1. * Package: sci-biology/vienna-rna-2.1.8
2. * Repository: gentoo
3. * Maintainer: sci-biology@gentoo.org
4. * USE: abi_x86_64 amd64 doc elibc_glibc kernel_linux openmp python_targets_python2_7 userland_GNU
5. * FEATURES: sandbox test userpriv usersandbox
6. Installed LAPACK for library directory lib64
7. [1] reference *
8. Installed BLAS for library directory lib64
9. [1] reference *
10. Installed CBLAS for library directory lib64
11. [1] gsl
12. [2] reference *
13. >>> Unpacking source...
14. >>> Unpacking ViennaRNA-2.1.8.tar.gz to /tmp/portage/sci-biology/vienna-rna-2.1.8/work
15. >>> Source unpacked in /tmp/portage/sci-biology/vienna-rna-2.1.8/work
16. >>> Preparing source in /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ...
17. * Applying vienna-rna-2.1.8-bindir.patch ...
18. [ ok ]
19. * Applying vienna-rna-2.1.1-prll.patch ...
20. [ ok ]
21. * Applying vienna-rna-2.1.1-impl-decl.patch ...
22. [ ok ]
23. * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8' ...
24. * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold' ...
25. * Running aclocal ...
26. * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70' ...
27. * Running aclocal ...
28. * Running aclocal ...
29. [ ok ]
30. [ ok ]
31. [ ok ]
32. * Running autoconf ...
33. * Running autoconf ...
34. [ ok ]
35. * Running autoheader ...
36. [ ok ]
37. * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester' ...
38. * Running autoconf ...
39. * Running aclocal ...
40. [ ok ]
41. * Running automake --add-missing --copy --force-missing ...
42. [ ok ]
43. * Running autoheader ...
44. [ ok ]
45. * Running automake --add-missing --copy --force-missing ...
46. [ ok ]
47. [ ok ]
48. * Running autoconf ...
49. [ ok ]
50. * Running elibtoolize in: ViennaRNA-2.1.8/
51. * Running elibtoolize in: ViennaRNA-2.1.8/Kinfold/
52. * Running elibtoolize in: ViennaRNA-2.1.8/RNAforester/
53. [ ok ]
54. * Running autoheader ...
55. * Running elibtoolize in: ViennaRNA-2.1.8/RNAforester/g2-0.70/
56. [ ok ]
57. * Running automake --add-missing --copy --force-missing ...
58. [ ok ]
59. >>> Source prepared.
60. >>> Configuring source in /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ...
61. >>> Working in BUILD_DIR: "/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8"
62. * econf: updating ViennaRNA-2.1.8/config.sub with /usr/share/gnuconfig/config.sub
63. * econf: updating ViennaRNA-2.1.8/config.guess with /usr/share/gnuconfig/config.guess
64. * econf: updating ViennaRNA-2.1.8/config/config.sub with /usr/share/gnuconfig/config.sub
65. * econf: updating ViennaRNA-2.1.8/config/config.guess with /usr/share/gnuconfig/config.guess
66. * econf: updating ViennaRNA-2.1.8/RNAforester/g2-0.70/config.sub with /usr/share/gnuconfig/config.sub
67. * econf: updating ViennaRNA-2.1.8/RNAforester/g2-0.70/config.guess with /usr/share/gnuconfig/config.guess
68. * econf: updating ViennaRNA-2.1.8/RNAforester/config.guess with /usr/share/gnuconfig/config.guess
69. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/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 --disable-dependency-tracking --disable-silent-rules --libdir=/usr/lib64 --docdir=/usr/share/doc/vienna-rna-2.1.8 --enable-shared --disable-static --with-cluster --enable-openmp
70. configure: loading site script /usr/share/config.site
71. checking whether make supports nested variables... yes
72. checking for a BSD-compatible install... /usr/bin/install -c
73. checking whether build environment is sane... yes
74. checking for a thread-safe mkdir -p... /bin/mkdir -p
75. checking for gawk... gawk
76. checking whether make sets $(MAKE)... yes
77. checking if malloc debugging is wanted... no
78. checking build system type... x86_64-pc-linux-gnu
79. checking host system type... x86_64-pc-linux-gnu
80. checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
81. checking whether the C++ compiler works... yes
82. checking for C++ compiler default output file name... a.out
83. checking for suffix of executables...
84. checking whether we are cross compiling... no
85. checking for suffix of object files... o
86. checking whether we are using the GNU C++ compiler... yes
87. checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
88. checking for style of include used by make... GNU
89. checking dependency style of x86_64-pc-linux-gnu-g++... none
90. checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
91. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
92. checking whether we are using the GNU C compiler... yes
93. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
94. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
95. checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
96. checking dependency style of x86_64-pc-linux-gnu-gcc... none
97. checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
98. checking whether x86_64-pc-linux-gnu-gcc accepts -fpic... yes
99. checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
100. checking whether make sets $(MAKE)... (cached) yes
101. checking for grep that handles long lines and -e... /bin/grep
102. checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp
103. checking for exp in -lm... yes
104. checking for egrep... /bin/grep -E
105. checking for ANSI C header files... yes
106. checking for sys/types.h... yes
107. checking for sys/stat.h... yes
108. checking for stdlib.h... yes
109. checking for string.h... yes
110. checking for memory.h... yes
111. checking for strings.h... yes
112. checking for inttypes.h... yes
113. checking for stdint.h... yes
114. checking for unistd.h... yes
115. checking for stdbool.h that conforms to C99... yes
116. checking for _Bool... yes
117. checking malloc.h usability... yes
118. checking malloc.h presence... yes
119. checking for malloc.h... yes
120. checking float.h usability... yes
121. checking float.h presence... yes
122. checking for float.h... yes
123. checking limits.h usability... yes
124. checking limits.h presence... yes
125. checking for limits.h... yes
126. checking for stdlib.h... (cached) yes
127. checking for string.h... (cached) yes
128. checking for strings.h... (cached) yes
129. checking for unistd.h... (cached) yes
130. checking for unistd.h... (cached) yes
131. checking math.h usability... yes
132. checking math.h presence... yes
133. checking for math.h... yes
134. checking for stdlib.h... (cached) yes
135. checking for GNU libc compatible malloc... yes
136. checking for stdlib.h... (cached) yes
137. checking for GNU libc compatible realloc... yes
138. checking for working strtod... yes
139. checking for floor... yes
140. checking for strdup... yes
141. checking for strstr... yes
142. checking for strchr... yes
143. checking for strrchr... yes
144. checking for strstr... (cached) yes
145. checking for strtol... yes
146. checking for strtoul... yes
147. checking for pow... yes
148. checking for rint... yes
149. checking for sqrt... yes
150. checking for erand48... yes
151. checking for memset... yes
152. checking for memmove... yes
153. checking for erand48... (cached) yes
154. checking for an ANSI C-conforming const... yes
155. checking for size_t... yes
156. checking for inline... inline
157. checking for interfaces/Perl/Makefile.am... yes
158. checking for Kinfold/Makefile.am... yes
159. checking for RNAforester/Makefile.am... yes
160. checking for Cluster/Makefile.am... yes
161. checking for libsvm-2.91/svm.cpp... yes
162. checking for libsvm-2.91/svm.h... yes
163. checking whether float precision is used for partition function arrays instead of double precision... no
164. checking for perl... /usr/bin/perl
165. checking for python... /usr/bin/python
166. checking for doxygen... /usr/bin/doxygen
167. checking for pdflatex... /usr/bin/pdflatex
168. checking for latex... /usr/bin/latex
169. checking for makeindex... /usr/bin/makeindex
170. checking for dot... /usr/bin/dot
171. checking for egrep... /bin/egrep
172. checking for perl... /usr/bin/perl
173. configure: WARNING: due to a bug in older versions of doxygen, latex will be used for reference manual generation even if pdflatex is available
174. checking that generated files are newer than configure... done
175. configure: creating ./config.status
176. config.status: creating interfaces/Perl/Makefile
177. config.status: creating interfaces/Perl/Makefile.PL
178. config.status: creating Cluster/Makefile
179. config.status: creating doc/doxygen.conf
180. config.status: creating misc/Makefile
181. config.status: creating misc/ViennaRNA.spec
182. config.status: creating misc/PKGBUILD
183. config.status: creating interfaces/Makefile
184. config.status: creating Makefile
185. config.status: creating RNAlib2.pc
186. config.status: creating Utils/Makefile
187. config.status: creating Progs/Makefile
188. config.status: creating lib/Makefile
189. config.status: creating man/Makefile
190. config.status: creating H/Makefile
191. config.status: creating doc/Makefile
192. config.status: creating man/cmdlopt.sh
193. config.status: creating config.h
194. config.status: executing depfiles commands
195. === configuring in Kinfold (/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold)
196. configure: running /bin/bash ./configure --disable-option-checking '--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' '--disable-dependency-tracking' '--disable-silent-rules' '--libdir=/usr/lib64' '--docdir=/usr/share/doc/vienna-rna-2.1.8' '--enable-shared' '--disable-static' '--with-cluster' '--enable-openmp' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches' --cache-file=/dev/null --srcdir=.
197. configure: loading site script /usr/share/config.site
198. checking whether make supports nested variables... yes
199. checking for a BSD-compatible install... /usr/bin/install -c
200. checking whether build environment is sane... yes
201. checking for a thread-safe mkdir -p... /bin/mkdir -p
202. checking for gawk... gawk
203. checking whether make sets $(MAKE)... yes
204. checking if malloc debugging is wanted... no
205. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
206. checking whether the C compiler works... yes
207. checking for C compiler default output file name... a.out
208. checking for suffix of executables...
209. checking whether we are cross compiling... no
210. checking for suffix of object files... o
211. checking whether we are using the GNU C compiler... yes
212. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
213. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
214. checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
215. checking for style of include used by make... GNU
216. checking dependency style of x86_64-pc-linux-gnu-gcc... none
217. checking build system type... x86_64-pc-linux-gnu
218. checking host system type... x86_64-pc-linux-gnu
219. checking for strdup... yes
220. checking for memset... yes
221. checking for strchr... yes
222. checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp
223. checking for ViennaRNA package... headers in "../H" and library... "../lib"
224. checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
225. checking for grep that handles long lines and -e... /bin/grep
226. checking for egrep... /bin/grep -E
227. checking for ANSI C header files... yes
228. checking for sys/types.h... yes
229. checking for sys/stat.h... yes
230. checking for stdlib.h... yes
231. checking for string.h... yes
232. checking for memory.h... yes
233. checking for strings.h... yes
234. checking for inttypes.h... yes
235. checking for stdint.h... yes
236. checking for unistd.h... yes
237. checking for stdlib.h... (cached) yes
238. checking for string.h... (cached) yes
239. checking for strings.h... (cached) yes
240. checking for unistd.h... (cached) yes
241. checking fold.h usability... yes
242. checking fold.h presence... yes
243. checking for fold.h... yes
244. checking for exp in -lm... yes
245. checking for stdlib.h... (cached) yes
246. checking for GNU libc compatible malloc... yes
247. checking for stdlib.h... (cached) yes
248. checking for GNU libc compatible realloc... yes
249. checking for an ANSI C-conforming const... yes
250. checking that generated files are newer than configure... done
251. configure: creating ./config.status
252. config.status: creating Example/Makefile
253. config.status: creating Makefile
254. config.status: creating config.h
255. config.status: executing depfiles commands
256. === configuring in RNAforester (/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester)
257. configure: running /bin/bash ./configure --disable-option-checking '--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' '--disable-dependency-tracking' '--disable-silent-rules' '--libdir=/usr/lib64' '--docdir=/usr/share/doc/vienna-rna-2.1.8' '--enable-shared' '--disable-static' '--with-cluster' '--enable-openmp' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches' --cache-file=/dev/null --srcdir=.
258. configure: loading site script /usr/share/config.site
259. checking whether make supports nested variables... yes
260. checking for a BSD-compatible install... /usr/bin/install -c
261. checking whether build environment is sane... yes
262. checking for a thread-safe mkdir -p... /bin/mkdir -p
263. checking for gawk... gawk
264. checking whether make sets $(MAKE)... yes
265. checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
266. checking whether the C++ compiler works... yes
267. checking for C++ compiler default output file name... a.out
268. checking for suffix of executables...
269. checking whether we are cross compiling... no
270. checking for suffix of object files... o
271. checking whether we are using the GNU C++ compiler... yes
272. checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
273. checking for style of include used by make... GNU
274. checking dependency style of x86_64-pc-linux-gnu-g++... none
275. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
276. checking whether we are using the GNU C compiler... yes
277. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
278. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
279. checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
280. checking dependency style of x86_64-pc-linux-gnu-gcc... none
281. checking for x86_64-pc-linux-gnu-g++ option to support OpenMP... -fopenmp
282. using (to be built) libRNA.a in ../lib
283. checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
284. checking for grep that handles long lines and -e... /bin/grep
285. checking for egrep... /bin/grep -E
286. checking for ANSI C header files... no
287. checking for sys/types.h... yes
288. checking for sys/stat.h... yes
289. checking for stdlib.h... yes
290. checking for string.h... yes
291. checking for memory.h... yes
292. checking for strings.h... yes
293. checking for inttypes.h... yes
294. checking for stdint.h... yes
295. checking for unistd.h... yes
296. checking g2.h usability... yes
297. checking g2.h presence... yes
298. checking for g2.h... yes
299. checking for an ANSI C-conforming const... yes
300. checking for inline... inline
301. checking for size_t... yes
302. checking that generated files are newer than configure... done
303. configure: creating ./config.status
304. config.status: creating Makefile
305. config.status: creating src/Makefile
306. config.status: creating man/Makefile
307. config.status: creating config.h
308. config.status: executing depfiles commands
309. === configuring in g2-0.70 (/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70)
310. configure: running /bin/bash ./configure --disable-option-checking '--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' '--disable-dependency-tracking' '--disable-silent-rules' '--libdir=/usr/lib64' '--docdir=/usr/share/doc/vienna-rna-2.1.8' '--enable-shared' '--disable-static' '--with-cluster' '--enable-openmp' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CXXFLAGS=-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CFLAGS=-O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches' --cache-file=/dev/null --srcdir=.
311. configure: loading site script /usr/share/config.site
312. checking build system type... x86_64-pc-linux-gnu
313. checking host system type... x86_64-pc-linux-gnu
314. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
315. checking whether the C compiler works... yes
316. checking for C compiler default output file name... a.out
317. checking for suffix of executables...
318. checking whether we are cross compiling... no
319. checking for suffix of object files... o
320. checking whether we are using the GNU C compiler... yes
321. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
322. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
323. checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
324. checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
325. checking whether we are using the GNU C++ compiler... yes
326. checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
327. checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
328. checking for a BSD-compatible install... /usr/bin/install -c
329. checking for find... find
330. checking for makedepend... makedepend
331. checking for dlopen in -ldl... yes
332. checking for X... libraries , headers
333. checking for gethostbyname... yes
334. checking for connect... yes
335. checking for remove... yes
336. checking for shmat... yes
337. checking for IceConnectionNumber in -lICE... yes
338. checking for main in -lm... yes
339. checking for main in -lX11... yes
340. checking for main in -lgd... yes
341. checking for gdImagePng... no
342. checking for grep that handles long lines and -e... /bin/grep
343. checking for egrep... /bin/grep -E
344. checking for ANSI C header files... yes
345. checking for sys/types.h... yes
346. checking for sys/stat.h... yes
347. checking for stdlib.h... yes
348. checking for string.h... yes
349. checking for memory.h... yes
350. checking for strings.h... yes
351. checking for inttypes.h... yes
352. checking for stdint.h... yes
353. checking for unistd.h... yes
354. checking limits.h usability... yes
355. checking limits.h presence... yes
356. checking for limits.h... yes
358. configure: creating ./config.status
359. config.status: creating Makefile
360. config.status: creating demo/Makefile
361. config.status: creating g2_perl/Makefile.PL
363. Supported devices:
364. PostScript
365. FIG
366. X11
368. Unsupported devices:
369. Win32
370. GD
372. Run 'make depend' to create dependencies.
374. configure:
375. Configure successful with the following options:
377. RNAlib Interfaces:
378. Perl Interface: yes
379. Python Interface: no
380. Ruby Interface: no
382. Extra Programs:
383. Analyse{Dists,Seqs}: yes
384. Kinfold: yes
385. RNAforester: yes
387. Other Options:
388. SVM: yes
389. Documentation: yes
390. (HTML): yes
391. (PDF): yes
392. -
393. Files will be installed in the following directories:
395. Executables: /usr/bin
396. Libraries: /usr/lib64
397. Header files: /usr/include
398. Extra Data: /usr/share
399. Man pages: /usr/share/man
400. Documentation: /usr/share/doc/vienna-rna-2.1.8
401. (HTML): /usr/share/doc/vienna-rna-2.1.8/html
402. (PDF): /usr/share/doc/vienna-rna-2.1.8
404. >>> Source configured.
405. >>> Compiling source in /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8 ...
406. >>> Working in BUILD_DIR: "/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8"
407. make -j24
408. make all-recursive
409. make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8'
410. Making all in lib
411. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib'
412. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c
413. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c
414. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c
415. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c
416. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c
417. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c
418. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c
419. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c
420. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c
421. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-utils.o `test -f 'utils.c' || echo './'`utils.c
422. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-fold.o `test -f 'fold.c' || echo './'`fold.c
423. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-naview.o `test -f 'naview.c' || echo './'`naview.c
424. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c
425. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c
426. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-params.o `test -f 'params.c' || echo './'`params.c
427. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c
428. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-list.o `test -f 'list.c' || echo './'`list.c
429. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c
430. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c
431. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c
432. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c
433. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c
434. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c
435. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c
436. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c
437. naview.c: In function 'dump_loops':
438. naview.c:341:3: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
439. printf("\nRoot loop is #%d\n",(root-loops)+1);
440. ^
441. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c
442. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.c
443. LPfold.c: In function 'putoutpU_splitup':
444. LPfold.c:1012:3: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'int' [-Wformat=]
445. fprintf(fp,"\t%s\n",ident);
446. ^
447. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-ribo.o `test -f 'ribo.c' || echo './'`ribo.c
448. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-findpath.o `test -f 'findpath.c' || echo './'`findpath.c
449. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-convert_epars.o `test -f 'convert_epars.c' || echo './'`convert_epars.c
450. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-MEA.o `test -f 'MEA.c' || echo './'`MEA.c
451. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-aliLfold.o `test -f 'aliLfold.c' || echo './'`aliLfold.c
452. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-mm.o `test -f 'mm.c' || echo './'`mm.c
453. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-2Dfold.o `test -f '2Dfold.c' || echo './'`2Dfold.c
454. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-2Dpfold.o `test -f '2Dpfold.c' || echo './'`2Dpfold.c
455. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-plex_functions.o `test -f 'plex_functions.c' || echo './'`plex_functions.c
456. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-plot_layouts.o `test -f 'plot_layouts.c' || echo './'`plot_layouts.c
457. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-ali_plex.o `test -f 'ali_plex.c' || echo './'`ali_plex.c
458. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-c_plex.o `test -f 'c_plex.c' || echo './'`c_plex.c
459. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-plex.o `test -f 'plex.c' || echo './'`plex.c
460. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-snofold.o `test -f 'snofold.c' || echo './'`snofold.c
461. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-snoop.o `test -f 'snoop.c' || echo './'`snoop.c
462. c_plex.c: In function 'find_max_C':
463. c_plex.c:1076:20: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
464. test.energy);
465. ^
466. c_plex.c: In function 'plot_max_C':
467. c_plex.c:1114:14: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
468. (begin_q -11) + test.j + strlen(test.structure)-l1-2 , test.energy);
469. ^
470. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-move_set.o `test -f 'move_set.c' || echo './'`move_set.c
471. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-gquad.o `test -f 'gquad.c' || echo './'`gquad.c
472. plex.c: In function 'find_max_XS':
473. plex.c:1518:18: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
474. position[pos+delta]);
475. ^
476. plex.c: In function 'plot_max_XS':
477. plex.c:1613:12: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
478. test.energy_backtrack + test.dG1 + test.dG2, test.energy_backtrack , test.dG1 , test.dG2);
479. ^
480. snoop.c: In function 'find_max_snoop':
481. snoop.c:1091:14: warning: format '%d' expects argument of type 'int', but argument 7 has type 'long int' [-Wformat=]
482. test.Duplex_Er, test.Loop_E, test.Loop_D,test.fullStemEnergy, target,s4);
483. ^
484. snoop.c: In function 'snoop_subopt_XS':
485. snoop.c:1604:14: warning: format '%d' expects argument of type 'int', but argument 7 has type 'long int' [-Wformat=]
486. test.Duplex_Er, test.Loop_E, test.Loop_D,dE , test.fullStemEnergy, s5,s4);
487. ^
488. plex.c: In function 'find_max':
489. plex.c:2676:18: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
490. test.energy,test.energy_backtrack);
491. ^
492. plex.c:2723:18: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
493. test.energy);
494. ^
495. plex.c: In function 'plot_max':
496. plex.c:2758:12: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
497. test.energy, test.energy_backtrack);
498. ^
499. plex.c:2780:12: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
500. test.energy);
501. ^
502. snoop.c: In function 'find_max_snoop_XS':
503. snoop.c:2100:14: warning: format '%d' expects argument of type 'int', but argument 7 has type 'long int' [-Wformat=]
504. test.Duplex_Er, test.Loop_E, test.Loop_D,dE ,test.fullStemEnergy, s5,s4);
505. ^
506. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o svm.o `test -f '../libsvm-2.91/svm.cpp' || echo './'`../libsvm-2.91/svm.cpp
507. ali_plex.c: In function 'alifind_max':
508. ali_plex.c:599:18: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
509. begin_q-11 + test.j +strlen(test.structure) -l1 -2 , test.energy);
510. ^
511. ali_plex.c: In function 'aliplot_max':
512. ali_plex.c:649:12: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
513. test.energy);
514. ^
515. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../libsvm-2.91 -fpic -fopenmp -fpic -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o libRNA_a-svm_utils.o `test -f 'svm_utils.c' || echo './'`svm_utils.c
516. ../libsvm-2.91/svm.cpp: In function 'svm_model* svm_load_model(const char*)':
517. ../libsvm-2.91/svm.cpp:2730:24: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
518. fscanf(fp,"%80s",cmd);
519. ^
520. ../libsvm-2.91/svm.cpp:2734:25: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
521. fscanf(fp,"%80s",cmd);
522. ^
523. ../libsvm-2.91/svm.cpp:2756:25: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
524. fscanf(fp,"%80s",cmd);
525. ^
526. ../libsvm-2.91/svm.cpp:2777:33: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
527. fscanf(fp,"%d",&param.degree);
528. ^
529. ../libsvm-2.91/svm.cpp:2779:33: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
530. fscanf(fp,"%lf",&param.gamma);
531. ^
532. ../libsvm-2.91/svm.cpp:2781:33: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
533. fscanf(fp,"%lf",&param.coef0);
534. ^
535. ../libsvm-2.91/svm.cpp:2783:36: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
536. fscanf(fp,"%d",&model->nr_class);
537. ^
538. ../libsvm-2.91/svm.cpp:2785:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
539. fscanf(fp,"%d",&model->l);
540. ^
541. ../libsvm-2.91/svm.cpp:2791:36: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
542. fscanf(fp,"%lf",&model->rho[i]);
543. ^
544. ../libsvm-2.91/svm.cpp:2798:37: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
545. fscanf(fp,"%d",&model->label[i]);
546. ^
547. ../libsvm-2.91/svm.cpp:2805:38: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
548. fscanf(fp,"%lf",&model->probA[i]);
549. ^
550. ../libsvm-2.91/svm.cpp:2812:38: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
551. fscanf(fp,"%lf",&model->probB[i]);
552. ^
553. ../libsvm-2.91/svm.cpp:2819:35: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
554. fscanf(fp,"%d",&model->nSV[i]);
555. ^
556. rm -f libRNA.a
557. ar cru libRNA.a libRNA_a-dist_vars.o libRNA_a-fold_vars.o libRNA_a-part_func.o libRNA_a-read_epars.o libRNA_a-treedist.o libRNA_a-energy_par.o libRNA_a-inverse.o libRNA_a-ProfileDist.o libRNA_a-RNAstruct.o libRNA_a-utils.o libRNA_a-fold.o libRNA_a-naview.o libRNA_a-PS_dot.o libRNA_a-stringdist.o libRNA_a-params.o libRNA_a-subopt.o libRNA_a-list.o libRNA_a-Lfold.o libRNA_a-cofold.o libRNA_a-part_func_co.o libRNA_a-ProfileAln.o libRNA_a-duplex.o libRNA_a-alifold.o libRNA_a-alipfold.o libRNA_a-aln_util.o libRNA_a-LPfold.o libRNA_a-part_func_up.o libRNA_a-ribo.o libRNA_a-findpath.o libRNA_a-convert_epars.o libRNA_a-MEA.o libRNA_a-aliLfold.o libRNA_a-mm.o libRNA_a-2Dfold.o libRNA_a-2Dpfold.o libRNA_a-plex_functions.o libRNA_a-plot_layouts.o libRNA_a-ali_plex.o libRNA_a-c_plex.o libRNA_a-plex.o libRNA_a-snofold.o libRNA_a-snoop.o libRNA_a-move_set.o libRNA_a-gquad.o svm.o libRNA_a-svm_utils.o
558. x86_64-pc-linux-gnu-ranlib libRNA.a
559. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib'
560. Making all in Progs
561. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs'
562. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAfold_cmdl.o RNAfold_cmdl.c
563. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAfold.o RNAfold.c
564. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAeval_cmdl.o RNAeval_cmdl.c
565. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAeval.o RNAeval.c
566. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAheat_cmdl.o RNAheat_cmdl.c
567. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAheat.o RNAheat.c
568. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNApdist_cmdl.o RNApdist_cmdl.c
569. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNApdist.o RNApdist.c
570. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAdistance_cmdl.o RNAdistance_cmdl.c
571. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAdistance.o RNAdistance.c
572. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAinverse_cmdl.o RNAinverse_cmdl.c
573. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAinverse.o RNAinverse.c
574. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAplot_cmdl.o RNAplot_cmdl.c
575. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAplot.o RNAplot.c
576. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAsubopt_cmdl.o RNAsubopt_cmdl.c
577. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAsubopt.o RNAsubopt.c
578. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNALfold_cmdl.o RNALfold_cmdl.c
579. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNALfold.o RNALfold.c
580. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAcofold_cmdl.o RNAcofold_cmdl.c
581. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAcofold.o RNAcofold.c
582. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNApaln_cmdl.o RNApaln_cmdl.c
583. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNApaln.o RNApaln.c
584. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAduplex_cmdl.o RNAduplex_cmdl.c
585. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAduplex.o RNAduplex.c
586. RNAduplex.c: In function 'main':
587. RNAduplex.c:161:5: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
588. if (istty) printf("lengths = %d,%d\n", strlen(s1), strlen(s2));
589. ^
590. RNAduplex.c:161:5: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' [-Wformat=]
591. RNAduplex.c: In function 'print_struc':
592. RNAduplex.c:203:10: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
593. dup->i, dup->j, dup->j+strlen(dup->structure)-l1-2, dup->energy);
594. ^
595. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAalifold_cmdl.o RNAalifold_cmdl.c
596. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAalifold.o RNAalifold.c
597. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAplfold_cmdl.o RNAplfold_cmdl.c
598. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAplfold.o RNAplfold.c
599. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAup_cmdl.o RNAup_cmdl.c
600. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAup.o RNAup.c
601. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAaliduplex_cmdl.o RNAaliduplex_cmdl.c
602. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAaliduplex.o RNAaliduplex.c
603. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNALalifold_cmdl.o RNALalifold_cmdl.c
604. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNALalifold.o RNALalifold.c
605. RNAaliduplex.c: In function 'print_struc':
606. RNAaliduplex.c:171:10: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
607. dup->i, dup->j, dup->j+strlen(dup->structure)-l1-2, dup->energy);
608. ^
609. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNA2Dfold_cmdl.o RNA2Dfold_cmdl.c
610. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNA2Dfold.o RNA2Dfold.c
611. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAparconv_cmdl.o RNAparconv_cmdl.c
612. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAparconv.o RNAparconv.c
613. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAPKplex_cmdl.o RNAPKplex_cmdl.c
614. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAPKplex.o RNAPKplex.c
615. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAplex_cmdl.o RNAplex_cmdl.c
616. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAplex.o RNAplex.c
617. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAsnoop_cmdl.o RNAsnoop_cmdl.c
618. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -I./../lib -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o RNAsnoop.o RNAsnoop.c
619. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAeval RNAeval_cmdl.o RNAeval.o -fopenmp ../lib/libRNA.a -lm -lm
620. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAheat RNAheat_cmdl.o RNAheat.o -fopenmp ../lib/libRNA.a -lm -lm
621. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNApdist RNApdist_cmdl.o RNApdist.o -fopenmp ../lib/libRNA.a -lm -lm
622. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAdistance RNAdistance_cmdl.o RNAdistance.o -fopenmp ../lib/libRNA.a -lm -lm
623. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAinverse RNAinverse_cmdl.o RNAinverse.o -fopenmp ../lib/libRNA.a -lm -lm
624. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAplot RNAplot_cmdl.o RNAplot.o -fopenmp ../lib/libRNA.a -lm -lm
625. RNAplex.c: In function 'main':
626. RNAplex.c:1100:9: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat=]
627. printf("lengths = %d,%d\n", strlen(s1), strlen(s2));
628. ^
629. RNAplex.c:1100:9: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' [-Wformat=]
630. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNALfold RNALfold_cmdl.o RNALfold.o -fopenmp ../lib/libRNA.a -lm -lm
631. RNAsnoop.c: In function 'print_struc':
632. RNAsnoop.c:546:10: warning: format '%d' expects argument of type 'int', but argument 7 has type 'long int' [-Wformat=]
633. dup->Duplex_El, dup->Duplex_Er, dup->Loop_E, dup->Loop_D,dup->fullStemEnergy,target,s4);
634. ^
635. RNAsnoop.c: In function 'aliprint_struc':
636. RNAsnoop.c:627:11: warning: format '%d' expects argument of type 'int', but argument 7 has type 'long int' [-Wformat=]
637. dup->Duplex_El/n_seq, dup->Duplex_Er/n_seq, dup->Loop_E/n_seq, dup->Loop_D/n_seq,dup->pscd/n_seq, dup->psct/n_seq,consens );
638. ^
639. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNApaln RNApaln_cmdl.o RNApaln.o -fopenmp ../lib/libRNA.a -lm -lm
640. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAduplex RNAduplex_cmdl.o RNAduplex.o -fopenmp ../lib/libRNA.a -lm -lm
641. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAcofold RNAcofold_cmdl.o RNAcofold.o -fopenmp ../lib/libRNA.a -lm -lm
642. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAfold RNAfold_cmdl.o RNAfold.o -fopenmp ../lib/libRNA.a -lm -lm
643. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAsubopt RNAsubopt_cmdl.o RNAsubopt.o -fopenmp ../lib/libRNA.a -lm -lm
644. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o -fopenmp ../lib/libRNA.a -lm -lm
645. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAplfold RNAplfold_cmdl.o RNAplfold.o -fopenmp ../lib/libRNA.a -lm -lm
646. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAalifold RNAalifold_cmdl.o RNAalifold.o -fopenmp ../lib/libRNA.a -lm -lm
647. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAup RNAup_cmdl.o RNAup.o -fopenmp ../lib/libRNA.a -lm -lm
648. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o -fopenmp ../lib/libRNA.a -lm -lm
649. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNALalifold RNALalifold_cmdl.o RNALalifold.o -fopenmp ../lib/libRNA.a -lm -lm
650. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAparconv RNAparconv_cmdl.o RNAparconv.o -fopenmp ../lib/libRNA.a -lm -lm
651. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.o -fopenmp ../lib/libRNA.a -lm -lm
652. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAsnoop RNAsnoop_cmdl.o RNAsnoop.o -fopenmp ../lib/libRNA.a -lm -lm
653. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o RNAplex RNAplex_cmdl.o RNAplex.o -fopenmp ../lib/libRNA.a -lm -lm
654. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs'
655. Making all in man
656. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man'
657. make[2]: Nothing to be done for 'all'.
658. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man'
659. Making all in Utils
660. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils'
661. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o b2ct.o b2ct.c
662. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o popt.o popt.c
663. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o ct2db_cmdl.o ct2db_cmdl.c
664. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o ct2db.o ct2db.c
665. if test -n "/usr/bin/perl"; then \
666. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' b2mt.pl ; \
667. fi
668. if test -n "/usr/bin/perl"; then \
669. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' ct2b.pl ; \
670. fi
671. if test -n "/usr/bin/perl"; then \
672. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' dpzoom.pl ; \
673. fi
674. if test -n "/usr/bin/perl"; then \
675. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' mountain.pl ; \
676. fi
677. if test -n "/usr/bin/perl"; then \
678. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' relplot.pl ; \
679. fi
680. if test -n "/usr/bin/perl"; then \
681. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' rotate_ss.pl ; \
682. fi
683. if test -n "/usr/bin/perl"; then \
684. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' cmount.pl ; \
685. fi
686. if test -n "/usr/bin/perl"; then \
687. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' colorrna.pl ; \
688. fi
689. if test -n "/usr/bin/perl"; then \
690. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' coloraln.pl ; \
691. fi
692. if test -n "/usr/bin/perl"; then \
693. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' refold.pl ; \
694. fi
695. if test -n "/usr/bin/perl"; then \
696. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' switch.pl ; \
697. fi
698. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o popt popt.o -L../lib -lRNA -lm -lm
699. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o b2ct b2ct.o -L../lib -lRNA -lm -lm
700. x86_64-pc-linux-gnu-gcc -fopenmp -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o ct2db ct2db_cmdl.o ct2db.o -L../lib -lRNA -lm -lm
701. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils'
702. Making all in H
703. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H'
704. make[2]: Nothing to be done for 'all'.
705. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H'
706. Making all in misc
707. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc'
708. make[2]: Nothing to be done for 'all'.
709. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc'
710. Making all in doc
711. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc'
712. /usr/bin/doxygen doxygen.conf
713. Warning: Tag `SYMBOL_CACHE_SIZE' at line 336 of file doxygen.conf has become obsolete.
714. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
715. Warning: doxygen no longer ships with the FreeSans font.
716. You may want to clear or change DOT_FONTNAME.
717. Otherwise you run the risk that the wrong font is being used for dot generated graphs.
718. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/fold.h:50: warning: group mfe_fold: ignoring title "Calculating Minimum Free Energy Structures" that does not match old title "Calculating Minimum Free Energy (MFE) Structures"
720. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/svm_utils.h:4: warning: Compound svm_model is not documented.
721. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:374: warning: Compound interact is not documented.
722. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:348: warning: Compound path_t is not documented.
723. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:328: warning: Compound move_t is not documented.
724. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:266: warning: Compound cofoldF is not documented.
725. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:278: warning: Compound ConcEnt is not documented.
726. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib/list.h:21: warning: Compound LIST is not documented.
727. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/dist_vars.h:46: warning: Compound swString is not documented.
728. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/dist_vars.h:41: warning: Compound Tree is not documented.
729. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:338: warning: Compound intermediate_t is not documented.
730. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:486: warning: Compound dupVar is not documented.
731. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:291: warning: Compound pairpro is not documented.
732. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/dist_vars.h:33: warning: Compound Postorder_list is not documented.
733. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/move_set.h:5: warning: Compound struct_en is not documented.
734. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib/list.h:16: warning: Compound LST_BUCKET is not documented.
735. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:443: warning: Compound folden is not documented.
736. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:452: warning: Compound snoopT is not documented.
737. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:415: warning: Compound duplexT is not documented.
738. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/gquad.h:244: warning: The following parameters of backtrack_GQuad_IntLoop_L(int c, int i, int j, int type, short *S, int **ggg, int maxdist, int *p, int *q, paramT *P) are not documented:
739. parameter 'maxdist'
740. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/plot_layouts.h:54: warning: unable to resolve reference to `bruccoleri_88' for \ref command
741. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:293: warning: The following parameters of hamming_bound(const char *s1, const char *s2, int n) are not documented:
742. parameter 'n'
743. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:326: warning: explicit link request to 'VRNA_INPUT_NOPRINT_COMMENTS' could not be resolved
744. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:326: warning: explicit link request to 'VRNA_INPUT_NOELIM_WS_SUFFIX' could not be resolved
745. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:480: warning: argument 'str1' of command @param is not found in the argument list of make_loop_index_pt(short *pt)
746. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:480: warning: argument 'str2' of command @param is not found in the argument list of make_loop_index_pt(short *pt)
747. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:480: warning: The following parameters of make_loop_index_pt(short *pt) are not documented:
748. parameter 'pt'
749. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/utils.h:591: warning: The following parameters of constrain_ptypes(const char *constraint, unsigned int length, char *ptype, int *BP, int min_loop_size, unsigned int idx_type) are not documented:
750. parameter 'BP'
751. citelist:4: warning: Unexpected new line character
752. citelist:12: warning: Unexpected new line character
753. citelist:20: warning: Unexpected new line character
754. citelist:21: warning: Unexpected new line character
755. citelist:37: warning: Unexpected new line character
756. citelist:62: warning: Unexpected new line character
757. citelist:63: warning: Unexpected new line character
758. citelist:73: warning: Unexpected new line character
759. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/fold.h:21: warning: unable to resolve reference to `zuker_81' for \ref command
760. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/alifold.h:350: warning: The following parameters of get_alipf_arrays(short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, double **qb_p, double **qm_p, double **q1k_p, double **qln_p, short **pscore) are not documented:
761. parameter 'pscore'
762. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H/data_structures.h:653: warning: explicit link request to 'FLT_OR_DBL' could not be resolved
763. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc/mainpage.h:139: warning: unable to resolve reference to `mp_ref' for \ref command
764. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc/mainpage.h:139: warning: unable to resolve reference to `mp_ref' for \ref command
765. cd latex; \
766. make; \
767. mv refman.pdf ../RNAlib-2.1.8.pdf
768. make[3]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc/latex'
769. make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
770. rm -f *.ps *.dvi *.aux *.toc *.idx *.ind *.ilg *.log *.out *.brf *.blg *.bbl refman.pdf
771. pdflatex refman
772. This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded format=pdflatex)
773. restricted \write18 enabled.
774. entering extended mode
775. (./refman.tex
776. LaTeX2e <2014/05/01>
777. Babel <3.9l> and hyphenation patterns for 30 languages loaded.
779. /usr/bin/makeindex refman.idx
780. This is makeindex, version 2.15 [TeX Live 2014] (kpathsea + Thai support).
781. Scanning input file refman.idx....done (574 entries accepted, 73 rejected).
782. Sorting entries.......done (5876 comparisons).
783. Generating output file refman.ind....done (1326 lines written, 0 warnings).
784. Output written in refman.ind.
785. Transcript written in refman.ilg.
786. bibtex refman
787. This is BibTeX, Version 0.99d (TeX Live 2014)
788. The top-level auxiliary file: refman.aux
789. A level-1 auxiliary file: group__mfe__fold.aux
790. A level-1 auxiliary file: group__pf__fold.aux
791. A level-1 auxiliary file: group__mea__fold.aux
792. A level-1 auxiliary file: group__centroid__fold.aux
793. A level-1 auxiliary file: group__subopt__fold.aux
794. A level-1 auxiliary file: group__subopt__zuker.aux
795. A level-1 auxiliary file: group__subopt__wuchty.aux
796. A level-1 auxiliary file: group__subopt__stochbt.aux
797. A level-1 auxiliary file: group__cofold.aux
798. A level-1 auxiliary file: group__mfe__cofold.aux
799. A level-1 auxiliary file: group__pf__cofold.aux
800. A level-1 auxiliary file: group__up__cofold.aux
801. A level-1 auxiliary file: group__consensus__fold.aux
802. A level-1 auxiliary file: group__consensus__mfe__fold.aux
803. A level-1 auxiliary file: group__consensus__pf__fold.aux
804. A level-1 auxiliary file: group__consensus__stochbt.aux
805. A level-1 auxiliary file: group__local__fold.aux
806. A level-1 auxiliary file: group__local__mfe__fold.aux
807. A level-1 auxiliary file: group__local__pf__fold.aux
808. A level-1 auxiliary file: group__local__consensus__fold.aux
809. A level-1 auxiliary file: group__energy__parameters.aux
810. A level-1 auxiliary file: group__energy__parameters__rw.aux
811. A level-1 auxiliary file: group__energy__parameters__convert.aux
812. A level-1 auxiliary file: group__eval.aux
813. A level-1 auxiliary file: group__inverse__fold.aux
814. A level-1 auxiliary file: group__class__fold.aux
815. A level-1 auxiliary file: group__kl__neighborhood.aux
816. A level-1 auxiliary file: group__kl__neighborhood__mfe.aux
817. A level-1 auxiliary file: group__kl__neighborhood__pf.aux
818. A level-1 auxiliary file: group__kl__neighborhood__stochbt.aux
819. A level-1 auxiliary file: group__dos.aux
820. A level-1 auxiliary file: group__parse.aux
821. The style file: plain.bst
822. Database file #1: viennarna.bib
823. pdflatex refman
824. This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded format=pdflatex)
825. restricted \write18 enabled.
826. entering extended mode
827. (./refman.tex
828. LaTeX2e <2014/05/01>
829. Babel <3.9l> and hyphenation patterns for 30 languages loaded.
831. pdflatex refman
832. This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded format=pdflatex)
833. restricted \write18 enabled.
834. entering extended mode
835. (./refman.tex
836. LaTeX2e <2014/05/01>
837. Babel <3.9l> and hyphenation patterns for 30 languages loaded.
839. latex_count=5 ; \
840. while egrep -s 'Rerun (LaTeX|to get cross-references right)' refman.log && [ $latex_count -gt 0 ] ;\
841. do \
842. echo "Rerunning latex...." ;\
843. pdflatex refman ;\
844. latex_count=`expr $latex_count - 1` ;\
845. done
846. /usr/bin/makeindex refman.idx
847. This is makeindex, version 2.15 [TeX Live 2014] (kpathsea + Thai support).
848. Scanning input file refman.idx....done (574 entries accepted, 73 rejected).
849. Sorting entries.......done (5876 comparisons).
850. Generating output file refman.ind....done (1326 lines written, 0 warnings).
851. Output written in refman.ind.
852. Transcript written in refman.ilg.
853. pdflatex refman
854. This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2014) (preloaded format=pdflatex)
855. restricted \write18 enabled.
856. entering extended mode
857. (./refman.tex
858. LaTeX2e <2014/05/01>
859. Babel <3.9l> and hyphenation patterns for 30 languages loaded.
861. make[3]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc/latex'
862. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc'
863. Making all in interfaces
864. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces'
865. Making all in Perl
866. make[3]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
867. /usr/bin/perl Makefile.PL INSTALLDIRS=vendor PREFIX=/usr INSTALL_BASE=
868. Generating a Unix-style Makefile.perl
869. Writing Makefile.perl for RNA
870. make -f Makefile.perl
871. make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
872. x86_64-pc-linux-gnu-gcc -c -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I../../H -O2 -pipe -ggdb -ftracer -frecord-gcc-switches -DVERSION=\"2.1.8\" -DXS_VERSION=\"2.1.8\" -fPIC "-I/usr/lib64/perl5/5.20.1/x86_64-linux-thread-multi/CORE" RNA_wrap.c
873. Running Mkbootstrap for RNA ()
874. cp RNA.pm blib/lib/RNA.pm
875. chmod 644 RNA.bs
876. RNA_wrap.c: In function 'my_alifold':
877. RNA_wrap.c:2316:23: warning: passing argument 1 of 'alifold' from incompatible pointer type
878. *energy = alifold(strings, struc);
879. ^
880. In file included from RNA_wrap.c:1578:0:
881. ../../H/../H/alifold.h:86:8: note: expected 'const char **' but argument is of type 'char **'
882. float alifold( const char **strings,
883. ^
884. RNA_wrap.c: In function '_wrap_LoopEnergy':
885. RNA_wrap.c:6632:5: warning: 'LoopEnergy' is deprecated (declared at ../../H/../H/fold.h:523) [-Wdeprecated-declarations]
886. result = (int)LoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8);
887. ^
888. RNA_wrap.c: In function '_wrap_HairpinE':
889. RNA_wrap.c:6707:5: warning: 'HairpinE' is deprecated (declared at ../../H/../H/fold.h:536) [-Wdeprecated-declarations]
890. result = (int)HairpinE(arg1,arg2,arg3,arg4,(char const *)arg5);
891. ^
892. RNA_wrap.c: In function '_wrap_initialize_fold':
893. RNA_wrap.c:6742:5: warning: 'initialize_fold' is deprecated (declared at ../../H/../H/fold.h:547) [-Wdeprecated-declarations]
894. initialize_fold(arg1);
895. ^
896. RNA_wrap.c: In function '_wrap_energy_of_struct':
897. RNA_wrap.c:6780:5: warning: 'energy_of_struct' is deprecated (declared at ../../H/../H/fold.h:563) [-Wdeprecated-declarations]
898. result = (float)energy_of_struct((char const *)arg1,(char const *)arg2);
899. ^
900. RNA_wrap.c: In function '_wrap_energy_of_struct_pt':
901. RNA_wrap.c:6835:5: warning: 'energy_of_struct_pt' is deprecated (declared at ../../H/../H/fold.h:582) [-Wdeprecated-declarations]
902. result = (int)energy_of_struct_pt((char const *)arg1,arg2,arg3,arg4);
903. ^
904. RNA_wrap.c: In function '_wrap_energy_of_circ_struct':
905. RNA_wrap.c:6879:5: warning: 'energy_of_circ_struct' is deprecated (declared at ../../H/../H/fold.h:601) [-Wdeprecated-declarations]
906. result = (float)energy_of_circ_struct((char const *)arg1,(char const *)arg2);
907. ^
908. RNA_wrap.c: In function '_wrap_initialize_cofold':
909. RNA_wrap.c:7403:5: warning: 'initialize_cofold' is deprecated (declared at ../../H/../H/cofold.h:180) [-Wdeprecated-declarations]
910. initialize_cofold(arg1);
911. ^
912. RNA_wrap.c: In function '_wrap_init_pf_fold':
913. RNA_wrap.c:8311:5: warning: 'init_pf_fold' is deprecated (declared at ../../H/../H/part_func.h:407) [-Wdeprecated-declarations]
914. init_pf_fold(arg1);
915. ^
916. RNA_wrap.c: In function '_wrap_centroid':
917. RNA_wrap.c:8347:5: warning: 'centroid' is deprecated (declared at ../../H/../H/part_func.h:413) [-Wdeprecated-declarations]
918. result = (char *)centroid(arg1,arg2);
919. ^
920. RNA_wrap.c: In function '_wrap_mean_bp_dist':
921. RNA_wrap.c:8377:5: warning: 'mean_bp_dist' is deprecated (declared at ../../H/../H/part_func.h:421) [-Wdeprecated-declarations]
922. result = (double)mean_bp_dist(arg1);
923. ^
924. RNA_wrap.c: In function '_wrap_expLoopEnergy':
925. RNA_wrap.c:8461:5: warning: 'expLoopEnergy' is deprecated (declared at ../../H/../H/part_func.h:426) [-Wdeprecated-declarations]
926. result = (double)expLoopEnergy(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8);
927. ^
928. RNA_wrap.c: In function '_wrap_expHairpinEnergy':
929. RNA_wrap.c:8536:5: warning: 'expHairpinEnergy' is deprecated (declared at ../../H/../H/part_func.h:438) [-Wdeprecated-declarations]
930. result = (double)expHairpinEnergy(arg1,arg2,arg3,arg4,(char const *)arg5);
931. ^
932. RNA_wrap.c: In function '_wrap_Make_bp_profile':
933. RNA_wrap.c:11742:5: warning: 'Make_bp_profile' is deprecated (declared at ../../H/../H/profiledist.h:56) [-Wdeprecated-declarations]
934. result = (float *)Make_bp_profile(arg1);
935. ^
936. RNA_wrap.c: In function '_wrap_copy_parameters':
937. RNA_wrap.c:13291:5: warning: 'copy_parameters' is deprecated (declared at ../../H/../H/params.h:126) [-Wdeprecated-declarations]
938. result = (paramT *)copy_parameters();
939. ^
940. RNA_wrap.c: In function '_wrap_set_parameters':
941. RNA_wrap.c:13317:5: warning: 'set_parameters' is deprecated (declared at ../../H/../H/params.h:127) [-Wdeprecated-declarations]
942. result = (paramT *)set_parameters(arg1);
943. ^
944. RNA_wrap.c: In function '_wrap_PS_dot_plot':
945. RNA_wrap.c:14984:5: warning: 'PS_dot_plot' is deprecated (declared at ../../H/../H/PS_dot.h:195) [-Wdeprecated-declarations]
946. result = (int)PS_dot_plot(arg1,arg2);
947. ^
948. rm -f blib/arch/auto/RNA/RNA.so
949. g++ -shared -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed RNA_wrap.o -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -fopenmp -o blib/arch/auto/RNA/RNA.so ../../lib/libRNA.a \
950. -lm \
952. chmod 755 blib/arch/auto/RNA/RNA.so
953. /usr/bin/perl5.20.1 -MExtUtils::Command::MM -e 'cp_nonempty' -- RNA.bs blib/arch/auto/RNA/RNA.bs 644
954. Manifying blib/man3/RNA.3pm
955. make[4]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
956. make[3]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
957. make[3]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces'
958. make[3]: Nothing to be done for 'all-am'.
959. make[3]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces'
960. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces'
961. Making all in Cluster
962. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Cluster'
963. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o split.o split.c
964. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o distance_matrix.o distance_matrix.c
965. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o cluster.o cluster.c
966. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o treeplot.o treeplot.c
967. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o AD_main.o AD_main.c
968. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c ./../lib/utils.c
969. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o statgeom.o statgeom.c
970. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o AS_main.o AS_main.c
971. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o PS3D.o PS3D.c
972. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o utils.o -lm -lm
973. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -Wl,-O1 -Wl,--as-needed -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o utils.o -lm -lm
974. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Cluster'
975. Making all in Kinfold
976. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold'
977. (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/missing autoheader)
978. rm -f stamp-h1
979. touch config.h.in
980. cd . && /bin/bash ./config.status config.h
981. config.status: creating config.h
982. config.status: config.h is unchanged
983. make all-recursive
984. make[3]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold'
985. Making all in Example
986. make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold/Example'
987. make[4]: Nothing to be done for 'all'.
988. make[4]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold/Example'
989. make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold'
990. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o baum.o baum.c
991. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o cache.o cache.c
992. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o globals.o globals.c
993. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o main.o main.c
994. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o nachbar.o nachbar.c
995. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o cmdline.o cmdline.c
996. globals.c: In function 'process_options_gg':
997. globals.c:298:25: warning: passing argument 2 of 'strncpy' makes pointer from integer without a cast
998. strncpy(GAV.ParamFile,255,args_info.Par_arg);
999. ^
1000. In file included from /usr/include/features.h:366:0,
1001. from /usr/include/stdio.h:27,
1002. from globals.c:9:
1003. /usr/include/bits/string3.h:117:1: note: expected 'const char * __restrict__' but argument is of type 'int'
1004. __NTH (strncpy (char *__restrict __dest, const char *__restrict __src,
1005. ^
1006. globals.c:298:29: warning: passing argument 3 of 'strncpy' makes integer from pointer without a cast
1007. strncpy(GAV.ParamFile,255,args_info.Par_arg);
1008. ^
1009. In file included from /usr/include/features.h:366:0,
1010. from /usr/include/stdio.h:27,
1011. from globals.c:9:
1012. /usr/include/bits/string3.h:117:1: note: expected 'size_t' but argument is of type 'char *'
1013. __NTH (strncpy (char *__restrict __dest, const char *__restrict __src,
1014. ^
1015. globals.c:334:9: warning: format '%g' expects argument of type 'float *', but argument 3 has type 'double *' [-Wformat=]
1016. &GAV.phi_bounds[2]) == 0)
1017. ^
1018. globals.c:334:9: warning: format '%g' expects argument of type 'float *', but argument 4 has type 'double *' [-Wformat=]
1019. globals.c:334:9: warning: format '%g' expects argument of type 'float *', but argument 5 has type 'double *' [-Wformat=]
1020. globals.c: In function 'process_options':
1021. globals.c:423:8: warning: format '%g' expects argument of type 'float *', but argument 3 has type 'double *' [-Wformat=]
1022. &GAV.phi_bounds[2]) == 0)
1023. ^
1024. globals.c:423:8: warning: format '%g' expects argument of type 'float *', but argument 4 has type 'double *' [-Wformat=]
1025. globals.c:423:8: warning: format '%g' expects argument of type 'float *', but argument 5 has type 'double *' [-Wformat=]
1026. nachbar.c: In function 'sel_nb':
1027. nachbar.c:302:2: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' [-Wformat=]
1028. sprintf(format, "%%-%ds %%6.2f %%10.3f", strlen(GAV.farbe_full)+1);
1029. ^
1030. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -fopenmp -L../lib -Wl,-O1 -Wl,--as-needed -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o -lRNA -lm
1031. make[4]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold'
1032. make[3]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold'
1033. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Kinfold'
1034. Making all in RNAforester
1035. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester'
1036. (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/bash /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/missing autoheader)
1037. rm -f stamp-h1
1038. touch config.h.in
1039. cd . && /bin/bash ./config.status config.h
1040. config.status: creating config.h
1041. config.status: config.h is unchanged
1042. make all-recursive
1043. make[3]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester'
1044. Making all in g2-0.70
1045. make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70'
1046. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_device.c -o src/g2_device.o
1047. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_control.c -o src/g2_ui_control.o
1048. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_util.c -o src/g2_util.o
1049. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_fif.c -o src/g2_fif.o
1050. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_virtual_device.c -o src/g2_virtual_device.o
1051. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_physical_device.c -o src/g2_physical_device.o
1052. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_graphic_pd.c -o src/g2_graphic_pd.o
1053. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_control_pd.c -o src/g2_control_pd.o
1054. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_graphic.c -o src/g2_ui_graphic.o
1055. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_virtual_device.c -o src/g2_ui_virtual_device.o
1056. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_device.c -o src/g2_ui_device.o
1057. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_splines.c -o src/g2_splines.o
1058. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/PS/g2_PS.c -o src/PS/g2_PS.o
1059. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/FIG/g2_FIG.c -o src/FIG/g2_FIG.o
1060. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DLINUX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/X11/g2_X11.c -o src/X11/g2_X11.o
1061. src/FIG/g2_FIG.c: In function 'g2_FIG_draw_string':
1062. src/FIG/g2_FIG.c:478:6: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
1063. fig->pen_color, fig->font_size, fig->font_size, fig->font_size*strlen(text), x, y);
1064. ^
1065. ar -cr libg2.a ./src/g2_device.o ./src/g2_ui_control.o ./src/g2_util.o ./src/g2_fif.o ./src/g2_virtual_device.o ./src/g2_physical_device.o ./src/g2_graphic_pd.o ./src/g2_control_pd.o ./src/g2_ui_graphic.o ./src/g2_ui_virtual_device.o ./src/g2_ui_device.o ./src/g2_splines.o ./src/PS/g2_PS.o ./src/FIG/g2_FIG.o ./src/X11/g2_X11.o
1066. test ! -n "x86_64-pc-linux-gnu-ranlib" || x86_64-pc-linux-gnu-ranlib libg2.a
1067. test -d ./include || mkdir ./include
1068. cp ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ./include/
1069. make[4]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/g2-0.70'
1070. Making all in src
1071. make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/src'
1072. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o Arguments.o Arguments.cpp
1073. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o glib.o glib.c
1074. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o main.o main.cpp
1075. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o ppforestbase.o ppforestbase.cpp
1076. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o progressive_align.o progressive_align.cpp
1077. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rna_profile_alignment.o rna_profile_alignment.cpp
1078. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rna_alignment.o rna_alignment.cpp
1079. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rna_algebra.o rna_algebra.cpp
1080. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rna_alphabet.o rna_alphabet.cpp
1081. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rnaforest.o rnaforest.cpp
1082. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rnaforestsz.o rnaforestsz.cpp
1083. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rnafuncs.o rnafuncs.cpp
1084. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o rnaforester_options.o rnaforester_options.cpp
1085. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -c -o wmatch.o wmatch.c
1086. glib.c: In function 'ReadGraph':
1087. glib.c:161:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
1088. fscanf(fp,"%d%d %c",size,&edges,&c);
1089. ^
1090. glib.c:170:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
1091. fscanf(fp,"%d%d%d%d",&degree,&vlabel,&xcoord,&ycoord);
1092. ^
1093. glib.c:176:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
1094. fscanf(fp,"%d%d", &adj_node, &elabel);
1095. ^
1096. glib.c: In function 'ReadEuclid':
1097. glib.c:225:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
1098. fscanf(fp,"%d %c",size,&c);
1099. ^
1100. glib.c:234:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
1101. fscanf(fp,"%d%d",&xcoord,&ycoord);
1102. ^
1103. glib.c: In function 'ReadMatrix':
1104. glib.c:272:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
1105. fscanf(fp,"%d %c",size,&c);
1106. ^
1107. glib.c:282:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
1108. fscanf(fp,"%d",&k);
1109. ^
1110. progressive_align.cpp: In function 'node_entry* makePairsGraph(const RNAProfileAliMapType&, const DoubleScoreProfileAlgebraType*, const Matrix<double>*, double)':
1111. progressive_align.cpp:341:30: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
1112. WriteGraph (graph,"test.out");
1113. ^
1114. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -L../g2-0.70 -L../../lib -L../../ViennaRNA -Wl,-O1 -Wl,--as-needed -fopenmp -o RNAforester Arguments.o glib.o main.o ppforestbase.o progressive_align.o rna_profile_alignment.o rna_alignment.o rna_algebra.o rna_alphabet.o rnaforest.o rnaforestsz.o rnafuncs.o rnaforester_options.o wmatch.o -lg2 -lRNA
1115. make[4]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/src'
1116. Making all in man
1117. make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/man'
1118. make[4]: Nothing to be done for 'all'.
1119. make[4]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester/man'
1120. make[4]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester'
1121. make[4]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester'
1122. make[3]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester'
1123. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/RNAforester'
1124. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8'
1125. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8'
1126. make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8'
1127. >>> Working in BUILD_DIR: "/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8"
1128. make -j24 -C Readseq build CC=x86_64-pc-linux-gnu-gcc
1129. make: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq'
1130. Compiling readseq...
1131. x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -O2 -pipe -ggdb -march=native -ftracer -frecord-gcc-switches -o readseq readseq.c ureadseq.c ureadasn.c
1132. readseq.c: In function 'formatstr':
1133. readseq.c:257:27: warning: return discards 'const' qualifier from pointer target type
1134. case kASNseqset : return formats[kASN1-1];
1135. ^
1136. readseq.c:259:31: warning: return discards 'const' qualifier from pointer target type
1137. case kPhylipSequential: return formats[kPhylip-1];
1138. ^
1139. readseq.c:263:8: warning: return discards 'const' qualifier from pointer target type
1140. else return formats[format-1];
1141. ^
1142. readseq.c: In function 'usage':
1143. readseq.c:328:3: warning: format not a string literal and no format arguments [-Wformat-security]
1144. fprintf(stderr,title);
1145. ^
1146. readseq.c: In function 'chooseFormat':
1147. readseq.c:419:7: warning: 'gets' is deprecated (declared at /usr/include/bits/stdio2.h:233) [-Wdeprecated-declarations]
1148. gets(sform);
1149. ^
1150. readseq.c: In function 'main':
1151. readseq.c:768:3: warning: format not a string literal and no format arguments [-Wformat-security]
1152. if (verbose || (!quietly && !gotinputfile)) fprintf( stderr, title);
1153. ^
1154. readseq.c:775:5: warning: 'gets' is deprecated (declared at /usr/include/bits/stdio2.h:233) [-Wdeprecated-declarations]
1155. gets(oname= onamestore);
1156. ^
1157. readseq.c:839:7: warning: 'gets' is deprecated (declared at /usr/include/bits/stdio2.h:233) [-Wdeprecated-declarations]
1158. gets(stemp= stempstore);
1159. ^
1160. readseq.c:885:9: warning: 'gets' is deprecated (declared at /usr/include/bits/stdio2.h:233) [-Wdeprecated-declarations]
1161. gets(stemp= stempstore);
1162. ^
1163. readseq.c:910:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1164. sprintf( stemp,"%s_%d", oname, whichSeq);
1165. ^
1166. readseq.c:912:13: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
1167. fprintf( stderr,"Writing sequence %d to file %s\n", whichSeq, stemp);
1168. ^
1169. readseq.c:955:17: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
1170. whichSeq, seqlen, checksum, formatstr(format), seqidptr);
1171. ^
1172. readseq.c:955:17: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1173. readseq.c:955:17: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1174. readseq.c:965:15: warning: format not a string literal and no format arguments [-Wformat-security]
1175. if (seqout == 0) fprintf( foo, kASN1headline);
1176. ^
1177. readseq.c:972:19: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
1178. if (phylvers >= 4) fprintf(foo," %d %d\n", i, seqlen);
1179. ^
1180. readseq.c:972:19: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1181. readseq.c:973:19: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
1182. else fprintf(foo," %d %d YF\n", i, seqlen);
1183. ^
1184. readseq.c:973:19: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1185. readseq.c:1076:19: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1186. cp, seqlen, checkall);
1187. ^
1188. readseq.c:1076:19: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=]
1189. readseq.c:1087:5: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1190. if (phylvers >= 4) fprintf(foo," %d %d\n", seqout, seqlen);
1191. ^
1192. readseq.c:1088:5: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1193. else fprintf(foo," %d %d YF\n", seqout, seqlen);
1194. ^
1195. readseq.c:1112:9: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1196. fprintf(foo," dimensions ntax=%d nchar=%d;\n", seqout, seqlen);
1197. ^
1198. readseq.c: In function 'chooseFormat':
1199. readseq.c:419:7: warning: ignoring return value of 'gets', declared with attribute warn_unused_result [-Wunused-result]
1200. gets(sform);
1201. ^
1202. readseq.c: In function 'main':
1203. readseq.c:757:5: warning: ignoring return value of 'tmpnam', declared with attribute warn_unused_result [-Wunused-result]
1204. tmpnam(tempname);
1205. ^
1206. readseq.c:775:5: warning: ignoring return value of 'gets', declared with attribute warn_unused_result [-Wunused-result]
1207. gets(oname= onamestore);
1208. ^
1209. readseq.c:839:7: warning: ignoring return value of 'gets', declared with attribute warn_unused_result [-Wunused-result]
1210. gets(stemp= stempstore);
1211. ^
1212. readseq.c:885:9: warning: ignoring return value of 'gets', declared with attribute warn_unused_result [-Wunused-result]
1213. gets(stemp= stempstore);
1214. ^
1215. readseq.c:911:13: warning: ignoring return value of 'freopen', declared with attribute warn_unused_result [-Wunused-result]
1216. freopen( stemp, "w", fout);
1217. ^
1218. ureadseq.c: In function 'seqFileFormatFp':
1219. ureadseq.c:1346:5: warning: format '%d' expects argument of type 'int *', but argument 3 has type 'long int *' [-Wformat=]
1220. sscanf( sp, "%d%d", &nspp, &nlen);
1221. ^
1222. ureadseq.c:1346:5: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long int *' [-Wformat=]
1223. ureadseq.c: In function 'writeSeq':
1224. ureadseq.c:1595:3: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
1225. sprintf(numform, "%d", seqlen);
1226. ^
1227. ureadseq.c:1624:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1228. fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen);
1229. ^
1230. ureadseq.c:1625:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1231. fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
1232. ^
1233. ureadseq.c:1625:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1234. ureadseq.c:1639:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1235. fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
1236. ^
1237. ureadseq.c:1639:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1238. ureadseq.c:1649:7: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
1239. for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j);
1240. ^
1241. ureadseq.c:1659:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1242. fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
1243. ^
1244. ureadseq.c:1659:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1245. ureadseq.c:1668:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1246. fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
1247. ^
1248. ureadseq.c:1668:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1249. ureadseq.c:1669:7: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
1250. fprintf(outf,"SQ %d BP\n", seqlen);
1251. ^
1252. ureadseq.c:1680:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1253. fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum);
1254. ^
1255. ureadseq.c:1680:7: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=]
1256. ureadseq.c:1689:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1257. fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum);
1258. ^
1259. ureadseq.c:1689:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1260. ureadseq.c:1695:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1261. fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
1262. ^
1263. ureadseq.c:1695:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1264. ureadseq.c:1726:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1265. fprintf(outf," repr raw, mol %s, length %d, topology linear,\n", cp, seqlen);
1266. ^
1267. ureadseq.c:1748:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1268. fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum);
1269. ^
1270. ureadseq.c:1748:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1271. ureadseq.c:1765:9: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1272. fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum);
1273. ^
1274. ureadseq.c:1765:9: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1275. ureadseq.c:1772:21: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1276. idword, seqlen, checksum);
1277. ^
1278. ureadseq.c:1772:21: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat=]
1279. ureadseq.c:1783:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1280. fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
1281. ^
1282. ureadseq.c:1783:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1283. ureadseq.c:1792:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=]
1284. fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
1285. ^
1286. ureadseq.c:1792:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat=]
1287. ureadseq.c:1833:9: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=]
1288. if (numline==1) fprintf(outf,"%-9d ",i+1);
1289. ^
1290. /tmp/portage/sci-biology/vienna-rna-2.1.8/temp/ccoGj8lo.o: In function `main':
1291. /tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq/readseq.c:757: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
1292. /tmp/portage/sci-biology/vienna-rna-2.1.8/temp/ccoGj8lo.o: In function `gets':
1293. /usr/include/bits/stdio2.h:236: warning: the `gets' function is dangerous and should not be used.
1294. make: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq'
1295. >>> Source compiled.
1296. >>> Test phase: sci-biology/vienna-rna-2.1.8
1297. >>> Working in BUILD_DIR: "/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8"
1298. make -j24 -C interfaces/Perl check
1299. make: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
1300. make -f Makefile.perl
1301. make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
1302. Running Mkbootstrap for RNA ()
1303. chmod 644 RNA.bs
1304. make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
1305. make check-local
1306. make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
1307. make -f Makefile.perl
1308. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
1309. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
1310. make -f Makefile.perl test
1311. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
1312. PERL_DL_NONLAZY=1 /usr/bin/perl5.20.1 "-Iblib/lib" "-Iblib/arch" test.pl
1313. 1..24
1314. # Running under perl version 5.020001 for linux
1315. # Current time local: Wed Nov 12 08:52:24 2014
1316. # Current time GMT: Wed Nov 12 08:52:24 2014
1317. # Using Test.pm version 1.26
1318. ok 1
1319. ok 2
1320. ok 3
1321. not ok 4
1322. # Failed test 4 in test.pl at line 42
1323. # test.pl line 42 is: ok($struct eq $struc1);
1324. WARNING: bases 1 and 16 (()) can't pair!
1325. WARNING: bases 2 and 15 (()) can't pair!
1326. WARNING: bases 3 and 14 (()) can't pair!
1327. WARNING: bases 5 and 13 (()) can't pair!
1328. WARNING: bases 6 and 12 (()) can't pair!
1329. WARNING: bases 7 and 11 (()) can't pair!
1330. not ok 5
1331. # Test 5 got: "16.7000007629395" (test.pl at line 44)
1332. # Expected: "0"
1333. # test.pl line 44 is: ok(RNA::energy_of_struct($seq1,$struc1), $mfe);
1334. not ok 6
1335. # Test 6 got: "................" (test.pl at line 49)
1336. # Expected: "(((..........)))"
1337. # test.pl line 49 is: ok($struct3, '(((..........)))');
1338. ok 7
1339. not ok 8
1340. # Test 8 got: "................((((((...))).)))" (test.pl at line 56)
1341. # Expected: "(((.(((...))))))((((((...))).)))"
1342. # test.pl line 56 is: ok($costruct, '(((.(((...))))))((((((...))).)))');
1343. ok 9
1344. ok 10
1345. not ok 11
1346. # Failed test 11 in test.pl at line 74
1347. # test.pl line 74 is: ok((abs($AB-0.0)+abs($AA-0.00578)+abs($BB-0.01100)+abs($A-0.48843)+abs($B-0.47801))<0.0001);
1348. not ok 12
1349. # Failed test 12 in test.pl at line 79
1350. # test.pl line 79 is: ok(($f<$mfe)&&($mfe-$f<0.8));
1351. ok 13
1352. ok 14
1353. ok 15
1354. not ok 16
1355. # Failed test 16 in test.pl at line 107
1356. # test.pl line 107 is: ok(($p1<0.999) && ($p1>0.99) && (abs($p1-$p2)<1.2e-7));
1357. ok 17
1358. ok 18
1359. ok 19
1360. please check the two postscript files test_ss.ps and test_dp.ps
1361. ok 20
1362. 1 suboptimals
1363. ................ 0.00
1364. ok 21
1365. not ok 22
1366. # Test 22 got: ".&." (test.pl at line 159)
1367. # Expected: "(.(.(((.....(((.&))))))...).)."
1368. # test.pl line 159 is: ok($duplex->{structure}, "(.(.(((.....(((.&))))))...).).");
1369. ok 23
1370. ok 24
1371. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
1372. make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
1373. make: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/interfaces/Perl'
1374. >>> Working in BUILD_DIR: "/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8"
1375. make -j24 -C Readseq test
1376. make: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq'
1378. Test for general read/write of all chars:
1379. ./readseq -p alphabet.std -otest.alpha
1380. diff test.alpha alphabet.std
1381. 1c1
1382. < >alphabet['!'..'~'], 83 bases, E14ECBE2 checksum.
1383. ---
1384. > >alphabet['!'..'~'], 83 bases, 9429 checksum.
1385. Makefile:51: recipe for target 'test' failed
1386. make: [test] Error 1 (ignored)
1388. Test for valid format conversions:
1389. ./readseq -v -p -f=ig nucleic.std -otest.ig
1390. readSeq (1Feb93), multi-format molbio sequence reader.
1391. Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino test
1392. ./readseq -v -p -f=gb test.ig -otest.gb
1393. readSeq (1Feb93), multi-format molbio sequence reader.
1394. Sequence 1, length= 228, checksum= 1B5655D0, format= 1. IG/Stanford, id= nucleic/amino
1395. ./readseq -v -p -f=nbrf test.gb -otest.nbrf
1396. readSeq (1Feb93), multi-format molbio sequence reader.
1397. Sequence 1, length= 228, checksum= 1B5655D0, format= 2. GenBank/GB, id= nucleic/amino 228 bp
1398. ./readseq -v -p -f=embl test.nbrf -otest.embl
1399. readSeq (1Feb93), multi-format molbio sequence reader.
1400. Sequence 1, length= 228, checksum= 1B5655D0, format= 3. NBRF, id= nucleic/amino
1401. ./readseq -v -p -f=gcg test.embl -otest.gcg
1402. readSeq (1Feb93), multi-format molbio sequence reader.
1403. Sequence 1, length= 228, checksum= 1B5655D0, format= 4. EMBL, id= nucleic/amino
1404. ./readseq -v -p -f=strider test.gcg -otest.strider
1405. readSeq (1Feb93), multi-format molbio sequence reader.
1406. Sequence 1, length= 228, checksum= 1B5655D0, format= 5. GCG, id= nucleic/amino
1407. ./readseq -v -p -f=fitch test.strider -otest.fitch
1408. readSeq (1Feb93), multi-format molbio sequence reader.
1409. Sequence 1, length= 228, checksum= 1B5655D0, format= 6. DNAStrider, id= nucleic/amino, 228 bases, 1B5655D0 checksum.
1410. ./readseq -v -p -f=fasta test.fitch -otest.fasta
1411. readSeq (1Feb93), multi-format molbio sequence reader.
1412. Sequence 1, length= 228, checksum= 1B5655D0, format= 7. Fitch, id= nucleic/amino, 228 bases, 1B5655D0 checksum.
1413. ./readseq -v -p -f=pir test.fasta -otest.pir
1414. readSeq (1Feb93), multi-format molbio sequence reader.
1415. Sequence 1, length= 228, checksum= 1B5655D0, format= 8. Pearson/Fasta, id= nucleic/amino, 228 bases, 1B5655D0 checksum.
1416. ./readseq -v -p -f=ig test.pir -otest.ig-b
1417. readSeq (1Feb93), multi-format molbio sequence reader.
1418. Sequence 1, length= 228, checksum= 1B5655D0, format= 14. PIR/CODATA, id= nucleic/amino,
1419. diff test.ig test.ig-b
1420. 1,2c1,2
1421. < ;nucleic/amino test, 228 bases, 1B5655D0 checksum.
1422. < nucleic/amino
1423. ---
1424. > ;nucleic/amino, , 228 bases, 1B5655D0 checksum.
1425. > nucleic/amino,
1426. Makefile:51: recipe for target 'test' failed
1427. make: [test] Error 1 (ignored)
1429. Test for multiple-sequence format conversions:
1430. ./readseq -p -f=ig multi.std -otest.m-ig
1431. ./readseq -p -f=gb test.m-ig -otest.m-gb
1432. ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf
1433. ./readseq -p -f=embl test.m-nbrf -otest.m-embl
1434. ./readseq -p -f=fasta test.m-embl -otest.m-fasta
1435. ./readseq -p -f=pir test.m-fasta -otest.m-pir
1436. ./readseq -p -f=msf test.m-pir -otest.m-msf
1437. ./readseq -p -f=paup test.m-msf -otest.m-paup
1438. ./readseq -p -f=ig test.m-paup -otest.m-ig-b
1439. diff test.m-ig test.m-ig-b
1440. 1,2c1,2
1441. < ;acarr58sst , 183 bases, 64754A4D checksum.
1442. < acarr58sst
1443. ---
1444. > ;acarr58ss, 183 bases, 64754A4D checksum.
1445. > acarr58ss
1446. 7c7
1447. < ;amgrrbst , 183 bases, C886D2FB checksum.
1448. ---
1449. > ;amgrrbst, 183 bases, C886D2FB checksum.
1450. 13c13
1451. < ;bmorrbst , 183 bases, 3E9C23D6 checksum.
1452. ---
1453. > ;bmorrbst, 183 bases, 3E9C23D6 checksum.
1454. 19c19
1455. < ;crerrbst , 183 bases, AC88A337 checksum.
1456. ---
1457. > ;crerrbst, 183 bases, AC88A337 checksum.
1458. 25,26c25,26
1459. < ;ddirr58sst , 183 bases, 1E3D23B8 checksum.
1460. < ddirr58sst
1461. ---
1462. > ;ddirr58ss, 183 bases, 1E3D23B8 checksum.
1463. > ddirr58ss
1464. Makefile:51: recipe for target 'test' failed
1465. make: [test] Error 1 (ignored)
1467. Expect differences in the header lines due to
1468. different format headers. If any sequence lines
1469. differ, or if the checksums differ, there is a problem.
1470. ----------------------
1472. To clean up test files, command me:
1473. make clean
1474. make: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Readseq'
1475. >>> Completed testing sci-biology/vienna-rna-2.1.8
1477. >>> Install vienna-rna-2.1.8 into /tmp/portage/sci-biology/vienna-rna-2.1.8/image/ category sci-biology
1478. >>> Working in BUILD_DIR: "/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8"
1479. make -j24 DESTDIR=/tmp/portage/sci-biology/vienna-rna-2.1.8/image/ install
1480. Making install in lib
1481. make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib'
1482. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib'
1483. make[2]: Nothing to be done for 'install-data-am'.
1484. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/lib64'
1485. /usr/bin/install -c -m 644 libRNA.a '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/lib64'
1486. ( cd '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/lib64' && x86_64-pc-linux-gnu-ranlib libRNA.a )
1487. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib'
1488. make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/lib'
1489. Making install in Progs
1490. make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs'
1491. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs'
1492. make[2]: Nothing to be done for 'install-data-am'.
1493. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/bin'
1494. /usr/bin/install -c RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex RNALalifold RNA2Dfold RNAparconv RNAPKplex RNAplex RNAsnoop '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/bin'
1495. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs'
1496. make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Progs'
1497. Making install in man
1498. make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man'
1499. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man'
1500. make[2]: Nothing to be done for 'install-exec-am'.
1501. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/man/man1'
1502. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/info'
1503. /usr/bin/install -c -m 644 RNA2Dfold.1 RNAaliduplex.1 RNAalifold.1 RNAcofold.1 RNAduplex.1 RNAeval.1 RNAfold.1 RNAheat.1 RNAinverse.1 RNALalifold.1 RNALfold.1 RNApaln.1 RNAparconv.1 RNAplfold.1 RNAplot.1 RNAsubopt.1 RNAup.1 RNAPKplex.1 RNAsnoop.1 RNAplex.1 RNAdistance.1 RNApdist.1 '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/man/man1'
1504. /usr/bin/install -c -m 644 ./RNAlib.info '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/info'
1505. install-info --info-dir='/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/info' '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/info/RNAlib.info'
1506. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man'
1507. make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/man'
1508. Making install in Utils
1509. make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils'
1510. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils'
1511. make[2]: Nothing to be done for 'install-exec-am'.
1512. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/bin'
1513. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/bin'
1514. /usr/bin/install -c b2ct popt ct2db '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/bin'
1515. /usr/bin/install -c b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl switch.pl Fold '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/bin'
1516. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils'
1517. make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/Utils'
1518. Making install in H
1519. make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H'
1520. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H'
1521. make[2]: Nothing to be done for 'install-exec-am'.
1522. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/include/ViennaRNA'
1523. /usr/bin/install -c -m 644 energy_par.h pair_mat.h RNAstruct.h dist_vars.h fold.h part_func.h stringdist.h edit_cost.h fold_vars.h profiledist.h treedist.h energy_const.h inverse.h PS_dot.h utils.h params.h subopt.h cofold.h duplex.h alifold.h aln_util.h part_func_co.h ProfileAln.h LPfold.h Lfold.h part_func_up.h ribo.h findpath.h loop_energies.h data_structures.h MEA.h mm.h naview.h 2Dfold.h 2Dpfold.h read_epars.h convert_epars.h PKplex.h plot_layouts.h ali_plex.h '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/include/ViennaRNA'
1524. /usr/bin/install -c -m 644 plex.h snofold.h snoop.h move_set.h gquad.h svm_utils.h '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/include/ViennaRNA'
1525. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H'
1526. make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/H'
1527. Making install in misc
1528. make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc'
1529. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc'
1530. make[2]: Nothing to be done for 'install-exec-am'.
1531. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/ViennaRNA'
1532. /usr/bin/install -c -m 644 rna_turner1999.par rna_turner2004.par rna_andronescu2007.par dna_mathews1999.par dna_mathews2004.par 2Dlandscape_mfe.gri 2Dlandscape_pf.gri '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/ViennaRNA'
1533. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc'
1534. make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/misc'
1535. Making install in doc
1536. make[1]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc'
1537. make[2]: Entering directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc'
1538. make[2]: Nothing to be done for 'install-exec-am'.
1539. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8'
1540. /usr/bin/install -c -m 644 RNAlib-2.1.8.tag RNAlib-2.1.8.pdf '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8'
1541. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1542. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8'
1543. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/ViennaRNA'
1544. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1545. /usr/bin/install -c -m 644 RNAlib-2.1.8.tag RNAlib-2.1.8.pdf '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8'
1546. /usr/bin/install -c -m 644 viennarna.bib '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/ViennaRNA'
1547. /usr/bin/install -c -m 644 html/1_88_84__epars_8h.html html/1_88_84__epars_8h.js html/1_88_84__epars_8h_source.html html/1_88_84__intloops_8h.html html/1_88_84__intloops_8h.js html/1_88_84__intloops_8h_source.html html/2Dfold_8h.html html/2Dfold_8h.js html/2Dfold_8h__incl.map html/2Dfold_8h__incl.md5 html/2Dfold_8h__incl.png html/2Dfold_8h_source.html html/2Dpfold_8h.html html/2Dpfold_8h.js html/2Dpfold_8h__incl.map html/2Dpfold_8h__incl.md5 html/2Dpfold_8h__incl.png html/2Dpfold_8h_source.html html/LPfold_8h.html html/LPfold_8h.js html/LPfold_8h__incl.map html/LPfold_8h__incl.md5 html/LPfold_8h__incl.png html/LPfold_8h_source.html html/Lfold_8h.html html/Lfold_8h.js html/Lfold_8h_source.html html/MEA_8h.html html/MEA_8h.js html/MEA_8h__incl.map html/MEA_8h__incl.md5 html/MEA_8h__incl.png html/MEA_8h_source.html html/PKplex_8h_source.html html/PS__dot_8h.html html/PS__dot_8h.js html/PS__dot_8h__incl.map html/PS__dot_8h__incl.md5 html/PS__dot_8h__incl.png html/PS__dot_8h_source.html '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1548. /usr/bin/install -c -m 644 html/1_88_84__epars_8h.html html/1_88_84__epars_8h.js html/1_88_84__epars_8h_source.html html/1_88_84__intloops_8h.html html/1_88_84__intloops_8h.js html/1_88_84__intloops_8h_source.html html/2Dfold_8h.html html/2Dfold_8h.js html/2Dfold_8h__incl.map html/2Dfold_8h__incl.md5 html/2Dfold_8h__incl.png html/2Dfold_8h_source.html html/2Dpfold_8h.html html/2Dpfold_8h.js html/2Dpfold_8h__incl.map html/2Dpfold_8h__incl.md5 html/2Dpfold_8h__incl.png html/2Dpfold_8h_source.html html/LPfold_8h.html html/LPfold_8h.js html/LPfold_8h__incl.map html/LPfold_8h__incl.md5 html/LPfold_8h__incl.png html/LPfold_8h_source.html html/Lfold_8h.html html/Lfold_8h.js html/Lfold_8h_source.html html/MEA_8h.html html/MEA_8h.js html/MEA_8h__incl.map html/MEA_8h__incl.md5 html/MEA_8h__incl.png html/MEA_8h_source.html html/PKplex_8h_source.html html/PS__dot_8h.html html/PS__dot_8h.js html/PS__dot_8h__incl.map html/PS__dot_8h__incl.md5 html/PS__dot_8h__incl.png html/PS__dot_8h_source.html '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1549. /usr/bin/install: cannot create regular file '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html/1_88_84__epars_8h.html': File exists
1550. /usr/bin/install -c -m 644 html/ProfileAln_8h_source.html html/RNAstruct_8h.html html/RNAstruct_8h.js html/RNAstruct_8h_source.html html/ali__plex_8h_source.html html/alifold_8h.html html/alifold_8h.js html/alifold_8h__incl.map html/alifold_8h__incl.md5 html/alifold_8h__incl.png html/alifold_8h_source.html html/aln__util_8h_source.html html/annotated.html html/annotated.js html/bc_s.png html/bdwn.png html/citelist.html html/classes.html html/closed.png html/cofold_8h.html html/cofold_8h.js html/cofold_8h__incl.map html/cofold_8h__incl.md5 html/cofold_8h__incl.png html/cofold_8h_source.html html/convert__epars_8h.html html/convert__epars_8h.js html/convert__epars_8h_source.html html/data__structures_8h.html html/data__structures_8h.js html/data__structures_8h__dep__incl.map html/data__structures_8h__dep__incl.md5 html/data__structures_8h__dep__incl.png html/data__structures_8h__incl.map html/data__structures_8h__incl.md5 html/data__structures_8h__incl.png html/data__structures_8h_source.html html/deprecated.html html/dir_97aefd0d527b934f1d99a682da8fe6a9.html html/dir_97aefd0d527b934f1d99a682da8fe6a9.js '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1551. Makefile:349: recipe for target 'install-dist_docdir_htmlDATA' failed
1552. make[2]: *** [install-dist_docdir_htmlDATA] Error 1
1553. make[2]: *** Waiting for unfinished jobs....
1554. /usr/bin/install -c -m 644 html/dir_97aefd0d527b934f1d99a682da8fe6a9_dep.map html/dir_97aefd0d527b934f1d99a682da8fe6a9_dep.md5 html/dir_97aefd0d527b934f1d99a682da8fe6a9_dep.png html/dir_d72344b28b4f2089ce25682c4e6eba22.html html/dir_d72344b28b4f2089ce25682c4e6eba22.js html/dir_d72344b28b4f2089ce25682c4e6eba22_dep.map html/dir_d72344b28b4f2089ce25682c4e6eba22_dep.md5 html/dir_d72344b28b4f2089ce25682c4e6eba22_dep.png html/dist__vars_8h.html html/dist__vars_8h.js html/dist__vars_8h__dep__incl.map html/dist__vars_8h__dep__incl.md5 html/dist__vars_8h__dep__incl.png html/dist__vars_8h_source.html html/doxygen.css html/doxygen.png html/duplex_8h.html html/duplex_8h.js html/duplex_8h__incl.map html/duplex_8h__incl.md5 html/duplex_8h__incl.png html/duplex_8h_source.html html/dynsections.js html/edit__cost_8h.html html/edit__cost_8h.js html/edit__cost_8h_source.html html/energy__const_8h.html html/energy__const_8h.js html/energy__const_8h__dep__incl.map html/energy__const_8h__dep__incl.md5 html/energy__const_8h__dep__incl.png html/energy__const_8h__incl.map html/energy__const_8h__incl.md5 html/energy__const_8h__incl.png html/energy__const_8h_source.html html/energy__par_8h_source.html html/files.html html/files.js html/findpath_8h.html html/findpath_8h.js '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1555. /usr/bin/install -c -m 644 html/findpath_8h__incl.map html/findpath_8h__incl.md5 html/findpath_8h__incl.png html/findpath_8h_source.html html/fold_8h.html html/fold_8h.js html/fold_8h__incl.map html/fold_8h__incl.md5 html/fold_8h__incl.png html/fold_8h_source.html html/fold__vars_8h.html html/fold__vars_8h.js html/fold__vars_8h__dep__incl.map html/fold__vars_8h__dep__incl.md5 html/fold__vars_8h__dep__incl.png html/fold__vars_8h__incl.map html/fold__vars_8h__incl.md5 html/fold__vars_8h__incl.png html/fold__vars_8h_source.html html/form_0.png html/form_1.png html/form_10.png html/form_11.png html/form_12.png html/form_13.png html/form_14.png html/form_15.png html/form_16.png html/form_17.png html/form_18.png html/form_19.png html/form_2.png html/form_20.png html/form_21.png html/form_22.png html/form_23.png html/form_24.png html/form_25.png html/form_26.png html/form_27.png '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1556. /usr/bin/install -c -m 644 html/form_28.png html/form_29.png html/form_3.png html/form_4.png html/form_5.png html/form_6.png html/form_7.png html/form_8.png html/form_9.png html/formula.repository html/ftv2blank.png html/ftv2cl.png html/ftv2doc.png html/ftv2folderclosed.png html/ftv2folderopen.png html/ftv2lastnode.png html/ftv2link.png html/ftv2mlastnode.png html/ftv2mnode.png html/ftv2mo.png html/ftv2node.png html/ftv2ns.png html/ftv2plastnode.png html/ftv2pnode.png html/ftv2splitbar.png html/ftv2vertline.png html/functions.html html/functions_vars.html html/globals.html html/globals_0x62.html html/globals_0x63.html html/globals_0x64.html html/globals_0x65.html html/globals_0x66.html html/globals_0x67.html html/globals_0x68.html html/globals_0x69.html html/globals_0x6a.html html/globals_0x6b.html html/globals_0x6c.html '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1557. /usr/bin/install -c -m 644 html/globals_0x6d.html html/globals_0x6e.html html/globals_0x6f.html html/globals_0x70.html html/globals_0x72.html html/globals_0x73.html html/globals_0x74.html html/globals_0x75.html html/globals_0x76.html html/globals_0x77.html html/globals_0x78.html html/globals_0x7a.html html/globals_defs.html html/globals_dup.js html/globals_func.html html/globals_vars.html html/gquad_8h.html html/gquad_8h.js html/gquad_8h__incl.map html/gquad_8h__incl.md5 html/gquad_8h__incl.png html/gquad_8h_source.html html/graph_legend.html html/graph_legend.md5 html/graph_legend.png html/group__centroid__fold.html html/group__centroid__fold.js html/group__centroid__fold.map html/group__centroid__fold.md5 html/group__centroid__fold.png html/group__class__fold.html html/group__class__fold.js html/group__class__fold.map html/group__class__fold.md5 html/group__class__fold.png html/group__cofold.html html/group__cofold.js html/group__cofold.map html/group__cofold.md5 html/group__cofold.png '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1558. /usr/bin/install -c -m 644 html/group__consensus__fold.html html/group__consensus__fold.js html/group__consensus__fold.map html/group__consensus__fold.md5 html/group__consensus__fold.png html/group__consensus__mfe__fold.html html/group__consensus__mfe__fold.js html/group__consensus__mfe__fold.map html/group__consensus__mfe__fold.md5 html/group__consensus__mfe__fold.png html/group__consensus__pf__fold.html html/group__consensus__pf__fold.js html/group__consensus__pf__fold.map html/group__consensus__pf__fold.md5 html/group__consensus__pf__fold.png html/group__consensus__stochbt.html html/group__consensus__stochbt.js html/group__consensus__stochbt.map html/group__consensus__stochbt.md5 html/group__consensus__stochbt.png html/group__dos.html html/group__dos.js html/group__dos.map html/group__dos.md5 html/group__dos.png html/group__energy__parameters.html html/group__energy__parameters.js html/group__energy__parameters.map html/group__energy__parameters.md5 html/group__energy__parameters.png html/group__energy__parameters__convert.html html/group__energy__parameters__convert.js html/group__energy__parameters__convert.map html/group__energy__parameters__convert.md5 html/group__energy__parameters__convert.png html/group__energy__parameters__rw.html html/group__energy__parameters__rw.js html/group__energy__parameters__rw.map html/group__energy__parameters__rw.md5 html/group__energy__parameters__rw.png '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1559. /usr/bin/install -c -m 644 html/group__eval.html html/group__eval.js html/group__eval.map html/group__eval.md5 html/group__eval.png html/group__folding__routines.html html/group__folding__routines.js html/group__folding__routines.map html/group__folding__routines.md5 html/group__folding__routines.png html/group__inverse__fold.html html/group__inverse__fold.js html/group__inverse__fold.map html/group__inverse__fold.md5 html/group__inverse__fold.png html/group__kl__neighborhood.html html/group__kl__neighborhood.js html/group__kl__neighborhood.map html/group__kl__neighborhood.md5 html/group__kl__neighborhood.png html/group__kl__neighborhood__mfe.html html/group__kl__neighborhood__mfe.js html/group__kl__neighborhood__mfe.map html/group__kl__neighborhood__mfe.md5 html/group__kl__neighborhood__mfe.png html/group__kl__neighborhood__pf.html html/group__kl__neighborhood__pf.js html/group__kl__neighborhood__pf.map html/group__kl__neighborhood__pf.md5 html/group__kl__neighborhood__pf.png html/group__kl__neighborhood__stochbt.html html/group__kl__neighborhood__stochbt.js html/group__kl__neighborhood__stochbt.map html/group__kl__neighborhood__stochbt.md5 html/group__kl__neighborhood__stochbt.png html/group__local__consensus__fold.html html/group__local__consensus__fold.js html/group__local__consensus__fold.map html/group__local__consensus__fold.md5 html/group__local__consensus__fold.png '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1560. /usr/bin/install -c -m 644 html/group__local__fold.html html/group__local__fold.js html/group__local__fold.map html/group__local__fold.md5 html/group__local__fold.png html/group__local__mfe__fold.html html/group__local__mfe__fold.js html/group__local__mfe__fold.map html/group__local__mfe__fold.md5 html/group__local__mfe__fold.png html/group__local__pf__fold.html html/group__local__pf__fold.js html/group__local__pf__fold.map html/group__local__pf__fold.md5 html/group__local__pf__fold.png html/group__mea__fold.html html/group__mea__fold.map html/group__mea__fold.md5 html/group__mea__fold.png html/group__mfe__cofold.html html/group__mfe__cofold.js html/group__mfe__cofold.map html/group__mfe__cofold.md5 html/group__mfe__cofold.png html/group__mfe__fold.html html/group__mfe__fold.js html/group__mfe__fold.map html/group__mfe__fold.md5 html/group__mfe__fold.png html/group__parse.html html/group__pf__cofold.html html/group__pf__cofold.js html/group__pf__cofold.map html/group__pf__cofold.md5 html/group__pf__cofold.png html/group__pf__fold.html html/group__pf__fold.js html/group__pf__fold.map html/group__pf__fold.md5 html/group__pf__fold.png '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1561. /usr/bin/install -c -m 644 html/group__subopt__fold.html html/group__subopt__fold.js html/group__subopt__fold.map html/group__subopt__fold.md5 html/group__subopt__fold.png html/group__subopt__stochbt.html html/group__subopt__stochbt.js html/group__subopt__stochbt.map html/group__subopt__stochbt.md5 html/group__subopt__stochbt.png html/group__subopt__wuchty.html html/group__subopt__wuchty.js html/group__subopt__wuchty.map html/group__subopt__wuchty.md5 html/group__subopt__wuchty.png html/group__subopt__zuker.html html/group__subopt__zuker.js html/group__subopt__zuker.map html/group__subopt__zuker.md5 html/group__subopt__zuker.png html/group__up__cofold.html html/group__up__cofold.js html/group__up__cofold.map html/group__up__cofold.md5 html/group__up__cofold.png html/index.html html/intl11_8h_source.html html/intl11dH_8h_source.html html/intl21_8h_source.html html/intl21dH_8h_source.html html/intl22_8h_source.html html/intl22dH_8h_source.html html/inverse_8h.html html/inverse_8h.js html/inverse_8h_source.html html/jquery.js html/list_8h_source.html html/loop__energies_8h.html html/loop__energies_8h.js html/loop__energies_8h__incl.map '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1562. /usr/bin/install -c -m 644 html/loop__energies_8h__incl.md5 html/loop__energies_8h__incl.png html/loop__energies_8h_source.html html/mainpage_8h_source.html html/mm_8h.html html/mm_8h.js html/mm_8h_source.html html/modules.html html/modules.js html/move__set_8h_source.html html/mp_example.html html/mp_parse.html html/mp_utils.html html/nav_f.png html/nav_g.png html/nav_h.png html/naview_8h.html html/naview_8h.js html/naview_8h__dep__incl.map html/naview_8h__dep__incl.md5 html/naview_8h__dep__incl.png html/naview_8h_source.html html/navtree.css html/navtree.js html/navtreeindex0.js html/navtreeindex1.js html/navtreeindex2.js html/navtreeindex3.js html/navtreeindex4.js html/navtreeindex5.js html/open.png html/pages.html html/pair__mat_8h_source.html html/params_8h.html html/params_8h.js html/params_8h__dep__incl.map html/params_8h__dep__incl.md5 html/params_8h__dep__incl.png html/params_8h__incl.map html/params_8h__incl.md5 '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1563. /usr/bin/install -c -m 644 html/params_8h__incl.png html/params_8h_source.html html/part__func_8h.html html/part__func_8h.js html/part__func_8h__incl.map html/part__func_8h__incl.md5 html/part__func_8h__incl.png html/part__func_8h_source.html html/part__func__co_8h.html html/part__func__co_8h.js html/part__func__co_8h__incl.map html/part__func__co_8h__incl.md5 html/part__func__co_8h__incl.png html/part__func__co_8h_source.html html/part__func__up_8h.html html/part__func__up_8h.js html/part__func__up_8h__incl.map html/part__func__up_8h__incl.md5 html/part__func__up_8h__incl.png html/part__func__up_8h_source.html html/plex_8h_source.html html/plot__layouts_8h.html html/plot__layouts_8h.js html/plot__layouts_8h__dep__incl.map html/plot__layouts_8h__dep__incl.md5 html/plot__layouts_8h__dep__incl.png html/plot__layouts_8h__incl.map html/plot__layouts_8h__incl.md5 html/plot__layouts_8h__incl.png html/plot__layouts_8h_source.html html/profiledist_8h.html html/profiledist_8h.js html/profiledist_8h__incl.map html/profiledist_8h__incl.md5 html/profiledist_8h__incl.png html/profiledist_8h_source.html html/read__epars_8h.html html/read__epars_8h.js html/read__epars_8h_source.html html/resize.js '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1564. /usr/bin/install -c -m 644 html/ribo_8h_source.html html/snofold_8h_source.html html/snoop_8h_source.html html/stringdist_8h.html html/stringdist_8h.js html/stringdist_8h__incl.map html/stringdist_8h__incl.md5 html/stringdist_8h__incl.png html/stringdist_8h_source.html html/structCOORDINATE.html html/structCOORDINATE.js html/structConcEnt.html html/structConcEnt.js html/structINTERVAL.html html/structINTERVAL.js html/structLIST.html html/structLIST.js html/structLIST__coll__graph.map html/structLIST__coll__graph.md5 html/structLIST__coll__graph.png html/structLST__BUCKET.html html/structLST__BUCKET.js html/structLST__BUCKET__coll__graph.map html/structLST__BUCKET__coll__graph.md5 html/structLST__BUCKET__coll__graph.png html/structPAIR.html html/structPAIR.js html/structPostorder__list.html html/structPostorder__list.js html/structSOLUTION.html html/structSOLUTION.js html/structTree.html html/structTree.js html/structTree__coll__graph.map html/structTree__coll__graph.md5 html/structTree__coll__graph.png html/structTwoDfold__solution.html html/structTwoDfold__solution.js html/structTwoDfold__vars.html html/structTwoDfold__vars.js '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1565. /usr/bin/install -c -m 644 html/structTwoDfold__vars__coll__graph.map html/structTwoDfold__vars__coll__graph.md5 html/structTwoDfold__vars__coll__graph.png html/structTwoDpfold__solution.html html/structTwoDpfold__solution.js html/structTwoDpfold__vars.html html/structTwoDpfold__vars.js html/structTwoDpfold__vars__coll__graph.map html/structTwoDpfold__vars__coll__graph.md5 html/structTwoDpfold__vars__coll__graph.png html/structbondT.html html/structbondT.js html/structbondTEn.html html/structbondTEn.js html/structcofoldF.html html/structcofoldF.js html/structconstrain.html html/structconstrain.js html/structcpair.html html/structcpair.js html/structdupVar.html html/structdupVar.js html/structduplexT.html html/structduplexT.js html/structfolden.html html/structfolden.js html/structinteract.html html/structinteract.js html/structintermediate__t.html html/structintermediate__t.js html/structintermediate__t__coll__graph.map html/structintermediate__t__coll__graph.md5 html/structintermediate__t__coll__graph.png html/structmodel__detailsT.html html/structmodel__detailsT.js html/structmove__t.html html/structmove__t.js html/structpair__info.html html/structpair__info.js html/structpairpro.html '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1566. /usr/bin/install -c -m 644 html/structpairpro.js html/structpairpro__coll__graph.map html/structpairpro__coll__graph.md5 html/structpairpro__coll__graph.png html/structparamT.html html/structparamT.js html/structparamT__coll__graph.map html/structparamT__coll__graph.md5 html/structparamT__coll__graph.png html/structpath__t.html html/structpath__t.js html/structpf__paramT.html html/structpf__paramT.js html/structpf__paramT__coll__graph.map html/structpf__paramT__coll__graph.md5 html/structpf__paramT__coll__graph.png html/structplist.html html/structplist.js html/structpu__contrib.html html/structpu__contrib.js html/structpu__out.html html/structpu__out.js html/structsect.html html/structsect.js html/structsnoopT.html html/structsnoopT.js html/structstruct__en.html html/structstruct__en.js html/structsvm__model.html html/structsvm__model.js html/structswString.html html/structswString.js html/subopt_8h.html html/subopt_8h.js html/subopt_8h__incl.map html/subopt_8h__incl.md5 html/subopt_8h__incl.png html/subopt_8h_source.html html/svgpan.js html/svm__utils_8h_source.html '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1567. /usr/bin/install -c -m 644 html/sync_off.png html/sync_on.png html/tab_a.png html/tab_b.png html/tab_h.png html/tab_s.png html/tabs.css html/treedist_8h.html html/treedist_8h.js html/treedist_8h__incl.map html/treedist_8h__incl.md5 html/treedist_8h__incl.png html/treedist_8h_source.html html/utils_8h.html html/utils_8h.js html/utils_8h__dep__incl.map html/utils_8h__dep__incl.md5 html/utils_8h__dep__incl.png html/utils_8h_source.html '/tmp/portage/sci-biology/vienna-rna-2.1.8/image//usr/share/doc/vienna-rna-2.1.8/html'
1568. make[2]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc'
1569. Makefile:482: recipe for target 'install-am' failed
1570. make[1]: *** [install-am] Error 2
1571. make[1]: Leaving directory '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8/doc'
1572. Makefile:457: recipe for target 'install-recursive' failed
1573. make: *** [install-recursive] Error 1
1574. * ERROR: sci-biology/vienna-rna-2.1.8::gentoo failed (install phase):
1575. * emake failed
1576. *
1577. * If you need support, post the output of `emerge --info '=sci-biology/vienna-rna-2.1.8::gentoo'`,
1578. * the complete build log and the output of `emerge -pqv '=sci-biology/vienna-rna-2.1.8::gentoo'`.
1579. * The complete build log is located at '/var/log/portage/sci-biology:vienna-rna-2.1.8:20141112-085103.log'.
1580. * The ebuild environment file is located at '/tmp/portage/sci-biology/vienna-rna-2.1.8/temp/environment'.
1581. * Working directory: '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8'
1582. * S: '/tmp/portage/sci-biology/vienna-rna-2.1.8/work/ViennaRNA-2.1.8'
1583. * QA Notice: make jobserver unavailable:
1584. *
1585. * make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.