1. * Package: sci-biology/cd-hit-4.5.4
2. * Repository: gentoo
3. * Maintainer: jlec@gentoo.org sci-biology@gentoo.org
4. * USE: amd64 elibc_glibc kernel_linux multilib openmp test userland_GNU
5. * FEATURES: sandbox test userpriv usersandbox
6. >>> Unpacking source...
7. >>> Unpacking cd-hit-v4.5.4-2011-03-07.tgz to /tmp/portage/sci-biology/cd-hit-4.5.4/work
8. >>> Source unpacked in /tmp/portage/sci-biology/cd-hit-4.5.4/work
9. >>> Preparing source in /tmp/portage/sci-biology/cd-hit-4.5.4/work/cd-hit-v4.5.4-2011-03-07 ...
10. * Applying 4.5.4-gentoo.patch ...
11. [ ok ]
12. >>> Source prepared.
13. >>> Configuring source in /tmp/portage/sci-biology/cd-hit-4.5.4/work/cd-hit-v4.5.4-2011-03-07 ...
14. >>> Source configured.
15. >>> Compiling source in /tmp/portage/sci-biology/cd-hit-4.5.4/work/cd-hit-v4.5.4-2011-03-07 ...
16. make -j24 openmp=yes
17. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -fopenmp cdhit-common.c++ -c
18. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -fopenmp cdhit-utility.c++ -c
19. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -fopenmp cdhit.c++ -c
20. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -fopenmp cdhit-est.c++ -c
21. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -fopenmp cdhit-2d.c++ -c
22. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -fopenmp cdhit-est-2d.c++ -c
23. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -fopenmp cdhit-div.c++ -c
24. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -fopenmp cdhit-454.c++ -c
25. cdhit-common.c++: In constructor 'TempFile::TempFile(const char*)':
26. cdhit-common.c++:68:34: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'TempFile*' [-Wformat]
27. cdhit-common.c++: In member function 'size_t SequenceDB::MinimalMemory(int, int, int, const Options&)':
28. cdhit-common.c++:2258:47: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat]
29. cdhit-common.c++:2262:71: warning: format '%i' expects argument of type 'int', but argument 4 has type 'size_t {aka long unsigned int}' [-Wformat]
30. cdhit-common.c++:2262:71: warning: format '%i' expects argument of type 'int', but argument 5 has type 'size_t {aka long unsigned int}' [-Wformat]
31. cdhit-common.c++:2266:78: warning: format '%i' expects argument of type 'int', but argument 4 has type 'size_t {aka long unsigned int}' [-Wformat]
32. cdhit-common.c++:2266:78: warning: format '%i' expects argument of type 'int', but argument 5 has type 'size_t {aka long unsigned int}' [-Wformat]
33. cdhit-common.c++:2271:52: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat]
34. cdhit-common.c++:2274:51: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat]
35. cdhit-common.c++:2279:30: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t {aka long unsigned int}' [-Wformat]
36. cdhit-common.c++: In member function 'void SequenceDB::DoClustering(int, const Options&)':
37. cdhit-common.c++:2476:90: warning: format '%i' expects argument of type 'int', but argument 2 has type 'std::vector<Sequence*, std::allocator<Sequence*> >::size_type {aka long unsigned int}' [-Wformat]
38. cdhit-common.c++:2487:65: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t {aka long unsigned int}' [-Wformat]
39. cdhit-common.c++: In member function 'void SequenceDB::DoClustering(const Options&)':
40. cdhit-common.c++:2994:65: warning: format '%i' expects argument of type 'int', but argument 2 has type 'size_t {aka long unsigned int}' [-Wformat]
41. In file included from cdhit-common.c++:28:0:
42. cdhit-common.h: In instantiation of 'void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<long int>]':
43. cdhit-common.c++:704:27: required from here
44. cdhit-common.h:95:4: error: 'push_back' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
45. cdhit-common.h:95:4: note: declarations in dependent base 'std::vector<NVector<long int>, std::allocator<NVector<long int> > >' are not found by unqualified lookup
46. cdhit-common.h:95:4: note: use 'this->push_back' instead
47. cdhit-common.h: In instantiation of 'void Vector<TYPE>::Append(const TYPE&) [with TYPE = NVector<int>]':
48. cdhit-common.c++:705:25: required from here
49. cdhit-common.h:95:4: error: 'push_back' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
50. cdhit-common.h:95:4: note: declarations in dependent base 'std::vector<NVector<int>, std::allocator<NVector<int> > >' are not found by unqualified lookup
51. cdhit-common.h:95:4: note: use 'this->push_back' instead
52. cdhit-common.h: In instantiation of 'void Vector<TYPE>::Append(const TYPE&) [with TYPE = Sequence*]':
53. cdhit-common.c++:1247:24: required from here
54. cdhit-common.h:95:4: error: 'push_back' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
55. cdhit-common.h:95:4: note: declarations in dependent base 'std::vector<Sequence*, std::allocator<Sequence*> >' are not found by unqualified lookup
56. cdhit-common.h:95:4: note: use 'this->push_back' instead
57. cdhit-common.h: In instantiation of 'void Vector<TYPE>::Append(const TYPE&) [with TYPE = int]':
58. cdhit-common.c++:1895:26: required from here
59. cdhit-common.h:95:4: error: 'push_back' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
60. cdhit-common.h:95:4: note: declarations in dependent base 'std::vector<int, std::allocator<int> >' are not found by unqualified lookup
61. cdhit-common.h:95:4: note: use 'this->push_back' instead
62. cdhit-common.c++: In member function 'void SequenceDB::WriteClusters(const char*, const char*, const Options&)':
63. cdhit-common.c++:1860:41: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
64. cdhit-common.c++:1864:32: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
65. cdhit-common.c++: In member function 'void SequenceDB::DivideSave(const char*, const char*, int, const Options&)':
66. cdhit-common.c++:1828:41: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
67. cdhit-common.c++:1832:32: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
68. cdhit-common.c++: In member function 'void SequenceDB::Read(const char*, const Options&)':
69. cdhit-common.c++:1650:44: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
70. make: *** [cdhit-common.o] Error 1
71. * ERROR: sci-biology/cd-hit-4.5.4 failed (compile phase):
72. * emake failed
73. *
74. * If you need support, post the output of `emerge --info '=sci-biology/cd-hit-4.5.4'`,
75. * the complete build log and the output of `emerge -pqv '=sci-biology/cd-hit-4.5.4'`.
76. * The complete build log is located at '/var/log/portage/sci-biology:cd-hit-4.5.4:20120619-232853.log'.
77. * For convenience, a symlink to the build log is located at '/tmp/portage/sci-biology/cd-hit-4.5.4/temp/build.log'.
78. * The ebuild environment file is located at '/tmp/portage/sci-biology/cd-hit-4.5.4/temp/environment'.
79. * Working directory: '/tmp/portage/sci-biology/cd-hit-4.5.4/work/cd-hit-v4.5.4-2011-03-07'
80. * S: '/tmp/portage/sci-biology/cd-hit-4.5.4/work/cd-hit-v4.5.4-2011-03-07'