-g++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Ddssp_EXPORTS -I/var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0/include  -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/dssp.dir/src/dssp-io.cpp.o -MF CMakeFiles/dssp.dir/src/dssp-io.cpp.o.d -o CMakeFiles/dssp.dir/src/dssp-io.cpp.o -c /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0/src/dssp-io.cpp
[5/9] /usr/bin/x86_64-pc-linux-gnu-g++ -DCACHE_DIR=\"/var/cache/libcifpp\" -DDATA_DIR=\"/usr/share/libcifpp\" -Ddssp_EXPORTS -I/var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0/include  -O2 -pipe -march=native -fno-diagnostics-color -Wall -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=gnu++17 -fPIC -fno-diagnostics-color -MD -MT CMakeFiles/dssp.dir/src/dssp.cpp.o -MF CMakeFiles/dssp.dir/src/dssp.cpp.o.d -o CMakeFiles/dssp.dir/src/dssp.cpp.o -c /var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0/src/dssp.cpp
ninja: build stopped: subcommand failed.
 * ERROR: sci-chemistry/dssp-4.4.0::gentoo failed (compile phase):
 *   ninja -v -j5 -l0 failed
 * 
 * Call stack:
 *     ebuild.sh, line  136:  Called src_compile
 *   environment, line 2165:  Called cmake_src_compile
 *   environment, line  892:  Called cmake_build
 *   environment, line  858:  Called eninja
 *   environment, line 1325:  Called die
 * The specific snippet of code:
 *       "$@" || die -n "${*} failed"
 * 
 * If you need support, post the output of `emerge --info '=sci-chemistry/dssp-4.4.0::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-chemistry/dssp-4.4.0::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-chemistry:dssp-4.4.0:20230720-093426.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/dssp-4.4.0/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/dssp-4.4.0/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0_build'
 * S: '/var/tmp/portage/sci-chemistry/dssp-4.4.0/work/dssp-4.4.0'