1. * Package: sci-biology/allpaths-3.1
2. * Repository: gentoo
3. * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
4. * USE: amd64 elibc_glibc kernel_linux multilib test userland_GNU
5. * FEATURES: sandbox test userpriv usersandbox
6. >>> Unpacking source...
7. >>> Unpacking allpaths-3.1.tgz to /tmp/portage/sci-biology/allpaths-3.1/work
8. >>> Unpacking AllPathsV3_Manual_r1.0.docx to /tmp/portage/sci-biology/allpaths-3.1/work
9. unpack AllPathsV3_Manual_r1.0.docx: file format not recognized. Ignoring.
10. >>> Source unpacked in /tmp/portage/sci-biology/allpaths-3.1/work
11. >>> Preparing source in /tmp/portage/sci-biology/allpaths-3.1/work/AllPaths ...
12. >>> Source prepared.
13. >>> Configuring source in /tmp/portage/sci-biology/allpaths-3.1/work/AllPaths ...
14. ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64
15. checking for gawk... gawk
16. checking for a sed that does not truncate output... /bin/sed
17. checking for bison... bison -y
18. checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
19. checking for C++ compiler default output file name... a.out
20. checking whether the C++ compiler works... yes
21. checking whether we are cross compiling... no
22. checking for suffix of executables...
23. checking for suffix of object files... o
24. checking whether we are using the GNU C++ compiler... yes
25. checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
26. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
27. checking whether we are using the GNU C compiler... yes
28. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
29. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
30. checking for flex... flex
31. checking lex output file root... lex.yy
32. checking lex library... -lfl
33. checking whether yytext is a pointer... yes
34. checking whether ln -s works... yes
35. checking whether make sets $(MAKE)... yes
36. checking to see if we need to include the Boost libraries... yes
37. checking to see if we need to include the Xerces libraries... no
38. checking to see if we need to include the GMP libraries... yes
39. checking for dirent.h that defines DIR... yes
40. checking for library containing opendir... none required
41. checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
42. checking for grep that handles long lines and -e... /bin/grep
43. checking for egrep... /bin/grep -E
44. checking for ANSI C header files... yes
45. checking for sys/wait.h that is POSIX.1 compatible... yes
46. checking for sys/types.h... yes
47. checking for sys/stat.h... yes
48. checking for stdlib.h... yes
49. checking for string.h... yes
50. checking for memory.h... yes
51. checking for strings.h... yes
52. checking for inttypes.h... yes
53. checking for stdint.h... yes
54. checking for unistd.h... yes
55. checking fcntl.h usability... yes
56. checking fcntl.h presence... yes
57. checking for fcntl.h... yes
58. checking float.h usability... yes
59. checking float.h presence... yes
60. checking for float.h... yes
61. checking limits.h usability... yes
62. checking limits.h presence... yes
63. checking for limits.h... yes
64. checking locale.h usability... yes
65. checking locale.h presence... yes
66. checking for locale.h... yes
67. checking for memory.h... (cached) yes
68. checking netinet/in.h usability... yes
69. checking netinet/in.h presence... yes
70. checking for netinet/in.h... yes
71. checking stddef.h usability... yes
72. checking stddef.h presence... yes
73. checking for stddef.h... yes
74. checking for stdlib.h... (cached) yes
75. checking for string.h... (cached) yes
76. checking for strings.h... (cached) yes
77. checking sys/file.h usability... yes
78. checking sys/file.h presence... yes
79. checking for sys/file.h... yes
80. checking sys/param.h usability... yes
81. checking sys/param.h presence... yes
82. checking for sys/param.h... yes
83. checking sys/time.h usability... yes
84. checking sys/time.h presence... yes
85. checking for sys/time.h... yes
86. checking for unistd.h... (cached) yes
87. checking wchar.h usability... yes
88. checking wchar.h presence... yes
89. checking for wchar.h... yes
90. configure: VENDOR wasn't set, setting to a default
91. checking for getline in -lm... yes
92. checking for stdbool.h that conforms to C99... yes
93. checking for _Bool... yes
94. checking for an ANSI C-conforming const... yes
95. checking for inline... inline
96. checking for mode_t... yes
97. checking for off_t... yes
98. checking for pid_t... yes
99. checking for C/C++ restrict keyword... __restrict
100. checking for size_t... yes
101. checking for ssize_t... yes
102. checking whether time.h and sys/time.h may both be included... yes
103. checking whether struct tm is in sys/time.h or time.h... time.h
104. checking for uint16_t... yes
105. checking for uint32_t... yes
106. checking for uint64_t... yes
107. checking for uint8_t... yes
108. checking for working volatile... yes
109. checking for ptrdiff_t... yes
110. checking for ulong... yes
111. checking whether closedir returns void... no
112. checking for error_at_line... yes
113. checking vfork.h usability... no
114. checking vfork.h presence... no
115. checking for vfork.h... no
116. checking for fork... yes
117. checking for vfork... yes
118. checking for working fork... yes
119. checking for working vfork... (cached) yes
120. checking whether x86_64-pc-linux-gnu-gcc needs -traditional... no
121. checking whether lstat dereferences a symlink specified with a trailing slash... yes
122. checking whether lstat accepts an empty string... no
123. checking whether lstat dereferences a symlink specified with a trailing slash... (cached) yes
124. checking for stdlib.h... (cached) yes
125. checking for GNU libc compatible malloc... yes
126. checking for working memcmp... yes
127. checking for stdlib.h... (cached) yes
128. checking for unistd.h... (cached) yes
129. checking for getpagesize... yes
130. checking for working mmap... yes
131. checking for stdlib.h... (cached) yes
132. checking for GNU libc compatible realloc... yes
133. checking sys/select.h usability... yes
134. checking sys/select.h presence... yes
135. checking for sys/select.h... yes
136. checking sys/socket.h usability... yes
137. checking sys/socket.h presence... yes
138. checking for sys/socket.h... yes
139. checking types of arguments for select... int,fd_set *,struct timeval *
140. checking return type of signal handlers... void
141. checking whether stat accepts an empty string... no
142. checking for strftime... yes
143. checking for alarm... yes
144. checking for atexit... yes
145. checking for bzero... yes
146. checking for dup2... yes
147. checking for floor... no
148. checking for ftruncate... yes
149. checking for getcwd... yes
150. checking for gethostname... yes
151. checking for getpagesize... (cached) yes
152. checking for gettimeofday... yes
153. checking for memchr... yes
154. checking for memmove... yes
155. checking for memset... yes
156. checking for mkdir... yes
157. checking for mkfifo... yes
158. checking for munmap... yes
159. checking for pow... no
160. checking for putenv... yes
161. checking for realpath... yes
162. checking for regcomp... yes
163. checking for rint... no
164. checking for rmdir... yes
165. checking for select... yes
166. checking for setenv... yes
167. checking for setlocale... yes
168. checking for sqrt... no
169. checking for strcasecmp... yes
170. checking for strchr... yes
171. checking for strdup... yes
172. checking for strerror... yes
173. checking for strncasecmp... yes
174. checking for strrchr... yes
175. checking for strstr... yes
176. checking for strtol... yes
177. checking for strtoul... yes
178. checking for uname... yes
179. checking to see that gcc is at least version 4.3.2... Yes, gcc version 4.7.1 is fine
180. checking for boostlib >= 1.37.0... yes
181. found boost version
182. checking for boost library name... Failed...
183. configure: Configure failed with the error message: Failed to resolve boost library name
184. configure:
185. configure: Common error conditions in the build process are documented on our wiki page,
186. configure: http://www.broadinstitute.org/crd/wiki/index.php/Build_FAQ
187. configure: We also offer email support at crdhelp@broadinstitute.org
188. configure: error: in `/tmp/portage/sci-biology/allpaths-3.1/work/AllPaths':
189. configure: error: configure failed.
190. See `config.log' for more details.
192. !!! Please attach the following file when seeking support:
193. !!! /tmp/portage/sci-biology/allpaths-3.1/work/AllPaths/config.log
194. * ERROR: sci-biology/allpaths-3.1 failed (configure phase):
195. * econf failed
196. *
197. * Call stack:
198. * ebuild.sh, line 85: Called src_configure
199. * environment, line 2144: Called base_src_configure
200. * environment, line 326: Called econf
201. * phase-helpers.sh, line 467: Called die
202. * The specific snippet of code:
203. * die "econf failed"
204. *
205. * If you need support, post the output of `emerge --info '=sci-biology/allpaths-3.1'`,
206. * the complete build log and the output of `emerge -pqv '=sci-biology/allpaths-3.1'`.
207. sed: couldn't open temporary file /etc/portage/package.mask/sedaQAKoZ: Permission denied