1. * Package: sci-biology/amos-3.1.0
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 amos-3.1.0.tar.gz to /tmp/portage/sci-biology/amos-3.1.0/work
8. >>> Source unpacked in /tmp/portage/sci-biology/amos-3.1.0/work
9. >>> Preparing source in /tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0 ...
10. >>> Source prepared.
11. >>> Configuring source in /tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0 ...
12. * econf: updating amos-3.1.0/config/config.sub with /usr/share/gnuconfig/config.sub
13. * econf: updating amos-3.1.0/config/config.guess with /usr/share/gnuconfig/config.guess
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 --disable-dependency-tracking
15. configure: loading site script /usr/share/config.site
16. configure: loading site script /usr/share/crossdev/include/site/linux
17. configure: loading site script /usr/share/crossdev/include/site/linux-gnu
18. configure: loading site script /usr/share/crossdev/include/site/x86_64-linux-gnu
19. checking for a BSD-compatible install... /usr/bin/install -c
20. checking whether build environment is sane... yes
21. checking for a thread-safe mkdir -p... /bin/mkdir -p
22. checking for gawk... gawk
23. checking whether make sets $(MAKE)... yes
24. checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
25. checking whether the C++ compiler works... yes
26. checking for C++ compiler default output file name... a.out
27. checking for suffix of executables...
28. checking whether we are cross compiling... no
29. checking for suffix of object files... o
30. checking whether we are using the GNU C++ compiler... yes
31. checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
32. checking for style of include used by make... GNU
33. checking dependency style of x86_64-pc-linux-gnu-g++... none
34. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
35. checking whether we are using the GNU C compiler... yes
36. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
37. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
38. checking dependency style of x86_64-pc-linux-gnu-gcc... none
39. checking for gawk... (cached) gawk
40. checking whether ln -s works... yes
41. checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
42. checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
43. checking for perl... /usr/bin/perl
44. checking for python... /usr/bin/python
45. checking for nucmer... /usr/bin/nucmer
46. checking for delta-filter... /usr/bin/delta-filter
47. checking for show-coords... /usr/bin/show-coords
48. checking for blat... /usr/bin/blat
49. checking for perl module Statistics::Descriptive... ok
50. checking for perl module XML::Parser... ok
51. checking for perl module DBI... ok
52. checking for pow in -lm... yes
53. checking for fopen in -lc... yes
54. checking for main in -lz... yes
55. checking for dirent.h that defines DIR... yes
56. checking for library containing opendir... none required
57. checking for grep that handles long lines and -e... /bin/grep
58. checking for egrep... /bin/grep -E
59. checking for ANSI C header files... yes
60. checking for sys/wait.h that is POSIX.1 compatible... yes
61. checking for sys/types.h... yes
62. checking for sys/stat.h... yes
63. checking for stdlib.h... yes
64. checking for string.h... yes
65. checking for memory.h... yes
66. checking for strings.h... yes
67. checking for inttypes.h... yes
68. checking for stdint.h... yes
69. checking for unistd.h... yes
70. checking fcntl.h usability... yes
71. checking fcntl.h presence... yes
72. checking for fcntl.h... yes
73. checking for inttypes.h... (cached) yes
74. checking limits.h usability... yes
75. checking limits.h presence... yes
76. checking for limits.h... yes
77. checking for stdlib.h... (cached) yes
78. checking for unistd.h... (cached) yes
79. checking for stdbool.h that conforms to C99... yes
80. checking for _Bool... yes
81. checking for an ANSI C-conforming const... yes
82. checking for inline... inline
83. checking for pid_t... yes
84. checking for size_t... yes
85. checking for mode_t... yes
86. checking whether struct tm is in sys/time.h or time.h... time.h
87. checking whether byte ordering is bigendian... no
88. checking for special C compiler options needed for large files... no
89. checking for _FILE_OFFSET_BITS value needed for large files... no
90. checking whether bitfields are packed htol... no
91. checking for X... libraries , headers
92. checking for gethostbyname... yes
93. checking for connect... yes
94. checking for remove... yes
95. checking for shmat... yes
96. checking for IceConnectionNumber in -lICE... yes
97. checking for Qt4... yes
98. checking whether Qt4 works... yes
99. checking for Boost... yes
100. checking whether Boost works... yes
101. checking for CA... no
102. checking whether CA works... no
103. checking getopt.h usability... yes
104. checking getopt.h presence... yes
105. checking for getopt.h... yes
106. checking for getopt_long_only... yes
107. checking for working strtod... yes
108. checking for isascii... yes
109. checking for strtol... yes
110. checking vfork.h usability... no
111. checking vfork.h presence... no
112. checking for vfork.h... no
113. checking for fork... yes
114. checking for vfork... yes
115. checking for working fork... yes
116. checking for working vfork... (cached) yes
117. checking sys/select.h usability... yes
118. checking sys/select.h presence... yes
119. checking for sys/select.h... yes
120. checking sys/socket.h usability... yes
121. checking sys/socket.h presence... yes
122. checking for sys/socket.h... yes
123. checking types of arguments for select... int,fd_set *,struct timeval *
124. checking for strftime... yes
125. checking for dup2... yes
126. checking for floor... yes
127. checking for localtime... yes
128. checking for lstat... yes
129. checking for memmove... yes
130. checking for memset... yes
131. checking for mkdir... yes
132. checking for pow... yes
133. checking for rmdir... yes
134. checking for sqrt... yes
135. checking for stat... yes
136. checking for strchr... yes
137. checking for strdup... yes
138. checking for strstr... yes
139. checking build system type... x86_64-pc-linux-gnu
140. checking host system type... x86_64-pc-linux-gnu
141. checking whether to build AMOScmp... (cached) no
142. checking whether to build minimus... (cached) no
143. checking whether to build Simulator... (cached) no
144. checking whether to build Experimental... (cached) no
145. checking whether to build all... (cached) yes
146. configure: creating ./config.status
147. config.status: creating Makefile
148. config.status: creating doc/Makefile
149. config.status: creating src/Makefile
150. config.status: creating src/GNU/Makefile
151. config.status: creating src/AMOS/Makefile
152. config.status: creating src/Bambus/Makefile
153. config.status: creating src/Bambus/Bundler/Makefile
154. config.status: creating src/Bambus/Output/Makefile
155. config.status: creating src/Bambus/Untangler/Makefile
156. config.status: creating src/Common/Makefile
157. config.status: creating src/Graph/Makefile
158. config.status: creating src/Slice/Makefile
159. config.status: creating src/CelMsg/Makefile
160. config.status: creating src/Message/Makefile
161. config.status: creating src/Bank/Makefile
162. config.status: creating src/Align/Makefile
163. config.status: creating src/Tigger/Makefile
164. config.status: creating src/Compare/Makefile
165. config.status: creating src/Casm/Makefile
166. config.status: creating src/CtgTrim/Makefile
167. config.status: creating src/Sim/Makefile
168. config.status: creating src/Validation/Makefile
169. config.status: creating src/Converters/Makefile
170. config.status: creating src/Utils/Makefile
171. config.status: creating src/PerlModules/Makefile
172. config.status: creating src/PythonModules/Makefile
173. config.status: creating src/Pipeline/Makefile
174. config.status: creating src/Staden/Makefile
175. config.status: creating src/Staden/read/Makefile
176. config.status: creating src/Staden/progs/Makefile
177. config.status: creating src/Contig/Makefile
178. config.status: creating src/Foundation/Makefile
179. config.status: creating src/hawkeye/Makefile
180. config.status: creating src/Experimental/Makefile
181. config.status: creating config.h
182. config.status: executing depfiles commands
184. -- AMOS Assembler 3.1.0 Configuration Results --
185. C compiler: x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches
186. C++ compiler: x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches
187. GCC version: x86_64-pc-linux-gnu-gcc (Gentoo 4.7.1 p1.0, pie-0.5.3) 4.7.1
188. Host System type: x86_64-pc-linux-gnu
189. Install prefix: /usr
190. Install eprefix: ${prefix}
192. See config.h for further configuration information.
193. Email <amos-help@lists.sourceforge.net> with questions and bug reports.
195. >>> Source configured.
196. >>> Compiling source in /tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0 ...
197. make -j24 -j1
198. make all-recursive
199. make[1]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0'
200. Making all in src
201. make[2]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src'
202. Making all in GNU
203. make[3]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/GNU'
204. make all-am
205. make[4]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/GNU'
206. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c gnu.c
207. rm -f libGNU.a
208. ar cru libGNU.a gnu.o
209. x86_64-pc-linux-gnu-ranlib libGNU.a
210. make[4]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/GNU'
211. make[3]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/GNU'
212. Making all in AMOS
213. make[3]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/AMOS'
214. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-BankStream_AMOS.o `test -f 'BankStream_AMOS.cc' || echo './'`BankStream_AMOS.cc
215. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
216. from utility_AMOS.hh:48,
217. from Bank_AMOS.hh:22,
218. from BankStream_AMOS.hh:13,
219. from BankStream_AMOS.cc:10:
220. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
221. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Bank_AMOS.o `test -f 'Bank_AMOS.cc' || echo './'`Bank_AMOS.cc
222. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
223. from utility_AMOS.hh:48,
224. from Bank_AMOS.hh:22,
225. from Bank_AMOS.cc:10:
226. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
227. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-ContigEdge_AMOS.o `test -f 'ContigEdge_AMOS.cc' || echo './'`ContigEdge_AMOS.cc
228. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
229. from utility_AMOS.hh:48,
230. from Message_AMOS.hh:14,
231. from Universal_AMOS.hh:13,
232. from Link_AMOS.hh:13,
233. from Edge_AMOS.hh:13,
234. from ContigEdge_AMOS.hh:13,
235. from ContigEdge_AMOS.cc:10:
236. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
237. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-ContigIterator_AMOS.o `test -f 'ContigIterator_AMOS.cc' || echo './'`ContigIterator_AMOS.cc
238. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
239. from utility_AMOS.hh:48,
240. from Message_AMOS.hh:14,
241. from Universal_AMOS.hh:13,
242. from Sequence_AMOS.hh:13,
243. from Contig_AMOS.hh:13,
244. from ContigIterator_AMOS.hh:15,
245. from ContigIterator_AMOS.cc:3:
246. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
247. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-ContigLink_AMOS.o `test -f 'ContigLink_AMOS.cc' || echo './'`ContigLink_AMOS.cc
248. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
249. from utility_AMOS.hh:48,
250. from Message_AMOS.hh:14,
251. from Universal_AMOS.hh:13,
252. from Link_AMOS.hh:13,
253. from ContigLink_AMOS.hh:13,
254. from ContigLink_AMOS.cc:10:
255. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
256. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Motif_AMOS.o `test -f 'Motif_AMOS.cc' || echo './'`Motif_AMOS.cc
257. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
258. from utility_AMOS.hh:48,
259. from Message_AMOS.hh:14,
260. from Universal_AMOS.hh:13,
261. from Motif_AMOS.hh:13,
262. from Motif_AMOS.cc:10:
263. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
264. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Contig_AMOS.o `test -f 'Contig_AMOS.cc' || echo './'`Contig_AMOS.cc
265. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
266. from utility_AMOS.hh:48,
267. from Message_AMOS.hh:14,
268. from Universal_AMOS.hh:13,
269. from Sequence_AMOS.hh:13,
270. from Contig_AMOS.hh:13,
271. from Contig_AMOS.cc:11:
272. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
273. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Edge_AMOS.o `test -f 'Edge_AMOS.cc' || echo './'`Edge_AMOS.cc
274. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
275. from utility_AMOS.hh:48,
276. from Message_AMOS.hh:14,
277. from Universal_AMOS.hh:13,
278. from Link_AMOS.hh:13,
279. from Edge_AMOS.hh:13,
280. from Edge_AMOS.cc:10:
281. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
282. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Feature_AMOS.o `test -f 'Feature_AMOS.cc' || echo './'`Feature_AMOS.cc
283. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
284. from utility_AMOS.hh:48,
285. from Message_AMOS.hh:14,
286. from Universal_AMOS.hh:13,
287. from Feature_AMOS.hh:13,
288. from Feature_AMOS.cc:10:
289. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
290. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Fragment_AMOS.o `test -f 'Fragment_AMOS.cc' || echo './'`Fragment_AMOS.cc
291. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
292. from utility_AMOS.hh:48,
293. from Message_AMOS.hh:14,
294. from Universal_AMOS.hh:13,
295. from Fragment_AMOS.hh:13,
296. from Fragment_AMOS.cc:10:
297. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
298. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Group_AMOS.o `test -f 'Group_AMOS.cc' || echo './'`Group_AMOS.cc
299. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
300. from utility_AMOS.hh:48,
301. from Message_AMOS.hh:14,
302. from Universal_AMOS.hh:13,
303. from Group_AMOS.hh:13,
304. from Group_AMOS.cc:10:
305. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
306. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-IDMap_AMOS.o `test -f 'IDMap_AMOS.cc' || echo './'`IDMap_AMOS.cc
307. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
308. from utility_AMOS.hh:48,
309. from Message_AMOS.hh:14,
310. from IDMap_AMOS.hh:13,
311. from IDMap_AMOS.cc:10:
312. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
313. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Index_AMOS.o `test -f 'Index_AMOS.cc' || echo './'`Index_AMOS.cc
314. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
315. from utility_AMOS.hh:48,
316. from Message_AMOS.hh:14,
317. from Universal_AMOS.hh:13,
318. from Link_AMOS.hh:13,
319. from Edge_AMOS.hh:13,
320. from ContigEdge_AMOS.hh:13,
321. from universals_AMOS.hh:13,
322. from Index_AMOS.hh:13,
323. from Index_AMOS.cc:10:
324. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
325. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Kmer_AMOS.o `test -f 'Kmer_AMOS.cc' || echo './'`Kmer_AMOS.cc
326. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
327. from utility_AMOS.hh:48,
328. from Message_AMOS.hh:14,
329. from Universal_AMOS.hh:13,
330. from Kmer_AMOS.hh:13,
331. from Kmer_AMOS.cc:10:
332. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
333. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Layout_AMOS.o `test -f 'Layout_AMOS.cc' || echo './'`Layout_AMOS.cc
334. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
335. from utility_AMOS.hh:48,
336. from Message_AMOS.hh:14,
337. from Universal_AMOS.hh:13,
338. from Layout_AMOS.hh:13,
339. from Layout_AMOS.cc:10:
340. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
341. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Library_AMOS.o `test -f 'Library_AMOS.cc' || echo './'`Library_AMOS.cc
342. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
343. from utility_AMOS.hh:48,
344. from Message_AMOS.hh:14,
345. from Universal_AMOS.hh:13,
346. from Library_AMOS.hh:13,
347. from Library_AMOS.cc:10:
348. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
349. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Link_AMOS.o `test -f 'Link_AMOS.cc' || echo './'`Link_AMOS.cc
350. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
351. from utility_AMOS.hh:48,
352. from Message_AMOS.hh:14,
353. from Universal_AMOS.hh:13,
354. from Link_AMOS.hh:13,
355. from Link_AMOS.cc:10:
356. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
357. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Message_AMOS.o `test -f 'Message_AMOS.cc' || echo './'`Message_AMOS.cc
358. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
359. from utility_AMOS.hh:48,
360. from Message_AMOS.hh:14,
361. from Message_AMOS.cc:10:
362. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
363. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Overlap_AMOS.o `test -f 'Overlap_AMOS.cc' || echo './'`Overlap_AMOS.cc
364. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
365. from utility_AMOS.hh:48,
366. from Message_AMOS.hh:14,
367. from Universal_AMOS.hh:13,
368. from Overlap_AMOS.hh:13,
369. from Overlap_AMOS.cc:10:
370. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
371. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Read_AMOS.o `test -f 'Read_AMOS.cc' || echo './'`Read_AMOS.cc
372. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
373. from utility_AMOS.hh:48,
374. from Message_AMOS.hh:14,
375. from Universal_AMOS.hh:13,
376. from Sequence_AMOS.hh:13,
377. from Read_AMOS.hh:13,
378. from Read_AMOS.cc:10:
379. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
380. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-ScaffoldEdge_AMOS.o `test -f 'ScaffoldEdge_AMOS.cc' || echo './'`ScaffoldEdge_AMOS.cc
381. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
382. from utility_AMOS.hh:48,
383. from Message_AMOS.hh:14,
384. from Universal_AMOS.hh:13,
385. from Link_AMOS.hh:13,
386. from Edge_AMOS.hh:13,
387. from ScaffoldEdge_AMOS.hh:13,
388. from ScaffoldEdge_AMOS.cc:10:
389. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
390. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-ScaffoldLink_AMOS.o `test -f 'ScaffoldLink_AMOS.cc' || echo './'`ScaffoldLink_AMOS.cc
391. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
392. from utility_AMOS.hh:48,
393. from Message_AMOS.hh:14,
394. from Universal_AMOS.hh:13,
395. from Link_AMOS.hh:13,
396. from ScaffoldLink_AMOS.hh:13,
397. from ScaffoldLink_AMOS.cc:10:
398. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
399. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Scaffold_AMOS.o `test -f 'Scaffold_AMOS.cc' || echo './'`Scaffold_AMOS.cc
400. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
401. from utility_AMOS.hh:48,
402. from Message_AMOS.hh:14,
403. from Universal_AMOS.hh:13,
404. from Scaffold_AMOS.hh:13,
405. from Scaffold_AMOS.cc:10:
406. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
407. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Sequence_AMOS.o `test -f 'Sequence_AMOS.cc' || echo './'`Sequence_AMOS.cc
408. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
409. from utility_AMOS.hh:48,
410. from Message_AMOS.hh:14,
411. from Universal_AMOS.hh:13,
412. from Sequence_AMOS.hh:13,
413. from Sequence_AMOS.cc:10:
414. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
415. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-Universal_AMOS.o `test -f 'Universal_AMOS.cc' || echo './'`Universal_AMOS.cc
416. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
417. from utility_AMOS.hh:48,
418. from Message_AMOS.hh:14,
419. from Universal_AMOS.hh:13,
420. from Universal_AMOS.cc:10:
421. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
422. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-datatypes_AMOS.o `test -f 'datatypes_AMOS.cc' || echo './'`datatypes_AMOS.cc
423. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
424. from utility_AMOS.hh:48,
425. from Message_AMOS.hh:14,
426. from datatypes_AMOS.hh:17,
427. from datatypes_AMOS.cc:10:
428. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
429. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-universals_AMOS.o `test -f 'universals_AMOS.cc' || echo './'`universals_AMOS.cc
430. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
431. from utility_AMOS.hh:48,
432. from Message_AMOS.hh:14,
433. from Universal_AMOS.hh:13,
434. from Link_AMOS.hh:13,
435. from Edge_AMOS.hh:13,
436. from ContigEdge_AMOS.hh:13,
437. from universals_AMOS.hh:13,
438. from universals_AMOS.cc:10:
439. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
440. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libAMOS_a-utility_AMOS.o `test -f 'utility_AMOS.cc' || echo './'`utility_AMOS.cc
441. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
442. from utility_AMOS.hh:48,
443. from utility_AMOS.cc:10:
444. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
445. rm -f libAMOS.a
446. ar cru libAMOS.a libAMOS_a-BankStream_AMOS.o libAMOS_a-Bank_AMOS.o libAMOS_a-ContigEdge_AMOS.o libAMOS_a-ContigIterator_AMOS.o libAMOS_a-ContigLink_AMOS.o libAMOS_a-Motif_AMOS.o libAMOS_a-Contig_AMOS.o libAMOS_a-Edge_AMOS.o libAMOS_a-Feature_AMOS.o libAMOS_a-Fragment_AMOS.o libAMOS_a-Group_AMOS.o libAMOS_a-IDMap_AMOS.o libAMOS_a-Index_AMOS.o libAMOS_a-Kmer_AMOS.o libAMOS_a-Layout_AMOS.o libAMOS_a-Library_AMOS.o libAMOS_a-Link_AMOS.o libAMOS_a-Message_AMOS.o libAMOS_a-Overlap_AMOS.o libAMOS_a-Read_AMOS.o libAMOS_a-ScaffoldEdge_AMOS.o libAMOS_a-ScaffoldLink_AMOS.o libAMOS_a-Scaffold_AMOS.o libAMOS_a-Sequence_AMOS.o libAMOS_a-Universal_AMOS.o libAMOS_a-datatypes_AMOS.o libAMOS_a-universals_AMOS.o libAMOS_a-utility_AMOS.o
447. x86_64-pc-linux-gnu-ranlib libAMOS.a
448. make[3]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/AMOS'
449. Making all in Common
450. make[3]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Common'
451. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o amp.o amp.cc
452. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o delcher.o delcher.cc
453. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o delta.o delta.cc
454. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o fasta.o fasta.cc
455. fasta.cc: In function 'int Fasta_Read_String(FILE*, char*&, long int&, char*, int)':
456. fasta.cc:366:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
457. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o prob.o prob.cc
458. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o fastq.o fastq.cc
459. rm -f libCommon.a
460. ar cru libCommon.a amp.o delcher.o delta.o fasta.o prob.o fastq.o
461. x86_64-pc-linux-gnu-ranlib libCommon.a
462. make[3]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Common'
463. Making all in Foundation
464. make[3]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Foundation'
465. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o CategoryInformation.o CategoryInformation.cc
466. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o ConfigFile.o ConfigFile.cc
467. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o ConfigSection.o ConfigSection.cc
468. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o Exceptions.o Exceptions.cc
469. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o FileSystem.o FileSystem.cc
470. FileSystem.cc: In static member function 'static char* FileSystem::getAbsolutePath()':
471. FileSystem.cc:136:29: warning: ignoring return value of 'char* getcwd(char*, size_t)', declared with attribute warn_unused_result [-Wunused-result]
472. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o LogCategory.o LogCategory.cc
473. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o Logger.o Logger.cc
474. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o LogMsg.o LogMsg.cc
475. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o OptionResult.o OptionResult.cc
476. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o Options.o Options.cc
477. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o AMOS_Foundation.o AMOS_Foundation.cc
478. rm -f libAMOSFoundation.a
479. ar cru libAMOSFoundation.a CategoryInformation.o ConfigFile.o ConfigSection.o Exceptions.o FileSystem.o LogCategory.o Logger.o LogMsg.o OptionResult.o Options.o AMOS_Foundation.o
480. x86_64-pc-linux-gnu-ranlib libAMOSFoundation.a
481. make[3]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Foundation'
482. Making all in Graph
483. make[3]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Graph'
484. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o Edge.o Edge.cc
485. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
486. from ../../src/AMOS/utility_AMOS.hh:48,
487. from INode.hh:5,
488. from Edge.hh:7,
489. from Edge.cc:2:
490. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
491. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o Graph.o Graph.cc
492. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
493. from ../../src/AMOS/utility_AMOS.hh:48,
494. from IGraph.hh:5,
495. from Graph.hh:9,
496. from Graph.cc:7:
497. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
498. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o Node.o Node.cc
499. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o SubGraph.o SubGraph.cc
500. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
501. from ../../src/AMOS/utility_AMOS.hh:48,
502. from IGraph.hh:5,
503. from SubGraph.hh:7,
504. from SubGraph.cc:3:
505. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
506. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o CompositeNode.o CompositeNode.cc
507. rm -f libGraph.a
508. ar cru libGraph.a Edge.o Graph.o Node.o SubGraph.o CompositeNode.o
509. x86_64-pc-linux-gnu-ranlib libGraph.a
510. make[3]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Graph'
511. Making all in Slice
512. make[3]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Slice'
513. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c getConsQC.c
514. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c getConsQV.c
515. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c newmem.c
516. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c utility.c
517. utility.c: In function 'libSlice_getVersion':
518. utility.c:72:9: warning: offset outside bounds of constant string [enabled by default]
519. rm -f libSlice.a
520. ar cru libSlice.a getConsQC.o getConsQV.o newmem.o utility.o
521. x86_64-pc-linux-gnu-ranlib libSlice.a
522. make[3]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Slice'
523. Making all in CelMsg
524. make[3]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/CelMsg'
525. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o CelMsg.o CelMsg.cc
526. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
527. from ../../src/AMOS/utility_AMOS.hh:48,
528. from ../../src/AMOS/Message_AMOS.hh:14,
529. from ../../src/AMOS/datatypes_AMOS.hh:17,
530. from CelMsg.hh:22,
531. from CelMsg.cc:17:
532. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
533. rm -f libCelMsg.a
534. ar cru libCelMsg.a CelMsg.o
535. x86_64-pc-linux-gnu-ranlib libCelMsg.a
536. make[3]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/CelMsg'
537. Making all in Message
538. make[3]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Message'
539. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o message-count.o message-count.cc
540. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
541. from ../../src/AMOS/utility_AMOS.hh:48,
542. from ../../src/AMOS/Message_AMOS.hh:14,
543. from ../../src/AMOS/messages_AMOS.hh:13,
544. from message-count.cc:13:
545. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
546. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o message-count message-count.o ../../src/AMOS/libAMOS.a -lz -lc -lm
547. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o message-extract.o message-extract.cc
548. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
549. from ../../src/AMOS/utility_AMOS.hh:48,
550. from ../../src/AMOS/Message_AMOS.hh:14,
551. from ../../src/AMOS/messages_AMOS.hh:13,
552. from message-extract.cc:13:
553. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
554. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o message-extract message-extract.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
555. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o message-validate.o message-validate.cc
556. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
557. from ../../src/AMOS/utility_AMOS.hh:48,
558. from ../../src/AMOS/Message_AMOS.hh:14,
559. from ../../src/AMOS/messages_AMOS.hh:13,
560. from message-validate.cc:13:
561. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
562. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o message-validate message-validate.o ../../src/AMOS/libAMOS.a -lz -lc -lm
563. make[3]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Message'
564. Making all in Bank
565. make[3]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Bank'
566. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o bank2contig.o bank2contig.cc
567. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
568. from ../../src/AMOS/utility_AMOS.hh:48,
569. from ../../src/AMOS/foundation_AMOS.hh:13,
570. from bank2contig.cc:1:
571. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
572. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o bank2contig bank2contig.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a -lz -lc -lm
573. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o bank2lib.o bank2lib.cc
574. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
575. from ../../src/AMOS/utility_AMOS.hh:48,
576. from ../../src/AMOS/foundation_AMOS.hh:13,
577. from bank2lib.cc:15:
578. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
579. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o bank2lib bank2lib.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a -lz -lc -lm
580. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o bank2coverage.o bank2coverage.cc
581. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
582. from ../../src/AMOS/utility_AMOS.hh:48,
583. from ../../src/AMOS/foundation_AMOS.hh:13,
584. from bank2coverage.cc:3:
585. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
586. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o bank2coverage bank2coverage.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Slice/libSlice.a -lz -lc -lm
587. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o bank2fasta-bank2fasta.o `test -f 'bank2fasta.cc' || echo './'`bank2fasta.cc
588. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
589. from ../../src/AMOS/utility_AMOS.hh:48,
590. from ../../src/AMOS/foundation_AMOS.hh:13,
591. from bank2fasta.cc:18:
592. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
593. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o bank2fasta bank2fasta-bank2fasta.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/GNU/libGNU.a -lz -lc -lm
594. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o bank2scaff.o bank2scaff.cc
595. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
596. from ../../src/AMOS/utility_AMOS.hh:48,
597. from ../../src/AMOS/foundation_AMOS.hh:13,
598. from bank2scaff.cc:1:
599. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
600. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o bank2scaff bank2scaff.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
601. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o bank-clean.o bank-clean.cc
602. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
603. from ../../src/AMOS/utility_AMOS.hh:48,
604. from ../../src/AMOS/foundation_AMOS.hh:13,
605. from bank-clean.cc:10:
606. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
607. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o bank-clean bank-clean.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
608. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o bank-combine.o bank-combine.cc
609. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
610. from ../../src/AMOS/utility_AMOS.hh:48,
611. from ../../src/AMOS/foundation_AMOS.hh:13,
612. from bank-combine.cc:11:
613. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
614. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o bank-combine bank-combine.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
615. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o bank-mapping.o bank-mapping.cc
616. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
617. from ../../src/AMOS/utility_AMOS.hh:48,
618. from ../../src/AMOS/foundation_AMOS.hh:13,
619. from bank-mapping.cc:14:
620. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
621. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o bank-mapping bank-mapping.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
622. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o bank-report.o bank-report.cc
623. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
624. from ../../src/AMOS/utility_AMOS.hh:48,
625. from ../../src/AMOS/foundation_AMOS.hh:13,
626. from bank-report.cc:14:
627. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
628. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o bank-report bank-report.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
629. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o bank-transact.o bank-transact.cc
630. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
631. from ../../src/AMOS/utility_AMOS.hh:48,
632. from ../../src/AMOS/foundation_AMOS.hh:13,
633. from bank-transact.cc:17:
634. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
635. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o bank-transact bank-transact.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
636. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o bank-tutorial.o bank-tutorial.cc
637. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
638. from ../../src/AMOS/utility_AMOS.hh:48,
639. from ../../src/AMOS/foundation_AMOS.hh:13,
640. from bank-tutorial.cc:1:
641. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
642. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o bank-tutorial bank-tutorial.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
643. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o dumpFeatures.o dumpFeatures.cc
644. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
645. from ../../src/AMOS/utility_AMOS.hh:48,
646. from ../../src/AMOS/foundation_AMOS.hh:13,
647. from dumpFeatures.cc:1:
648. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
649. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o dumpFeatures dumpFeatures.o ../../src/Foundation/libAMOSFoundation.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/GNU/libGNU.a -lz -lc -lm
650. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o dumpmates.o dumpmates.cc
651. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
652. from ../../src/AMOS/utility_AMOS.hh:48,
653. from ../../src/AMOS/foundation_AMOS.hh:13,
654. from dumpmates.cc:10:
655. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
656. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o dumpmates dumpmates.o ../../src/AMOS/libAMOS.a -lz -lc -lm
657. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o dumpreads.o dumpreads.cc
658. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
659. from ../../src/AMOS/utility_AMOS.hh:48,
660. from ../../src/AMOS/foundation_AMOS.hh:13,
661. from dumpreads.cc:10:
662. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
663. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o dumpreads dumpreads.o ../../src/AMOS/libAMOS.a -lz -lc -lm
664. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o extractContig.o extractContig.cc
665. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
666. from ../../src/AMOS/utility_AMOS.hh:48,
667. from ../../src/AMOS/foundation_AMOS.hh:13,
668. from extractContig.cc:1:
669. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
670. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o extractContig extractContig.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
671. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o findMissingMates.o findMissingMates.cc
672. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
673. from ../../src/AMOS/utility_AMOS.hh:48,
674. from ../../src/AMOS/foundation_AMOS.hh:13,
675. from findMissingMates.cc:10:
676. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
677. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o findMissingMates findMissingMates.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
678. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o grow-readbank.o grow-readbank.cc
679. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
680. from ../../src/AMOS/utility_AMOS.hh:48,
681. from ../../src/AMOS/foundation_AMOS.hh:13,
682. from grow-readbank.cc:10:
683. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
684. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o grow-readbank grow-readbank.o ../../src/CelMsg/libCelMsg.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
685. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o listReadPlacedStatus.o listReadPlacedStatus.cc
686. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
687. from ../../src/AMOS/utility_AMOS.hh:48,
688. from ../../src/AMOS/foundation_AMOS.hh:13,
689. from listReadPlacedStatus.cc:1:
690. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
691. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o listReadPlacedStatus listReadPlacedStatus.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
692. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o listGCContent.o listGCContent.cc
693. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
694. from ../../src/AMOS/utility_AMOS.hh:48,
695. from ../../src/AMOS/foundation_AMOS.hh:13,
696. from listGCContent.cc:1:
697. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
698. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o listGCContent listGCContent.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
699. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o load-overlaps.o load-overlaps.cc
700. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
701. from ../../src/AMOS/utility_AMOS.hh:48,
702. from ../../src/AMOS/foundation_AMOS.hh:13,
703. from load-overlaps.cc:10:
704. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
705. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o load-overlaps load-overlaps.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
706. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o loadFeatures.o loadFeatures.cc
707. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
708. from ../../src/AMOS/utility_AMOS.hh:48,
709. from ../../src/AMOS/foundation_AMOS.hh:13,
710. from loadFeatures.cc:1:
711. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
712. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o loadFeatures loadFeatures.o ../../src/Foundation/libAMOSFoundation.a ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
713. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o normalizeScaffold.o normalizeScaffold.cc
714. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
715. from ../../src/AMOS/utility_AMOS.hh:48,
716. from ../../src/AMOS/foundation_AMOS.hh:13,
717. from normalizeScaffold.cc:1:
718. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
719. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o normalizeScaffold normalizeScaffold.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
720. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o renameReads.o renameReads.cc
721. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
722. from ../../src/AMOS/utility_AMOS.hh:48,
723. from ../../src/AMOS/foundation_AMOS.hh:13,
724. from renameReads.cc:1:
725. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
726. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o renameReads renameReads.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
727. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o resetFragLibrary.o resetFragLibrary.cc
728. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
729. from ../../src/AMOS/utility_AMOS.hh:48,
730. from ../../src/AMOS/foundation_AMOS.hh:13,
731. from resetFragLibrary.cc:1:
732. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
733. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o resetFragLibrary resetFragLibrary.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
734. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o revScaffold.o revScaffold.cc
735. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
736. from ../../src/AMOS/utility_AMOS.hh:48,
737. from ../../src/AMOS/foundation_AMOS.hh:13,
738. from revScaffold.cc:1:
739. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
740. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o revScaffold revScaffold.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
741. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o select-reads.o select-reads.cc
742. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
743. from ../../src/AMOS/utility_AMOS.hh:48,
744. from ../../src/AMOS/foundation_AMOS.hh:13,
745. from select-reads.cc:10:
746. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
747. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o select-reads select-reads.o ../../src/AMOS/libAMOS.a -lz -lc -lm
748. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o simplifyLibraries-simplifyLibraries.o `test -f 'simplifyLibraries.cc' || echo './'`simplifyLibraries.cc
749. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
750. from ../../src/AMOS/utility_AMOS.hh:48,
751. from ../../src/AMOS/foundation_AMOS.hh:13,
752. from simplifyLibraries.cc:1:
753. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
754. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o simplifyLibraries simplifyLibraries-simplifyLibraries.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/GNU/libGNU.a -lz -lc -lm
755. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o simpleContigLoader.o simpleContigLoader.cc
756. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
757. from ../../src/AMOS/utility_AMOS.hh:48,
758. from ../../src/AMOS/foundation_AMOS.hh:13,
759. from simpleContigLoader.cc:1:
760. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
761. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o simpleContigLoader simpleContigLoader.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
762. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o updateBankPositions.o updateBankPositions.cc
763. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
764. from ../../src/AMOS/utility_AMOS.hh:48,
765. from ../../src/AMOS/foundation_AMOS.hh:13,
766. from updateBankPositions.cc:1:
767. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
768. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o updateBankPositions updateBankPositions.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
769. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o updateClrRanges.o updateClrRanges.cc
770. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
771. from ../../src/AMOS/utility_AMOS.hh:48,
772. from ../../src/AMOS/foundation_AMOS.hh:13,
773. from updateClrRanges.cc:1:
774. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
775. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o updateClrRanges updateClrRanges.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
776. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Common -I../../src/Slice -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o updateLibSizes.o updateLibSizes.cc
777. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
778. from ../../src/AMOS/utility_AMOS.hh:48,
779. from ../../src/AMOS/foundation_AMOS.hh:13,
780. from updateLibSizes.cc:1:
781. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
782. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o updateLibSizes updateLibSizes.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a -lz -lc -lm
783. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o dumpContigsAsReads-dumpContigsAsReads.o `test -f 'dumpContigsAsReads.cc' || echo './'`dumpContigsAsReads.cc
784. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
785. from ../../src/AMOS/utility_AMOS.hh:48,
786. from ../../src/AMOS/foundation_AMOS.hh:13,
787. from dumpContigsAsReads.cc:18:
788. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
789. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o dumpContigsAsReads dumpContigsAsReads-dumpContigsAsReads.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/GNU/libGNU.a -lz -lc -lm
790. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/Common -I../../src/AMOS -I../../src/GNU -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o partitionBank-partitionBank.o `test -f 'partitionBank.cc' || echo './'`partitionBank.cc
791. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
792. from ../../src/AMOS/utility_AMOS.hh:48,
793. from ../../src/AMOS/foundation_AMOS.hh:13,
794. from partitionBank.cc:10:
795. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
796. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o partitionBank partitionBank-partitionBank.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/GNU/libGNU.a -lz -lc -lm
797. make[3]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Bank'
798. Making all in Align
799. make[3]: Entering directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Align'
800. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o align.o align.cc
801. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
802. from ../../src/AMOS/utility_AMOS.hh:48,
803. from ../../src/AMOS/Message_AMOS.hh:14,
804. from ../../src/AMOS/datatypes_AMOS.hh:17,
805. from align.hh:13,
806. from align.cc:9:
807. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
808. align.cc: In member function 'void Multi_Alignment_t::Print_Alignments_To_Consensus(FILE*, std::vector<char*>)':
809. align.cc:1939:64: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::basic_string<char>::size_type {aka long unsigned int}' [-Wformat]
810. rm -f libAlign.a
811. ar cru libAlign.a align.o
812. x86_64-pc-linux-gnu-ranlib libAlign.a
813. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o align_poly.o align_poly.cc
814. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
815. from ../../src/AMOS/utility_AMOS.hh:48,
816. from ../../src/AMOS/Message_AMOS.hh:14,
817. from ../../src/AMOS/datatypes_AMOS.hh:17,
818. from align_poly.hh:14,
819. from align_poly.cc:10:
820. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
821. align_poly.cc: In member function 'void Multi_Alignment_t::Print_Alignments_To_Consensus(FILE*, std::vector<char*>)':
822. align_poly.cc:1764:64: warning: format '%d' expects argument of type 'int', but argument 3 has type 'std::basic_string<char>::size_type {aka long unsigned int}' [-Wformat]
823. rm -f libAlign_poly.a
824. ar cru libAlign_poly.a align_poly.o
825. x86_64-pc-linux-gnu-ranlib libAlign_poly.a
826. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o arrive.o arrive.cc
827. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o arrive arrive.o -lz -lc -lm
828. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o arrive2.o arrive2.cc
829. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o arrive2 arrive2.o ../../src/Common/libCommon.a -lz -lc -lm
830. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o genome-complexity-fast.o genome-complexity-fast.cc
831. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
832. from ../../src/AMOS/utility_AMOS.hh:48,
833. from ../../src/AMOS/foundation_AMOS.hh:13,
834. from genome-complexity-fast.cc:1:
835. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
836. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o genome-complexity genome-complexity-fast.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a ../../src/GNU/libGNU.a -lz -lc -lm
837. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o genome-complexity-fast genome-complexity-fast.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a ../../src/GNU/libGNU.a -lz -lc -lm
838. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o count-kmers.o count-kmers.cc
839. In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/ext/hash_map:61:0,
840. from ../../src/AMOS/utility_AMOS.hh:48,
841. from ../../src/AMOS/foundation_AMOS.hh:13,
842. from count-kmers.cc:1:
843. /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.1/include/g++-v4/backward/backward_warning.h:33:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
844. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o count-kmers count-kmers.o ../../src/Common/libCommon.a ../../src/AMOS/libAMOS.a ../../src/Foundation/libAMOSFoundation.a -lz -lc -lm
845. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/CelMsg -I../../src/Slice -I../../src/Common -I../../src/AMOS -I../../src/GNU -I../../src/Foundation -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o find-tandem.o find-tandem.cc
846. find-tandem.cc: In function 'int main(int, char**)':
847. find-tandem.cc:243:3: error: 'optarg' was not declared in this scope
848. find-tandem.cc:245:63: error: 'getopt' was not declared in this scope
849. find-tandem.cc:258:55: error: 'optopt' was not declared in this scope
850. make[3]: *** [find-tandem.o] Error 1
851. make[3]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src/Align'
852. make[2]: *** [all-recursive] Error 1
853. make[2]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0/src'
854. make[1]: *** [all-recursive] Error 1
855. make[1]: Leaving directory `/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0'
856. make: *** [all] Error 2
857. * ERROR: sci-biology/amos-3.1.0 failed (compile phase):
858. * emake failed
859. *
860. * If you need support, post the output of `emerge --info '=sci-biology/amos-3.1.0'`,
861. * the complete build log and the output of `emerge -pqv '=sci-biology/amos-3.1.0'`.
862. * The complete build log is located at '/var/log/portage/sci-biology:amos-3.1.0:20120707-102601.log'.
863. * For convenience, a symlink to the build log is located at '/tmp/portage/sci-biology/amos-3.1.0/temp/build.log'.
864. * The ebuild environment file is located at '/tmp/portage/sci-biology/amos-3.1.0/temp/environment'.
865. * Working directory: '/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0'
866. * S: '/tmp/portage/sci-biology/amos-3.1.0/work/amos-3.1.0'