1. * Package: sci-libs/openmm-4.1.1
2. * Repository: gentoo
3. * Maintainer: ottxor@gentoo.org sci-chemistry@gentoo.org
4. * USE: amd64 elibc_glibc kernel_linux userland_GNU
5. * FEATURES: sandbox test userpriv usersandbox
6. Installed LAPACK for library directory lib64
7. [1] reference *
8. Installed BLAS for library directory lib64
9. [1] reference *
10. Installed CBLAS for library directory lib64
11. [1] gsl
12. [2] reference *
13. >>> Unpacking source...
14. >>> Unpacking OpenMM4.1.1-Source.zip to /tmp/portage/sci-libs/openmm-4.1.1/work
15. >>> Source unpacked in /tmp/portage/sci-libs/openmm-4.1.1/work
16. >>> Preparing source in /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source ...
17. >>> Source prepared.
18. >>> Configuring source in /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source ...
19. >>> Working in BUILD_DIR: "/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build"
20. cmake --no-warn-unused-cli -C /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/gentoo_common_config.cmake -G Unix Makefiles -DCMAKE_INSTALL_PREFIX=/usr -DOPENMM_BUILD_CUDA_LIB=OFF -DOPENMM_BUILD_OPENCL_LIB=OFF -DCUDA_BUILD_CUBIN=ON -DOPENMM_BUILD_RPMD_PLUGIN=OFF -DOPENMM_BUILD_PYTHON_WRAPPERS=OFF -DCMAKE_BUILD_TYPE=Gentoo -DCMAKE_INSTALL_DO_STRIP=OFF -DCMAKE_USER_MAKE_RULES_OVERRIDE=/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/gentoo_rules.cmake /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source
21. Not searching for unused variables given on the command line.
22. loading initial cache file /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/gentoo_common_config.cmake
23. Re-run cmake no build system arguments
24. -- The C compiler identification is GNU 4.7.2
25. -- The CXX compiler identification is GNU 4.7.2
26. -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc
27. -- Check for working C compiler: /usr/bin/x86_64-pc-linux-gnu-gcc -- works
28. -- Detecting C compiler ABI info
29. -- Detecting C compiler ABI info - done
30. -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++
31. -- Check for working CXX compiler: /usr/bin/x86_64-pc-linux-gnu-g++ -- works
32. -- Detecting CXX compiler ABI info
33. -- Detecting CXX compiler ABI info - done
34. -- Found Java: /etc/java-config-2/current-system-vm/bin/java (found version "1.7.0.09")
35. -- Found OPENCL: /usr/lib64/libOpenCL.so
36. -- <<< Gentoo configuration >>>
37. Build type Gentoo
38. Install path /usr
39. Compiler flags:
40. C -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches
41. C++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches
42. Linker flags:
43. Executable -Wl,-O1 -Wl,--as-needed
44. Module -Wl,-O1 -Wl,--as-needed
45. Shared -Wl,-O1 -Wl,--as-needed
47. -- Configuring done
48. -- Generating done
49. -- Build files have been written to: /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build
50. >>> Source configured.
51. >>> Compiling source in /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source ...
52. >>> Working in BUILD_DIR: "/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build"
53. make -j24 VERBOSE=1
54. /usr/bin/cmake -H/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source -B/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build --check-build-system CMakeFiles/Makefile.cmake 0
55. /usr/bin/cmake -E cmake_progress_start /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/CMakeFiles /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/CMakeFiles/progress.marks
56. make -f CMakeFiles/Makefile2 all
57. make[1]: Entering directory `/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build'
58. make -f wrappers/CMakeFiles/ApiWrappers.dir/build.make wrappers/CMakeFiles/ApiWrappers.dir/depend
59. make -f plugins/amoeba/wrappers/CMakeFiles/AmoebaApiWrappers.dir/build.make plugins/amoeba/wrappers/CMakeFiles/AmoebaApiWrappers.dir/depend
60. make[2]: Entering directory `/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build'
61. cd /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/wrappers /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/wrappers /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/wrappers/CMakeFiles/ApiWrappers.dir/DependInfo.cmake
62. make[2]: Entering directory `/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build'
63. cd /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/plugins/amoeba/wrappers /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/plugins/amoeba/wrappers /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/plugins/amoeba/wrappers/CMakeFiles/AmoebaApiWrappers.dir/DependInfo.cmake
64. Dependee "/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/wrappers/CMakeFiles/ApiWrappers.dir/DependInfo.cmake" is newer than depender "/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/wrappers/CMakeFiles/ApiWrappers.dir/depend.internal".
65. Dependee "/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/wrappers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/wrappers/CMakeFiles/ApiWrappers.dir/depend.internal".
66. Scanning dependencies of target ApiWrappers
67. Dependee "/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/plugins/amoeba/wrappers/CMakeFiles/AmoebaApiWrappers.dir/DependInfo.cmake" is newer than depender "/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/plugins/amoeba/wrappers/CMakeFiles/AmoebaApiWrappers.dir/depend.internal".
68. Dependee "/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/plugins/amoeba/wrappers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/plugins/amoeba/wrappers/CMakeFiles/AmoebaApiWrappers.dir/depend.internal".
69. Scanning dependencies of target AmoebaApiWrappers
70. make[2]: Leaving directory `/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build'
71. make -f wrappers/CMakeFiles/ApiWrappers.dir/build.make wrappers/CMakeFiles/ApiWrappers.dir/build
72. make[2]: Leaving directory `/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build'
73. make -f plugins/amoeba/wrappers/CMakeFiles/AmoebaApiWrappers.dir/build.make plugins/amoeba/wrappers/CMakeFiles/AmoebaApiWrappers.dir/build
74. make[2]: Entering directory `/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build'
75. /usr/bin/cmake -E cmake_progress_report /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/CMakeFiles
76. make[2]: Entering directory `/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build'
77. /usr/bin/cmake -E cmake_progress_report /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/CMakeFiles 1
78. [ 0%] [ 1%] Generating OpenMMApi.xml
79. cd /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/wrappers && /usr/bin/gccxml -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/./include -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/./include/openmm -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/./include/openmm/internal -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/openmmapi/include -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/openmmapi/include/openmm -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/openmmapi/include/openmm/internal -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/olla/include -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/olla/include/openmm -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/olla/include/openmm/internal -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/jama/include -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/jama/include/openmm -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/jama/include/openmm/internal -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/quern/include -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/quern/include/openmm -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/quern/include/openmm/internal -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/lepton/include -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/lepton/include/openmm -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/lepton/include/openmm/internal -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/sfmt/include -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/sfmt/include/openmm -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/sfmt/include/openmm/internal -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/lbfgs/include -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/lbfgs/include/openmm -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/lbfgs/include/openmm/internal -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/platforms/reference/include -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/platforms/reference/include/openmm -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/platforms/reference/include/openmm/internal -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/validate/include -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/validate/include/openmm -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/libraries/validate/include/openmm/internal /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/openmmapi/include/OpenMM.h -fxml=OpenMMApi.xml
80. Generating AmoebaOpenMMApi.xml
81. cd /tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build/plugins/amoeba/wrappers && /usr/bin/gccxml -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/openmmapi/include -I/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/olla/include /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/plugins/amoeba/openmmapi/include/OpenMMAmoeba.h -fxml=AmoebaOpenMMApi.xml
82. In file included from /usr/include/endian.h:60,
83. from /usr/include/ctype.h:40,
84. from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/include/g++-v4/cctype:44,
85. from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/include/g++-v4/bits/localefwd.h:44,
86. from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/include/g++-v4/string:45,
87. from /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/openmmapi/include/openmm/AndersenThermostat.h:36,
88. from /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/openmmapi/include/OpenMM.h:35:
89. /usr/include/bits/byteswap.h: In function 'unsigned int __bswap_32(unsigned int)':
90. /usr/include/bits/byteswap.h:47: error: '__builtin_bswap32' was not declared in this scope
91. /usr/include/bits/byteswap.h: In function '__uint64_t __bswap_64(__uint64_t)':
92. /usr/include/bits/byteswap.h:111: error: '__builtin_bswap64' was not declared in this scope
93. In file included from /usr/include/endian.h:60,
94. from /usr/include/ctype.h:40,
95. from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/include/g++-v4/cctype:44,
96. from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/include/g++-v4/bits/localefwd.h:44,
97. from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/include/g++-v4/string:45,
98. from /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/openmmapi/include/openmm/OpenMMException.h:36,
99. from /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionForce.h:36,
100. from /tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source/plugins/amoeba/openmmapi/include/OpenMMAmoeba.h:39:
101. /usr/include/bits/byteswap.h: In function 'unsigned int __bswap_32(unsigned int)':
102. /usr/include/bits/byteswap.h:47: error: '__builtin_bswap32' was not declared in this scope
103. /usr/include/bits/byteswap.h: In function '__uint64_t __bswap_64(__uint64_t)':
104. /usr/include/bits/byteswap.h:111: error: '__builtin_bswap64' was not declared in this scope
105. make[2]: *** [plugins/amoeba/wrappers/AmoebaOpenMMApi.xml] Error 1
106. make[2]: Leaving directory `/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build'
107. make[1]: *** [plugins/amoeba/wrappers/CMakeFiles/AmoebaApiWrappers.dir/all] Error 2
108. make[1]: *** Waiting for unfinished jobs....
109. make[2]: *** [wrappers/OpenMMApi.xml] Error 1
110. make[2]: Leaving directory `/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build'
111. make[1]: *** [wrappers/CMakeFiles/ApiWrappers.dir/all] Error 2
112. make[1]: Leaving directory `/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build'
113. make: *** [all] Error 2
114. * ERROR: sci-libs/openmm-4.1.1 failed (compile phase):
115. * emake failed
116. *
117. * If you need support, post the output of `emerge --info '=sci-libs/openmm-4.1.1'`,
118. * the complete build log and the output of `emerge -pqv '=sci-libs/openmm-4.1.1'`.
119. * The complete build log is located at '/var/log/portage/sci-libs:openmm-4.1.1:20130202-162313.log'.
120. * For convenience, a symlink to the build log is located at '/tmp/portage/sci-libs/openmm-4.1.1/temp/build.log'.
121. * The ebuild environment file is located at '/tmp/portage/sci-libs/openmm-4.1.1/temp/environment'.
122. * Working directory: '/tmp/portage/sci-libs/openmm-4.1.1/work/openmm-4.1.1_build'
123. * S: '/tmp/portage/sci-libs/openmm-4.1.1/work/OpenMM4.1.1-Source'