1. * Package: sci-biology/vienna-rna-1.8.5
2. * Repository: gentoo
3. * Maintainer: sci-biology@gentoo.org
4. * USE: amd64 elibc_glibc kernel_linux multilib test userland_GNU
5. * FEATURES: sandbox test userpriv usersandbox
6. >>> Unpacking source...
7. >>> Unpacking ViennaRNA-1.8.5.tar.gz to /tmp/portage/sci-biology/vienna-rna-1.8.5/work
8. >>> Source unpacked in /tmp/portage/sci-biology/vienna-rna-1.8.5/work
9. >>> Preparing source in /tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5 ...
10. * Applying vienna-rna-1.6.5-c-fixes.patch ...
11. [ ok ]
12. * Applying vienna-rna-1.7.2-LDFLAGS.patch ...
13. [ ok ]
14. * Applying vienna-rna-1.8.3-gcc4.3.patch ...
15. [ ok ]
16. * Applying vienna-rna-1.8.3-disable-gd.patch ...
17. [ ok ]
18. * Applying vienna-rna-1.8.4-jobserver-fix.patch ...
19. [ ok ]
20. * Applying vienna-rna-1.8.4-bindir.patch ...
21. [ ok ]
22. * Applying vienna-rna-1.8.4-overflows.patch ...
23. [ ok ]
24. * Applying vienna-rna-1.8.4-implicits.patch ...
25. [ ok ]
26. * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5' ...
27. * Running aclocal ...
28. * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold' ...
29. * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester' ...
30. * Running aclocal ...
31. * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70' ...
32. * Running aclocal ...
33. * Running aclocal ...
34. [ ok ]
35. [ ok ]
36. [ ok ]
37. [ ok ]
38. * Running autoconf ...
39. * Running autoconf ...
40. [ ok ]
41. * Running autoheader ...
42. [ ok ]
43. * Running autoconf ...
44. * Running autoconf ...
45. [ ok ]
46. * Running automake --add-missing --copy ...
47. [ ok ]
48. * Running autoheader ...
49. [ ok ]
50. * Running autoheader ...
51. [ ok ]
52. * Running automake --add-missing --copy ...
53. [ ok ]
54. * Running automake --add-missing --copy ...
55. [ ok ]
56. [ ok ]
57. [ ok ]
58. * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester' ...
59. * Running eautoreconf in '/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70' ...
60. * Running aclocal ...
61. * Running aclocal ...
62. [ ok ]
63. * Running autoconf ...
64. [ ok ]
65. [ ok ]
66. * Running autoconf ...
67. [ ok ]
68. * Running autoheader ...
69. [ ok ]
70. * Running automake --add-missing --copy ...
71. [ ok ]
72. >>> Source prepared.
73. >>> Configuring source in /tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5 ...
74. * econf: updating ViennaRNA-1.8.5/config.guess with /usr/share/gnuconfig/config.guess
75. * econf: updating ViennaRNA-1.8.5/RNAforester/g2-0.70/config.guess with /usr/share/gnuconfig/config.guess
76. * econf: updating ViennaRNA-1.8.5/RNAforester/g2-0.70/config.sub with /usr/share/gnuconfig/config.sub
77. * econf: updating ViennaRNA-1.8.5/RNAforester/config.guess with /usr/share/gnuconfig/config.guess
78. * econf: updating ViennaRNA-1.8.5/config.sub with /usr/share/gnuconfig/config.sub
79. ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --with-cluster
80. configure: loading site script /usr/share/config.site
81. configure: loading site script /usr/share/crossdev/include/site/linux
82. configure: loading site script /usr/share/crossdev/include/site/linux-gnu
83. configure: loading site script /usr/share/crossdev/include/site/x86_64-linux-gnu
84. checking for a BSD-compatible install... /usr/bin/install -c
85. checking whether build environment is sane... yes
86. checking for a thread-safe mkdir -p... /bin/mkdir -p
87. checking for gawk... gawk
88. checking whether make sets $(MAKE)... yes
89. checking if malloc debugging is wanted... no
90. checking build system type... x86_64-pc-linux-gnu
91. checking host system type... x86_64-pc-linux-gnu
92. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
93. checking whether the C compiler works... yes
94. checking for C compiler default output file name... a.out
95. checking for suffix of executables...
96. checking whether we are cross compiling... no
97. checking for suffix of object files... o
98. checking whether we are using the GNU C compiler... yes
99. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
100. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
101. checking for style of include used by make... GNU
102. checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3
103. checking whether x86_64-pc-linux-gnu-gcc accepts -fpic... yes
104. checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
105. checking whether x86_64-pc-linux-gnu-gcc and cc understand -c and -o together... yes
106. checking for perl... /usr/bin/perl
107. checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
108. checking for grep that handles long lines and -e... /bin/grep
109. checking for egrep... /bin/grep -E
110. checking for ANSI C header files... yes
111. checking for sys/types.h... yes
112. checking for sys/stat.h... yes
113. checking for stdlib.h... yes
114. checking for string.h... yes
115. checking for memory.h... yes
116. checking for strings.h... yes
117. checking for inttypes.h... yes
118. checking for stdint.h... yes
119. checking for unistd.h... yes
120. checking malloc.h usability... yes
121. checking malloc.h presence... yes
122. checking for malloc.h... yes
123. checking for strings.h... (cached) yes
124. checking for unistd.h... (cached) yes
125. checking for an ANSI C-conforming const... yes
126. checking for size_t... yes
127. checking for inline... inline
128. checking for strdup... yes
129. checking for strstr... yes
130. checking for strchr... yes
131. checking for erand48... yes
132. checking that generated files are newer than configure... done
133. configure: creating ./config.status
134. config.status: creating Makefile
135. config.status: creating ViennaRNA.spec
136. config.status: creating Utils/Makefile
137. config.status: creating Progs/Makefile
138. config.status: creating lib/Makefile
139. config.status: creating man/Makefile
140. config.status: creating Cluster/Makefile
141. config.status: creating H/Makefile
142. config.status: creating Perl/Makefile
143. config.status: creating man/RNAheat.1
144. config.status: creating man/RNAsubopt.1
145. config.status: creating man/RNAdistance.1
146. config.status: creating man/RNAinverse.1
147. config.status: creating man/RNAeval.1
148. config.status: creating man/RNAfold.1
149. config.status: creating man/RNApdist.1
150. config.status: creating man/RNAplot.1
151. config.status: creating man/RNALfold.1
152. config.status: creating man/RNAalifold.1
153. config.status: creating man/RNAduplex.1
154. config.status: creating man/RNAcofold.1
155. config.status: creating man/RNAplfold.1
156. config.status: creating man/RNAup.1
157. config.status: creating man/RNApaln.1
158. config.status: creating man/RNAaliduplex.1
159. config.status: creating config.h
160. config.status: executing depfiles commands
161. === configuring in RNAforester (/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester)
162. configure: running /bin/sh ./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' '--libdir=/usr/lib64' '--with-cluster' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CFLAGS=-O2 -pipe -ggdb -march=native -ftracer' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' --cache-file=/dev/null --srcdir=.
163. configure: loading site script /usr/share/config.site
164. configure: loading site script /usr/share/crossdev/include/site/linux
165. configure: loading site script /usr/share/crossdev/include/site/linux-gnu
166. configure: loading site script /usr/share/crossdev/include/site/x86_64-linux-gnu
167. checking for a BSD-compatible install... /usr/bin/install -c
168. checking whether build environment is sane... yes
169. checking for a thread-safe mkdir -p... /bin/mkdir -p
170. checking for gawk... gawk
171. checking whether make sets $(MAKE)... yes
172. checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
173. checking whether the C++ compiler works... yes
174. checking for C++ compiler default output file name... a.out
175. checking for suffix of executables...
176. checking whether we are cross compiling... no
177. checking for suffix of object files... o
178. checking whether we are using the GNU C++ compiler... yes
179. checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
180. checking for style of include used by make... GNU
181. checking dependency style of x86_64-pc-linux-gnu-g++... gcc3
182. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
183. checking whether we are using the GNU C compiler... yes
184. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
185. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
186. checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3
187. using (to be built) libRNA.a in ../lib
188. checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
189. checking for grep that handles long lines and -e... /bin/grep
190. checking for egrep... /bin/grep -E
191. checking for ANSI C header files... no
192. checking for sys/types.h... yes
193. checking for sys/stat.h... yes
194. checking for stdlib.h... yes
195. checking for string.h... yes
196. checking for memory.h... yes
197. checking for strings.h... yes
198. checking for inttypes.h... yes
199. checking for stdint.h... yes
200. checking for unistd.h... yes
201. checking g2.h usability... yes
202. checking g2.h presence... yes
203. checking for g2.h... yes
204. checking for an ANSI C-conforming const... yes
205. checking for inline... inline
206. checking for size_t... yes
207. checking that generated files are newer than configure... done
208. configure: creating ./config.status
209. config.status: creating Makefile
210. config.status: creating src/Makefile
211. config.status: creating man/Makefile
212. config.status: creating config.h
213. config.status: executing depfiles commands
214. === configuring in g2-0.70 (/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70)
215. configure: running /bin/sh ./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' '--libdir=/usr/lib64' '--with-cluster' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CFLAGS=-O2 -pipe -ggdb -march=native -ftracer' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' 'CXXFLAGS=-O2 -pipe -ggdb -march=native -ftracer' --cache-file=/dev/null --srcdir=.
216. configure: loading site script /usr/share/config.site
217. configure: loading site script /usr/share/crossdev/include/site/linux
218. configure: loading site script /usr/share/crossdev/include/site/linux-gnu
219. configure: loading site script /usr/share/crossdev/include/site/x86_64-linux-gnu
220. checking build system type... x86_64-pc-linux-gnu
221. checking host system type... x86_64-pc-linux-gnu
222. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
223. checking whether the C compiler works... yes
224. checking for C compiler default output file name... a.out
225. checking for suffix of executables...
226. checking whether we are cross compiling... no
227. checking for suffix of object files... o
228. checking whether we are using the GNU C compiler... yes
229. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
230. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
231. checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
232. checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
233. checking whether we are using the GNU C++ compiler... yes
234. checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
235. checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
236. checking for a BSD-compatible install... /usr/bin/install -c
237. checking for find... find
238. checking for makedepend... makedepend
239. checking for dlopen in -ldl... yes
240. checking for X... libraries , headers
241. checking for gethostbyname... yes
242. checking for connect... yes
243. checking for remove... yes
244. checking for shmat... yes
245. checking for IceConnectionNumber in -lICE... yes
246. checking for main in -lm... yes
247. checking for main in -lX11... yes
248. checking for main in -lgd... yes
249. checking for gdImagePng... no
250. checking for grep that handles long lines and -e... /bin/grep
251. checking for egrep... /bin/grep -E
252. checking for ANSI C header files... yes
253. checking for sys/types.h... yes
254. checking for sys/stat.h... yes
255. checking for stdlib.h... yes
256. checking for string.h... yes
257. checking for memory.h... yes
258. checking for strings.h... yes
259. checking for inttypes.h... yes
260. checking for stdint.h... yes
261. checking for unistd.h... yes
262. checking limits.h usability... yes
263. checking limits.h presence... yes
264. checking for limits.h... yes
266. configure: creating ./config.status
267. config.status: creating Makefile
268. config.status: creating demo/Makefile
269. config.status: creating g2_perl/Makefile.PL
271. Supported devices:
272. PostScript
273. FIG
274. X11
276. Unsupported devices:
277. Win32
278. GD
280. Run 'make depend' to create dependencies.
282. === configuring in Kinfold (/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold)
283. configure: running /bin/sh ./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' '--libdir=/usr/lib64' '--with-cluster' 'build_alias=x86_64-pc-linux-gnu' 'host_alias=x86_64-pc-linux-gnu' 'CFLAGS=-O2 -pipe -ggdb -march=native -ftracer' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' --cache-file=/dev/null --srcdir=.
284. configure: loading site script /usr/share/config.site
285. configure: loading site script /usr/share/crossdev/include/site/linux
286. configure: loading site script /usr/share/crossdev/include/site/linux-gnu
287. configure: loading site script /usr/share/crossdev/include/site/x86_64-linux-gnu
288. checking for a BSD-compatible install... /usr/bin/install -c
289. checking whether build environment is sane... yes
290. checking for a thread-safe mkdir -p... /bin/mkdir -p
291. checking for gawk... gawk
292. checking whether make sets $(MAKE)... yes
293. checking if malloc debugging is wanted... no
294. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
295. checking whether the C compiler works... yes
296. checking for C compiler default output file name... a.out
297. checking for suffix of executables...
298. checking whether we are cross compiling... no
299. checking for suffix of object files... o
300. checking whether we are using the GNU C compiler... yes
301. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
302. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
303. checking for style of include used by make... GNU
304. checking dependency style of x86_64-pc-linux-gnu-gcc... gcc3
305. checking build system type... x86_64-pc-linux-gnu
306. checking host system type... x86_64-pc-linux-gnu
307. checking for strdup... yes
308. checking for memset... yes
309. checking for strchr... yes
310. checking for ViennaRNA package... headers in "../H" and library... "../lib"
311. checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
312. checking for grep that handles long lines and -e... /bin/grep
313. checking for egrep... /bin/grep -E
314. checking for ANSI C header files... yes
315. checking for sys/types.h... yes
316. checking for sys/stat.h... yes
317. checking for stdlib.h... yes
318. checking for string.h... yes
319. checking for memory.h... yes
320. checking for strings.h... yes
321. checking for inttypes.h... yes
322. checking for stdint.h... yes
323. checking for unistd.h... yes
324. checking for stdlib.h... (cached) yes
325. checking for string.h... (cached) yes
326. checking for strings.h... (cached) yes
327. checking for unistd.h... (cached) yes
328. checking fold.h usability... yes
329. checking fold.h presence... yes
330. checking for fold.h... yes
331. checking for exp in -lm... yes
332. checking for stdlib.h... (cached) yes
333. checking for GNU libc compatible malloc... (cached) yes
334. checking for stdlib.h... (cached) yes
335. checking for GNU libc compatible realloc... (cached) yes
336. checking for an ANSI C-conforming const... yes
337. checking that generated files are newer than configure... done
338. configure: creating ./config.status
339. config.status: creating Example/Makefile
340. config.status: creating Makefile
341. config.status: creating config.h
342. config.status: executing depfiles commands
343. configure:
344. Configure successful with the following options:
346. Perl Extension: yes
347. Analyse{Dists,Seqs}: yes
348. Kinfold: yes
349. RNAforester: yes
351. Files will be installed in the following directories:
353. Executables: /usr/bin
354. Libraries: /usr/lib64
355. Header files: /usr/include
356. Extra Data: /usr/share
357. Man pages: /usr/share/man
359. >>> Source configured.
360. >>> Compiling source in /tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5 ...
361. make -j24 clean
362. Making clean in Kinfold
363. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
364. Making clean in Example
365. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold/Example'
366. make[2]: Nothing to be done for `clean'.
367. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold/Example'
368. Making clean in .
369. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
370. test -z "Kinfold" || rm -f Kinfold
371. rm -f *.o
372. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
373. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
374. Making clean in RNAforester
375. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
376. Making clean in man
377. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/man'
378. make[2]: Nothing to be done for `clean'.
379. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/man'
380. Making clean in src
381. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/src'
382. test -z "RNAforester" || rm -f RNAforester
383. rm -f *.o
384. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/src'
385. Making clean in g2-0.70
386. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70'
387. (cd ./demo ; make clean)
388. make[3]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70/demo'
389. rm g2_test g2_arc g2_splines_demo demo_cpp simple_PS simple_FIG simple_X11 pointer handles g2testf g2testf.f demo_f *~ core *.ps *.fig *.eps *.png *.jpg *.fig.bak
390. rm: cannot remove 'g2_test': No such file or directory
391. rm: cannot remove 'g2_arc': No such file or directory
392. rm: cannot remove 'g2_splines_demo': No such file or directory
393. rm: cannot remove 'demo_cpp': No such file or directory
394. rm: cannot remove 'simple_PS': No such file or directory
395. rm: cannot remove 'simple_FIG': No such file or directory
396. rm: cannot remove 'simple_X11': No such file or directory
397. rm: cannot remove 'pointer': No such file or directory
398. rm: cannot remove 'handles': No such file or directory
399. rm: cannot remove 'g2testf': No such file or directory
400. rm: cannot remove 'g2testf.f': No such file or directory
401. rm: cannot remove 'demo_f': No such file or directory
402. rm: cannot remove '*~': No such file or directory
403. rm: cannot remove 'core': No such file or directory
404. rm: cannot remove '*.ps': No such file or directory
405. rm: cannot remove '*.fig': No such file or directory
406. rm: cannot remove '*.eps': No such file or directory
407. rm: cannot remove '*.png': No such file or directory
408. rm: cannot remove '*.jpg': No such file or directory
409. rm: cannot remove '*.fig.bak': No such file or directory
410. make[3]: [clean] Error 1 (ignored)
411. make[3]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70/demo'
412. rm -f ./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
413. rm -f libg2.a config.cache config.log Makefile.bak config.status
414. rm -f ./include/*.h
415. find . -name "*~" -exec rm -f {} \;
416. (cd ./g2_perl ; make clean)
417. make[3]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70/g2_perl'
418. make[3]: *** No rule to make target `clean'. Stop.
419. make[3]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70/g2_perl'
420. make[2]: [clean] Error 2 (ignored)
421. rm -f ./g2_perl/test.ps
422. rm -f ./g2_perl/test.png
423. rm -f ./g2_perl/test.jpg
424. rm -f ./g2_perl/test.fig
425. rm -f ./g2_perl/Makefile.old
426. rm -f ./libg2.so.0.0.70
427. rm -f libg2.0.70.a
428. rm -f a.out
429. rm -fr doc/html/ doc/latex/ doc/g2_refman.ps doc/g2_refman.pdf
430. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70'
431. Making clean in .
432. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
433. make[2]: Nothing to be done for `clean-am'.
434. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
435. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
436. Making clean in Cluster
437. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Cluster'
438. test -z "AnalyseDists AnalyseSeqs" || rm -f AnalyseDists AnalyseSeqs
439. rm -f *.o
440. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Cluster'
441. Making clean in Perl
442. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
443. /usr/bin/perl Makefile.PL INSTALLDIRS=vendor LDDLFLAGS="-Wl,-O1 -Wl,--as-needed -shared"
444. Writing Makefile.perl for RNA
445. Writing MYMETA.yml and MYMETA.json
446. make -f Makefile.perl clean
447. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
448. rm -f \
449. *.a core \
450. core.[0-9] blib/arch/auto/RNA/extralibs.all \
451. core.[0-9][0-9] RNA.bso \
452. pm_to_blib.ts MYMETA.json \
453. core.[0-9][0-9][0-9][0-9] MYMETA.yml \
454. RNA.x RNA.bs \
455. perl tmon.out \
456. *.o pm_to_blib \
457. blib/arch/auto/RNA/extralibs.ld blibdirs.ts \
458. core.[0-9][0-9][0-9][0-9][0-9] *perl.core \
459. core.*perl.*.? Makefile.perl.aperl \
460. RNA.def perl \
461. core.[0-9][0-9][0-9] mon.out \
462. libRNA.def perlmain.c \
463. perl.exe so_locations \
464. RNA.exp
465. rm -rf \
466. blib
467. mv Makefile.perl Makefile.perl.old > /dev/null 2>&1
468. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
469. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
470. Making clean in H
471. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H'
472. make[1]: Nothing to be done for `clean'.
473. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H'
474. Making clean in Utils
475. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils'
476. test -z "b2ct popt" || rm -f b2ct popt
477. rm -f *.o
478. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils'
479. Making clean in man
480. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man'
481. test -z "RNAlib.dvi RNAlib.pdf RNAlib.ps RNAlib.html" \
482. || rm -rf RNAlib.dvi RNAlib.pdf RNAlib.ps RNAlib.html
483. rm -rf RNAlib.aux RNAlib.cp RNAlib.cps RNAlib.fn RNAlib.fns RNAlib.ky \
484. RNAlib.kys RNAlib.log RNAlib.pg RNAlib.pgs RNAlib.tmp \
485. RNAlib.toc RNAlib.tp RNAlib.tps RNAlib.vr RNAlib.vrs
486. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man'
487. Making clean in Progs
488. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs'
489. test -z "RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex" || rm -f RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex
490. rm -f *.o
491. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs'
492. Making clean in lib
493. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib'
494. test -z "libRNA.a" || rm -f libRNA.a
495. rm -f *.o
496. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib'
497. Making clean in .
498. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
499. make[1]: Nothing to be done for `clean-am'.
500. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
501. make -j24
502. make all-recursive
503. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
504. Making all in lib
505. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib'
506. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-dist_vars.o -MD -MP -MF .deps/libRNA_a-dist_vars.Tpo -c -o libRNA_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c
507. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-fold_vars.o -MD -MP -MF .deps/libRNA_a-fold_vars.Tpo -c -o libRNA_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c
508. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-part_func.o -MD -MP -MF .deps/libRNA_a-part_func.Tpo -c -o libRNA_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c
509. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-read_epars.o -MD -MP -MF .deps/libRNA_a-read_epars.Tpo -c -o libRNA_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c
510. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-treedist.o -MD -MP -MF .deps/libRNA_a-treedist.Tpo -c -o libRNA_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c
511. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-energy_par.o -MD -MP -MF .deps/libRNA_a-energy_par.Tpo -c -o libRNA_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c
512. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-inverse.o -MD -MP -MF .deps/libRNA_a-inverse.Tpo -c -o libRNA_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c
513. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-ProfileDist.o -MD -MP -MF .deps/libRNA_a-ProfileDist.Tpo -c -o libRNA_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c
514. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-RNAstruct.o -MD -MP -MF .deps/libRNA_a-RNAstruct.Tpo -c -o libRNA_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c
515. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-utils.o -MD -MP -MF .deps/libRNA_a-utils.Tpo -c -o libRNA_a-utils.o `test -f 'utils.c' || echo './'`utils.c
516. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-fold.o -MD -MP -MF .deps/libRNA_a-fold.Tpo -c -o libRNA_a-fold.o `test -f 'fold.c' || echo './'`fold.c
517. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-naview.o -MD -MP -MF .deps/libRNA_a-naview.Tpo -c -o libRNA_a-naview.o `test -f 'naview.c' || echo './'`naview.c
518. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-PS_dot.o -MD -MP -MF .deps/libRNA_a-PS_dot.Tpo -c -o libRNA_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c
519. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-stringdist.o -MD -MP -MF .deps/libRNA_a-stringdist.Tpo -c -o libRNA_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c
520. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-params.o -MD -MP -MF .deps/libRNA_a-params.Tpo -c -o libRNA_a-params.o `test -f 'params.c' || echo './'`params.c
521. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-subopt.o -MD -MP -MF .deps/libRNA_a-subopt.Tpo -c -o libRNA_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c
522. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-list.o -MD -MP -MF .deps/libRNA_a-list.Tpo -c -o libRNA_a-list.o `test -f 'list.c' || echo './'`list.c
523. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-Lfold.o -MD -MP -MF .deps/libRNA_a-Lfold.Tpo -c -o libRNA_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c
524. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-cofold.o -MD -MP -MF .deps/libRNA_a-cofold.Tpo -c -o libRNA_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c
525. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-part_func_co.o -MD -MP -MF .deps/libRNA_a-part_func_co.Tpo -c -o libRNA_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c
526. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-ProfileAln.o -MD -MP -MF .deps/libRNA_a-ProfileAln.Tpo -c -o libRNA_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c
527. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-duplex.o -MD -MP -MF .deps/libRNA_a-duplex.Tpo -c -o libRNA_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c
528. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-alifold.o -MD -MP -MF .deps/libRNA_a-alifold.Tpo -c -o libRNA_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c
529. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-alipfold.o -MD -MP -MF .deps/libRNA_a-alipfold.Tpo -c -o libRNA_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c
530. mv -f .deps/libRNA_a-dist_vars.Tpo .deps/libRNA_a-dist_vars.Po
531. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-aln_util.o -MD -MP -MF .deps/libRNA_a-aln_util.Tpo -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c
532. inverse.c: In function 'pf_cost':
533. inverse.c:488:4: warning: passing argument 1 of 'pf_fold' discards 'const' qualifier from pointer target type [enabled by default]
534. In file included from inverse.c:20:0:
535. ./../H/part_func.h:6:15: note: expected 'char *' but argument is of type 'const char *'
536. naview.c: In function 'dump_loops':
537. naview.c:334:3: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat]
538. stringdist.c:24:0: warning: "INFINITY" redefined [enabled by default]
539. In file included from /usr/include/math.h:40:0,
540. from stringdist.c:12:
541. /usr/include/bits/inf.h:27:0: note: this is the location of the previous definition
542. mv -f .deps/libRNA_a-fold_vars.Tpo .deps/libRNA_a-fold_vars.Po
543. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-LPfold.o -MD -MP -MF .deps/libRNA_a-LPfold.Tpo -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c
544. duplex.c: In function 'aliduplexfold':
545. duplex.c:385:3: warning: passing argument 3 of 'alibacktrack' from incompatible pointer type [enabled by default]
546. duplex.c:37:16: note: expected 'const short int **' but argument is of type 'short int **'
547. duplex.c:385:3: warning: passing argument 4 of 'alibacktrack' from incompatible pointer type [enabled by default]
548. duplex.c:37:16: note: expected 'const short int **' but argument is of type 'short int **'
549. alipfold.c: In function 'make_pscores':
550. alipfold.c:1154:5: warning: passing argument 1 of 'get_ribosum' from incompatible pointer type [enabled by default]
551. In file included from alipfold.c:22:0:
552. ./../H/ribo.h:1:16: note: expected 'char **' but argument is of type 'const char * const*'
553. duplex.c: In function 'aliduplex_subopt':
554. duplex.c:462:7: warning: passing argument 3 of 'alibacktrack' from incompatible pointer type [enabled by default]
555. duplex.c:37:16: note: expected 'const short int **' but argument is of type 'short int **'
556. duplex.c:462:7: warning: passing argument 4 of 'alibacktrack' from incompatible pointer type [enabled by default]
557. duplex.c:37:16: note: expected 'const short int **' but argument is of type 'short int **'
558. alifold.c: In function 'make_pscores':
559. alifold.c:722:5: warning: passing argument 1 of 'get_ribosum' from incompatible pointer type [enabled by default]
560. In file included from alifold.c:23:0:
561. ./../H/ribo.h:1:16: note: expected 'char **' but argument is of type 'const char * const*'
562. mv -f .deps/libRNA_a-list.Tpo .deps/libRNA_a-list.Po
563. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-part_func_up.o -MD -MP -MF .deps/libRNA_a-part_func_up.Tpo -c -o libRNA_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.c
564. mv -f .deps/libRNA_a-aln_util.Tpo .deps/libRNA_a-aln_util.Po
565. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-ribo.o -MD -MP -MF .deps/libRNA_a-ribo.Tpo -c -o libRNA_a-ribo.o `test -f 'ribo.c' || echo './'`ribo.c
566. mv -f .deps/libRNA_a-utils.Tpo .deps/libRNA_a-utils.Po
567. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-findpath.o -MD -MP -MF .deps/libRNA_a-findpath.Tpo -c -o libRNA_a-findpath.o `test -f 'findpath.c' || echo './'`findpath.c
568. mv -f .deps/libRNA_a-energy_par.Tpo .deps/libRNA_a-energy_par.Po
569. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -ggdb -march=native -ftracer -MT libRNA_a-MEA.o -MD -MP -MF .deps/libRNA_a-MEA.Tpo -c -o libRNA_a-MEA.o `test -f 'MEA.c' || echo './'`MEA.c
570. mv -f .deps/libRNA_a-ProfileDist.Tpo .deps/libRNA_a-ProfileDist.Po
571. mv -f .deps/libRNA_a-ProfileAln.Tpo .deps/libRNA_a-ProfileAln.Po
572. mv -f .deps/libRNA_a-stringdist.Tpo .deps/libRNA_a-stringdist.Po
573. mv -f .deps/libRNA_a-params.Tpo .deps/libRNA_a-params.Po
574. mv -f .deps/libRNA_a-MEA.Tpo .deps/libRNA_a-MEA.Po
575. mv -f .deps/libRNA_a-RNAstruct.Tpo .deps/libRNA_a-RNAstruct.Po
576. mv -f .deps/libRNA_a-inverse.Tpo .deps/libRNA_a-inverse.Po
577. mv -f .deps/libRNA_a-treedist.Tpo .deps/libRNA_a-treedist.Po
578. mv -f .deps/libRNA_a-findpath.Tpo .deps/libRNA_a-findpath.Po
579. mv -f .deps/libRNA_a-PS_dot.Tpo .deps/libRNA_a-PS_dot.Po
580. mv -f .deps/libRNA_a-naview.Tpo .deps/libRNA_a-naview.Po
581. mv -f .deps/libRNA_a-read_epars.Tpo .deps/libRNA_a-read_epars.Po
582. mv -f .deps/libRNA_a-ribo.Tpo .deps/libRNA_a-ribo.Po
583. mv -f .deps/libRNA_a-duplex.Tpo .deps/libRNA_a-duplex.Po
584. mv -f .deps/libRNA_a-subopt.Tpo .deps/libRNA_a-subopt.Po
585. mv -f .deps/libRNA_a-Lfold.Tpo .deps/libRNA_a-Lfold.Po
586. mv -f .deps/libRNA_a-LPfold.Tpo .deps/libRNA_a-LPfold.Po
587. mv -f .deps/libRNA_a-alifold.Tpo .deps/libRNA_a-alifold.Po
588. mv -f .deps/libRNA_a-part_func_co.Tpo .deps/libRNA_a-part_func_co.Po
589. mv -f .deps/libRNA_a-part_func_up.Tpo .deps/libRNA_a-part_func_up.Po
590. mv -f .deps/libRNA_a-cofold.Tpo .deps/libRNA_a-cofold.Po
591. mv -f .deps/libRNA_a-part_func.Tpo .deps/libRNA_a-part_func.Po
592. mv -f .deps/libRNA_a-alipfold.Tpo .deps/libRNA_a-alipfold.Po
593. mv -f .deps/libRNA_a-fold.Tpo .deps/libRNA_a-fold.Po
594. rm -f libRNA.a
595. 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-MEA.o
596. x86_64-pc-linux-gnu-ranlib libRNA.a
597. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib'
598. Making all in Progs
599. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs'
600. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAfold.o -MD -MP -MF .deps/RNAfold.Tpo -c -o RNAfold.o RNAfold.c
601. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAeval.o -MD -MP -MF .deps/RNAeval.Tpo -c -o RNAeval.o RNAeval.c
602. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAheat.o -MD -MP -MF .deps/RNAheat.Tpo -c -o RNAheat.o RNAheat.c
603. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNApdist.o -MD -MP -MF .deps/RNApdist.Tpo -c -o RNApdist.o RNApdist.c
604. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAdistance.o -MD -MP -MF .deps/RNAdistance.Tpo -c -o RNAdistance.o RNAdistance.c
605. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAinverse.o -MD -MP -MF .deps/RNAinverse.Tpo -c -o RNAinverse.o RNAinverse.c
606. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAplot.o -MD -MP -MF .deps/RNAplot.Tpo -c -o RNAplot.o RNAplot.c
607. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAsubopt.o -MD -MP -MF .deps/RNAsubopt.Tpo -c -o RNAsubopt.o RNAsubopt.c
608. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNALfold.o -MD -MP -MF .deps/RNALfold.Tpo -c -o RNALfold.o RNALfold.c
609. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAcofold.o -MD -MP -MF .deps/RNAcofold.Tpo -c -o RNAcofold.o RNAcofold.c
610. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNApaln.o -MD -MP -MF .deps/RNApaln.Tpo -c -o RNApaln.o RNApaln.c
611. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAduplex.o -MD -MP -MF .deps/RNAduplex.Tpo -c -o RNAduplex.o RNAduplex.c
612. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAalifold.o -MD -MP -MF .deps/RNAalifold.Tpo -c -o RNAalifold.o RNAalifold.c
613. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAplfold.o -MD -MP -MF .deps/RNAplfold.Tpo -c -o RNAplfold.o RNAplfold.c
614. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAup.o -MD -MP -MF .deps/RNAup.Tpo -c -o RNAup.o RNAup.c
615. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT RNAaliduplex.o -MD -MP -MF .deps/RNAaliduplex.Tpo -c -o RNAaliduplex.o RNAaliduplex.c
616. RNAduplex.c: In function 'main':
617. RNAduplex.c:158:7: warning: format '%d' expects argument of type 'int', but argument 2 has type 'size_t' [-Wformat]
618. RNAduplex.c:158:7: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' [-Wformat]
619. RNAduplex.c: In function 'print_struc':
620. RNAduplex.c:188:3: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat]
621. RNAaliduplex.c: In function 'main':
622. RNAaliduplex.c:128:5: warning: passing argument 1 of 'aliduplex_subopt' from incompatible pointer type [enabled by default]
623. In file included from RNAaliduplex.c:14:0:
624. ./../H/duplex.h:14:17: note: expected 'const char **' but argument is of type 'char **'
625. RNAaliduplex.c:128:5: warning: passing argument 2 of 'aliduplex_subopt' from incompatible pointer type [enabled by default]
626. In file included from RNAaliduplex.c:14:0:
627. ./../H/duplex.h:14:17: note: expected 'const char **' but argument is of type 'char **'
628. RNAaliduplex.c:135:5: warning: passing argument 1 of 'aliduplexfold' from incompatible pointer type [enabled by default]
629. RNAaliduplex.c:22:16: note: expected 'const char **' but argument is of type 'char **'
630. RNAaliduplex.c:135:5: warning: passing argument 2 of 'aliduplexfold' from incompatible pointer type [enabled by default]
631. RNAaliduplex.c:22:16: note: expected 'const char **' but argument is of type 'char **'
632. RNAaliduplex.c: In function 'print_struc':
633. RNAaliduplex.c:150:3: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat]
634. RNAup.c: In function 'main':
635. RNAup.c:110:5: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[201]' [-Wformat]
636. RNAinverse.c:31:0: warning: "INFINITY" redefined [enabled by default]
637. In file included from /usr/include/math.h:40:0,
638. from RNAinverse.c:9:
639. /usr/include/bits/inf.h:27:0: note: this is the location of the previous definition
640. mv -f .deps/RNAplot.Tpo .deps/RNAplot.Po
641. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAplot RNAplot.o ../lib/libRNA.a -lm
642. mv -f .deps/RNAaliduplex.Tpo .deps/RNAaliduplex.Po
643. mv -f .deps/RNAeval.Tpo .deps/RNAeval.Po
644. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAaliduplex RNAaliduplex.o ../lib/libRNA.a -lm
645. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAeval RNAeval.o ../lib/libRNA.a -lm
646. mv -f .deps/RNAduplex.Tpo .deps/RNAduplex.Po
647. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAduplex RNAduplex.o ../lib/libRNA.a -lm
648. mv -f .deps/RNAheat.Tpo .deps/RNAheat.Po
649. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAheat RNAheat.o ../lib/libRNA.a -lm
650. mv -f .deps/RNAinverse.Tpo .deps/RNAinverse.Po
651. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAinverse RNAinverse.o ../lib/libRNA.a -lm
652. mv -f .deps/RNALfold.Tpo .deps/RNALfold.Po
653. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNALfold RNALfold.o ../lib/libRNA.a -lm
654. mv -f .deps/RNAsubopt.Tpo .deps/RNAsubopt.Po
655. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAsubopt RNAsubopt.o ../lib/libRNA.a -lm
656. mv -f .deps/RNApdist.Tpo .deps/RNApdist.Po
657. mv -f .deps/RNAplfold.Tpo .deps/RNAplfold.Po
658. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNApdist RNApdist.o ../lib/libRNA.a -lm
659. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAplfold RNAplfold.o ../lib/libRNA.a -lm
660. mv -f .deps/RNAfold.Tpo .deps/RNAfold.Po
661. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAfold RNAfold.o ../lib/libRNA.a -lm
662. mv -f .deps/RNApaln.Tpo .deps/RNApaln.Po
663. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNApaln RNApaln.o ../lib/libRNA.a -lm
664. mv -f .deps/RNAdistance.Tpo .deps/RNAdistance.Po
665. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAdistance RNAdistance.o ../lib/libRNA.a -lm
666. mv -f .deps/RNAcofold.Tpo .deps/RNAcofold.Po
667. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAcofold RNAcofold.o ../lib/libRNA.a -lm
668. mv -f .deps/RNAalifold.Tpo .deps/RNAalifold.Po
669. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAalifold RNAalifold.o ../lib/libRNA.a -lm
670. mv -f .deps/RNAup.Tpo .deps/RNAup.Po
671. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o RNAup RNAup.o ../lib/libRNA.a -lm
672. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs'
673. Making all in man
674. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man'
675. make[2]: Nothing to be done for `all'.
676. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man'
677. Making all in Utils
678. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils'
679. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT b2ct.o -MD -MP -MF .deps/b2ct.Tpo -c -o b2ct.o b2ct.c
680. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -ggdb -march=native -ftracer -MT popt.o -MD -MP -MF .deps/popt.Tpo -c -o popt.o popt.c
681. if test -n "/usr/bin/perl"; then \
682. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' b2mt.pl ; \
683. fi
684. if test -n "/usr/bin/perl"; then \
685. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' ct2b.pl ; \
686. fi
687. if test -n "/usr/bin/perl"; then \
688. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' dpzoom.pl ; \
689. fi
690. if test -n "/usr/bin/perl"; then \
691. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' mountain.pl ; \
692. fi
693. if test -n "/usr/bin/perl"; then \
694. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' relplot.pl ; \
695. fi
696. if test -n "/usr/bin/perl"; then \
697. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' rotate_ss.pl ; \
698. fi
699. if test -n "/usr/bin/perl"; then \
700. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' cmount.pl ; \
701. fi
702. if test -n "/usr/bin/perl"; then \
703. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' colorrna.pl ; \
704. fi
705. if test -n "/usr/bin/perl"; then \
706. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' coloraln.pl ; \
707. fi
708. if test -n "/usr/bin/perl"; then \
709. /usr/bin/perl -npi -e 's|^#!\S+|#!/usr/bin/perl|' refold.pl ; \
710. fi
711. mv -f .deps/popt.Tpo .deps/popt.Po
712. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o popt popt.o -L../lib -lRNA -lm
713. mv -f .deps/b2ct.Tpo .deps/b2ct.Po
714. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o b2ct b2ct.o -L../lib -lRNA -lm
715. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils'
716. Making all in H
717. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H'
718. make[2]: Nothing to be done for `all'.
719. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H'
720. Making all in Perl
721. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
722. /usr/bin/perl Makefile.PL INSTALLDIRS=vendor LDDLFLAGS="-Wl,-O1 -Wl,--as-needed -shared"
723. Writing Makefile.perl for RNA
724. Writing MYMETA.yml and MYMETA.json
725. make -f Makefile.perl
726. make[3]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
727. x86_64-pc-linux-gnu-gcc -c -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -pipe -ggdb -march=native -ftracer -DVERSION=\"0.2\" -DXS_VERSION=\"0.2\" -fPIC "-I/usr/lib64/perl5/5.16.0/x86_64-linux/CORE" RNA_wrap.c
728. Running Mkbootstrap for RNA ()
729. cp RNA.pm blib/lib/RNA.pm
730. chmod 644 RNA.bs
731. cp RNA.bs blib/arch/auto/RNA/RNA.bs
732. chmod 644 blib/arch/auto/RNA/RNA.bs
733. In file included from RNA_wrap.c:1547:0:
734. ../H/part_func_co.h:28:9: warning: 'struct plist' declared inside parameter list [enabled by default]
735. rm -f blib/arch/auto/RNA/RNA.so
736. x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -shared RNA_wrap.o -o blib/arch/auto/RNA/RNA.so ../lib/libRNA.a \
737. -lm \
739. chmod 755 blib/arch/auto/RNA/RNA.so
740. Manifying blib/man3/RNA.3pm
741. make[3]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
742. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
743. Making all in Cluster
744. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Cluster'
745. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -ggdb -march=native -ftracer -MT split.o -MD -MP -MF .deps/split.Tpo -c -o split.o split.c
746. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -ggdb -march=native -ftracer -MT distance_matrix.o -MD -MP -MF .deps/distance_matrix.Tpo -c -o distance_matrix.o distance_matrix.c
747. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -ggdb -march=native -ftracer -MT cluster.o -MD -MP -MF .deps/cluster.Tpo -c -o cluster.o cluster.c
748. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -ggdb -march=native -ftracer -MT treeplot.o -MD -MP -MF .deps/treeplot.Tpo -c -o treeplot.o treeplot.c
749. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -ggdb -march=native -ftracer -MT AD_main.o -MD -MP -MF .deps/AD_main.Tpo -c -o AD_main.o AD_main.c
750. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -ggdb -march=native -ftracer -c ./../lib/utils.c
751. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -ggdb -march=native -ftracer -MT statgeom.o -MD -MP -MF .deps/statgeom.Tpo -c -o statgeom.o statgeom.c
752. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -ggdb -march=native -ftracer -MT AS_main.o -MD -MP -MF .deps/AS_main.Tpo -c -o AS_main.o AS_main.c
753. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -O2 -pipe -ggdb -march=native -ftracer -MT PS3D.o -MD -MP -MF .deps/PS3D.Tpo -c -o PS3D.o PS3D.c
754. mv -f .deps/AD_main.Tpo .deps/AD_main.Po
755. mv -f .deps/PS3D.Tpo .deps/PS3D.Po
756. mv -f .deps/AS_main.Tpo .deps/AS_main.Po
757. mv -f .deps/cluster.Tpo .deps/cluster.Po
758. mv -f .deps/split.Tpo .deps/split.Po
759. mv -f .deps/treeplot.Tpo .deps/treeplot.Po
760. mv -f .deps/statgeom.Tpo .deps/statgeom.Po
761. mv -f .deps/distance_matrix.Tpo .deps/distance_matrix.Po
762. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o utils.o -lm
763. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -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
764. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Cluster'
765. Making all in RNAforester
766. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
767. make all-recursive
768. make[3]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
769. Making all in g2-0.70
770. make[4]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70'
771. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
772. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
773. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
774. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
775. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
776. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
777. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
778. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
779. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
780. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
781. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
782. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
783. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
784. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
785. x86_64-pc-linux-gnu-gcc -I./src -O2 -pipe -ggdb -march=native -ftracer -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
786. src/FIG/g2_FIG.c: In function 'g2_FIG_draw_string':
787. src/FIG/g2_FIG.c:478:6: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat]
788. 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
789. test ! -n "x86_64-pc-linux-gnu-ranlib" || x86_64-pc-linux-gnu-ranlib libg2.a
790. test -d ./include || mkdir ./include
791. cp ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ./include/
792. make[4]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70'
793. Making all in src
794. make[4]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/src'
795. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT Arguments.o -MD -MP -MF .deps/Arguments.Tpo -c -o Arguments.o Arguments.cpp
796. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT glib.o -MD -MP -MF .deps/glib.Tpo -c -o glib.o glib.c
797. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp
798. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT ppforestbase.o -MD -MP -MF .deps/ppforestbase.Tpo -c -o ppforestbase.o ppforestbase.cpp
799. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT progressive_align.o -MD -MP -MF .deps/progressive_align.Tpo -c -o progressive_align.o progressive_align.cpp
800. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT rna_profile_alignment.o -MD -MP -MF .deps/rna_profile_alignment.Tpo -c -o rna_profile_alignment.o rna_profile_alignment.cpp
801. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT rna_alignment.o -MD -MP -MF .deps/rna_alignment.Tpo -c -o rna_alignment.o rna_alignment.cpp
802. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT rna_algebra.o -MD -MP -MF .deps/rna_algebra.Tpo -c -o rna_algebra.o rna_algebra.cpp
803. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT rna_alphabet.o -MD -MP -MF .deps/rna_alphabet.Tpo -c -o rna_alphabet.o rna_alphabet.cpp
804. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT rnaforest.o -MD -MP -MF .deps/rnaforest.Tpo -c -o rnaforest.o rnaforest.cpp
805. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT rnaforestsz.o -MD -MP -MF .deps/rnaforestsz.Tpo -c -o rnaforestsz.o rnaforestsz.cpp
806. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT rnafuncs.o -MD -MP -MF .deps/rnafuncs.Tpo -c -o rnafuncs.o rnafuncs.cpp
807. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT rnaforester_options.o -MD -MP -MF .deps/rnaforester_options.Tpo -c -o rnaforester_options.o rnaforester_options.cpp
808. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../g2-0.70/include/ -O2 -pipe -ggdb -march=native -ftracer -MT wmatch.o -MD -MP -MF .deps/wmatch.Tpo -c -o wmatch.o wmatch.c
809. glib.c: In function 'ReadMatrix':
810. glib.c:272:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
811. glib.c:282:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
812. glib.c: In function 'ReadEuclid':
813. glib.c:225:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
814. glib.c:234:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
815. glib.c: In function 'ReadGraph':
816. glib.c:161:8: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
817. glib.c:170:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
818. glib.c:176:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
819. mv -f .deps/rna_alphabet.Tpo .deps/rna_alphabet.Po
820. mv -f .deps/glib.Tpo .deps/glib.Po
821. In file included from rnaforest.h:22:0,
822. from rnaforest.cpp:24:
823. rnafuncs.h:42:3: warning: 'typedef' was ignored in this declaration [enabled by default]
824. In file included from rnafuncs.cpp:23:0:
825. rnafuncs.h:42:3: warning: 'typedef' was ignored in this declaration [enabled by default]
826. In file included from rna_profile_alignment.cpp:37:0:
827. rnafuncs.h:42:3: warning: 'typedef' was ignored in this declaration [enabled by default]
828. progressive_align.cpp: In function 'node_entry* makePairsGraph(const RNAProfileAliMapType&, const DoubleScoreProfileAlgebraType*, const Matrix<double>*, double)':
829. progressive_align.cpp:341:30: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
830. In file included from rnaforestsz.cpp:15:0:
831. rnafuncs.h:42:3: warning: 'typedef' was ignored in this declaration [enabled by default]
832. In file included from rnaforest.h:22:0,
833. from rna_alignment.h:24,
834. from rna_alignment.cpp:22:
835. rnafuncs.h:42:3: warning: 'typedef' was ignored in this declaration [enabled by default]
836. mv -f .deps/ppforestbase.Tpo .deps/ppforestbase.Po
837. mv -f .deps/wmatch.Tpo .deps/wmatch.Po
838. In file included from rnaforest.h:22:0,
839. from rna_alignment.h:24,
840. from main.cpp:52:
841. rnafuncs.h:42:3: warning: 'typedef' was ignored in this declaration [enabled by default]
842. mv -f .deps/rnaforest.Tpo .deps/rnaforest.Po
843. mv -f .deps/rna_algebra.Tpo .deps/rna_algebra.Po
844. mv -f .deps/rnaforestsz.Tpo .deps/rnaforestsz.Po
845. mv -f .deps/rna_alignment.Tpo .deps/rna_alignment.Po
846. mv -f .deps/Arguments.Tpo .deps/Arguments.Po
847. mv -f .deps/rnafuncs.Tpo .deps/rnafuncs.Po
848. mv -f .deps/rnaforester_options.Tpo .deps/rnaforester_options.Po
849. mv -f .deps/rna_profile_alignment.Tpo .deps/rna_profile_alignment.Po
850. mv -f .deps/progressive_align.Tpo .deps/progressive_align.Po
851. mv -f .deps/main.Tpo .deps/main.Po
852. x86_64-pc-linux-gnu-g++ -O2 -pipe -ggdb -march=native -ftracer -L../g2-0.70 -L../../lib -Wl,-O1 -Wl,--as-needed -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
853. make[4]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/src'
854. Making all in man
855. make[4]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/man'
856. make[4]: Nothing to be done for `all'.
857. make[4]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/man'
858. make[4]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
859. make[4]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
860. make[3]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
861. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
862. Making all in Kinfold
863. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
864. make all-recursive
865. make[3]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
866. Making all in Example
867. make[4]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold/Example'
868. make[4]: Nothing to be done for `all'.
869. make[4]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold/Example'
870. make[4]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
871. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -MT baum.o -MD -MP -MF .deps/baum.Tpo -c -o baum.o baum.c
872. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -MT cache.o -MD -MP -MF .deps/cache.Tpo -c -o cache.o cache.c
873. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -MT globals.o -MD -MP -MF .deps/globals.Tpo -c -o globals.o globals.c
874. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c
875. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -MT nachbar.o -MD -MP -MF .deps/nachbar.Tpo -c -o nachbar.o nachbar.c
876. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../H -O2 -pipe -ggdb -march=native -ftracer -MT cmdline.o -MD -MP -MF .deps/cmdline.Tpo -c -o cmdline.o cmdline.c
877. nachbar.c: In function 'sel_nb':
878. nachbar.c:301:2: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' [-Wformat]
879. globals.c: In function 'process_options_gg':
880. globals.c:320:9: warning: format '%g' expects argument of type 'float *', but argument 3 has type 'double *' [-Wformat]
881. globals.c:320:9: warning: format '%g' expects argument of type 'float *', but argument 4 has type 'double *' [-Wformat]
882. globals.c:320:9: warning: format '%g' expects argument of type 'float *', but argument 5 has type 'double *' [-Wformat]
883. globals.c: In function 'process_options':
884. globals.c:406:8: warning: format '%g' expects argument of type 'float *', but argument 3 has type 'double *' [-Wformat]
885. globals.c:406:8: warning: format '%g' expects argument of type 'float *', but argument 4 has type 'double *' [-Wformat]
886. globals.c:406:8: warning: format '%g' expects argument of type 'float *', but argument 5 has type 'double *' [-Wformat]
887. mv -f .deps/cache.Tpo .deps/cache.Po
888. mv -f .deps/main.Tpo .deps/main.Po
889. mv -f .deps/nachbar.Tpo .deps/nachbar.Po
890. mv -f .deps/globals.Tpo .deps/globals.Po
891. mv -f .deps/baum.Tpo .deps/baum.Po
892. mv -f .deps/cmdline.Tpo .deps/cmdline.Po
893. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -L../lib -Wl,-O1 -Wl,--as-needed -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o -lRNA -lm
894. make[4]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
895. make[3]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
896. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
897. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
898. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
899. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
900. make -j24 -C Readseq
901. make: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Readseq'
902. Compiling readseq...
903. x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -O2 -pipe -ggdb -march=native -ftracer -o readseq readseq.c ureadseq.c
904. readseq.c: In function 'formatstr':
905. readseq.c:261:27: warning: return discards 'const' qualifier from pointer target type [enabled by default]
906. readseq.c:263:31: warning: return discards 'const' qualifier from pointer target type [enabled by default]
907. readseq.c:267:8: warning: return discards 'const' qualifier from pointer target type [enabled by default]
908. readseq.c: In function 'usage':
909. readseq.c:332:3: warning: format not a string literal and no format arguments [-Wformat-security]
910. readseq.c: In function 'main':
911. readseq.c:772:3: warning: format not a string literal and no format arguments [-Wformat-security]
912. readseq.c:914:13: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
913. readseq.c:916:13: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat]
914. readseq.c:959:17: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat]
915. readseq.c:959:17: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
916. readseq.c:959:17: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat]
917. readseq.c:969:15: warning: format not a string literal and no format arguments [-Wformat-security]
918. readseq.c:976:19: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat]
919. readseq.c:976:19: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
920. readseq.c:977:19: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat]
921. readseq.c:977:19: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
922. readseq.c:1080:19: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
923. readseq.c:1080:19: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat]
924. readseq.c:1091:5: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
925. readseq.c:1092:5: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
926. readseq.c:1116:9: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
927. readseq.c:761:11: warning: ignoring return value of 'tmpnam', declared with attribute warn_unused_result [-Wunused-result]
928. readseq.c:779:9: warning: ignoring return value of 'gets', declared with attribute warn_unused_result [-Wunused-result]
929. readseq.c:843:11: warning: ignoring return value of 'gets', declared with attribute warn_unused_result [-Wunused-result]
930. readseq.c:889:13: warning: ignoring return value of 'gets', declared with attribute warn_unused_result [-Wunused-result]
931. readseq.c:915:20: warning: ignoring return value of 'freopen', declared with attribute warn_unused_result [-Wunused-result]
932. readseq.c: In function 'chooseFormat':
933. readseq.c:423:11: warning: ignoring return value of 'gets', declared with attribute warn_unused_result [-Wunused-result]
934. ureadseq.c: In function 'seqFileFormatFp':
935. ureadseq.c:1346:5: warning: format '%d' expects argument of type 'int *', but argument 3 has type 'long int *' [-Wformat]
936. ureadseq.c:1346:5: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long int *' [-Wformat]
937. ureadseq.c: In function 'writeSeq':
938. ureadseq.c:1595:3: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat]
939. ureadseq.c:1624:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
940. ureadseq.c:1625:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
941. ureadseq.c:1625:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat]
942. ureadseq.c:1639:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
943. ureadseq.c:1639:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat]
944. ureadseq.c:1649:7: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat]
945. ureadseq.c:1659:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
946. ureadseq.c:1659:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat]
947. ureadseq.c:1668:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
948. ureadseq.c:1668:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat]
949. ureadseq.c:1669:7: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat]
950. ureadseq.c:1680:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
951. ureadseq.c:1680:7: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat]
952. ureadseq.c:1689:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
953. ureadseq.c:1689:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat]
954. ureadseq.c:1695:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
955. ureadseq.c:1695:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat]
956. ureadseq.c:1726:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
957. ureadseq.c:1748:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
958. ureadseq.c:1748:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat]
959. ureadseq.c:1765:9: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
960. ureadseq.c:1765:9: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat]
961. ureadseq.c:1772:21: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
962. ureadseq.c:1772:21: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long unsigned int' [-Wformat]
963. ureadseq.c:1783:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
964. ureadseq.c:1783:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat]
965. ureadseq.c:1791:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
966. ureadseq.c:1791:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat]
967. ureadseq.c:1797:7: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat]
968. ureadseq.c:1797:7: warning: format '%X' expects argument of type 'unsigned int', but argument 5 has type 'long unsigned int' [-Wformat]
969. ureadseq.c:1838:9: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat]
970. /tmp/portage/sci-biology/vienna-rna-1.8.5/temp/ccJXpb0B.o: In function `main':
971. /tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Readseq/readseq.c:761: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
972. /tmp/portage/sci-biology/vienna-rna-1.8.5/temp/ccJXpb0B.o: In function `gets':
973. /usr/include/bits/stdio2.h:229: warning: the `gets' function is dangerous and should not be used.
974. make: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Readseq'
975. >>> Source compiled.
976. make -j24 check
977. make -f Makefile.perl
978. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
979. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
980. make check-local
981. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
982. make -f Makefile.perl
983. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
984. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
985. make -f Makefile.perl test
986. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
987. PERL_DL_NONLAZY=1 /usr/bin/perl5.16.0 "-Iblib/lib" "-Iblib/arch" test.pl
988. 1..24
989. # Running under perl version 5.016000 for linux
990. # Current time local: Thu Jun 21 20:01:08 2012
991. # Current time GMT: Thu Jun 21 20:01:08 2012
992. # Using Test.pm version 1.25_02
993. ok 1
994. ok 2
995. ok 3
996. ok 4
997. ok 5
998. ok 6
999. ok 7
1000. ok 8
1001. ok 9
1002. ok 10
1003. ok 11
1004. ok 12
1005. ok 13
1006. ok 14
1007. ok 15
1008. ok 16
1009. ok 17
1010. ok 18
1011. ok 19
1012. please check the two postscript files test_ss.ps and test_dp.ps
1013. ok 20
1014. 14 suboptimals
1015. (((.((....)).))) -5.50
1016. (((.(((...)))))) -5.30
1017. .((.((....)).)). -5.10
1018. (((.((.....))))) -5.00
1019. .((.(((...))))). -4.90
1020. .((.((.....)))). -4.60
1021. ....(((...)))... -2.80
1022. ....((.....))... -2.50
1023. (((..((....))))) -2.20
1024. .((..((....)))). -1.80
1025. ....((....)).... -1.10
1026. .....((....))... -0.90
1027. (((..........))) -0.80
1028. ((..((....))..)) -0.50
1029. ok 21
1030. ok 22
1031. ok 23
1032. ok 24
1033. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
1034. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
1035. make -j24 test
1037. Test for general read/write of all chars:
1038. ./readseq -p alphabet.std -otest.alpha
1039. diff -w test.alpha alphabet.std
1040. 1c1
1041. < >alphabet['!'..'~'], 83 bases, E14ECBE2 checksum.
1042. ---
1043. > >alphabet['!'..'~'], 83 bases, 9429 checksum.
1044. make: [test] Error 1 (ignored)
1046. Test for valid format conversions:
1047. ./readseq -p -f=ig nucleic.std -otest.ig
1048. ./readseq -p -f=gb test.ig -otest.gb
1049. ./readseq -p -f=nbrf test.gb -otest.nbrf
1050. ./readseq -p -f=embl test.nbrf -otest.embl
1051. ./readseq -p -f=gcg test.embl -otest.gcg
1052. ./readseq -p -f=strider test.gcg -otest.strider
1053. ./readseq -p -f=fitch test.strider -otest.fitch
1054. ./readseq -p -f=fasta test.fitch -otest.fasta
1055. ./readseq -p -f=pir test.fasta -otest.pir
1056. ./readseq -p -f=ig test.pir -otest.ig-b
1057. diff -w test.ig test.ig-b
1058. 1,2c1,2
1059. < ;nucleic/amino test, 228 bases, 1B5655D0 checksum.
1060. < nucleic/amino
1061. ---
1062. > ;nucleic/amino, , 228 bases, 1B5655D0 checksum.
1063. > nucleic/amino,
1064. make: [test] Error 1 (ignored)
1066. Test for multiple-sequence format conversions:
1067. ./readseq -p -f=ig multi.std -otest.m-ig
1068. ./readseq -p -f=gb test.m-ig -otest.m-gb
1069. ./readseq -p -f=nbrf test.m-gb -otest.m-nbrf
1070. ./readseq -p -f=embl test.m-nbrf -otest.m-embl
1071. ./readseq -p -f=fasta test.m-embl -otest.m-fasta
1072. ./readseq -p -f=pir test.m-fasta -otest.m-pir
1073. ./readseq -p -f=msf test.m-pir -otest.m-msf
1074. ./readseq -p -f=paup test.m-msf -otest.m-paup
1075. ./readseq -p -f=ig test.m-paup -otest.m-ig-b
1076. diff -w test.m-ig test.m-ig-b
1077. 1,2c1,2
1078. < ;acarr58sst , 183 bases, 64754A4D checksum.
1079. < acarr58sst
1080. ---
1081. > ;acarr58ss, 183 bases, 64754A4D checksum.
1082. > acarr58ss
1083. 25,26c25,26
1084. < ;ddirr58sst , 183 bases, 1E3D23B8 checksum.
1085. < ddirr58sst
1086. ---
1087. > ;ddirr58ss, 183 bases, 1E3D23B8 checksum.
1088. > ddirr58ss
1089. make: [test] Error 1 (ignored)
1091. Expect differences in the header lines due to
1092. different format headers. If any sequence lines
1093. differ, or if the checksums differ, there is a problem.
1094. ----------------------
1096. To clean up test files, command me:
1097. make clean
1099. >>> Install vienna-rna-1.8.5 into /tmp/portage/sci-biology/vienna-rna-1.8.5/image/ category sci-biology
1100. make -j24 DESTDIR=/tmp/portage/sci-biology/vienna-rna-1.8.5/image/ install
1101. Making install in lib
1102. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib'
1103. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib'
1104. make[2]: Nothing to be done for `install-data-am'.
1105. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/lib64'
1106. /usr/bin/install -c -m 644 libRNA.a '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/lib64'
1107. ( cd '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/lib64' && x86_64-pc-linux-gnu-ranlib libRNA.a )
1108. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib'
1109. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/lib'
1110. Making install in Progs
1111. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs'
1112. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs'
1113. make[2]: Nothing to be done for `install-data-am'.
1114. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/bin'
1115. /usr/bin/install -c RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/bin'
1116. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs'
1117. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Progs'
1118. Making install in man
1119. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man'
1120. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man'
1121. make[2]: Nothing to be done for `install-exec-am'.
1122. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/man/man1'
1123. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/info'
1124. /usr/bin/install -c -m 644 RNAheat.1 RNAsubopt.1 RNAdistance.1 RNAinverse.1 RNAcofold.1 RNAeval.1 RNAfold.1 RNApdist.1 RNAplot.1 RNAalifold.1 RNALfold.1 RNAduplex.1 RNAplfold.1 RNAup.1 RNApaln.1 RNAaliduplex.1 '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/man/man1'
1125. /usr/bin/install -c -m 644 ./RNAlib.info '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/info'
1126. install-info --info-dir='/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/info' '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/info/RNAlib.info'
1127. install-info: warning: no info dir entry in `/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/info/RNAlib.info'
1128. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man'
1129. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/man'
1130. Making install in Utils
1131. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils'
1132. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils'
1133. make[2]: Nothing to be done for `install-exec-am'.
1134. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/bin'
1135. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/bin'
1136. /usr/bin/install -c b2ct popt '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/bin'
1137. /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 Fold '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/bin'
1138. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils'
1139. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Utils'
1140. Making install in H
1141. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H'
1142. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H'
1143. make[2]: Nothing to be done for `install-exec-am'.
1144. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/include/ViennaRNA'
1145. /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 MEA.h '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/include/ViennaRNA'
1146. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H'
1147. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/H'
1148. Making install in Perl
1149. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
1150. make -f Makefile.perl
1151. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
1152. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
1153. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
1154. make -f Makefile.perl
1155. make[2]: Nothing to be done for `install-data-am'.
1156. make[3]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
1157. make[3]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
1158. make -f Makefile.perl install
1159. make[3]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
1160. Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
1161. Installing /tmp/portage/sci-biology/vienna-rna-1.8.5/image/usr/lib64/perl5/vendor_perl/5.16.0/x86_64-linux/auto/RNA/RNA.so
1162. Installing /tmp/portage/sci-biology/vienna-rna-1.8.5/image/usr/lib64/perl5/vendor_perl/5.16.0/x86_64-linux/auto/RNA/RNA.bs
1163. Installing /tmp/portage/sci-biology/vienna-rna-1.8.5/image/usr/lib64/perl5/vendor_perl/5.16.0/x86_64-linux/RNA.pm
1164. Installing /tmp/portage/sci-biology/vienna-rna-1.8.5/image/usr/share/man/man3/RNA.3pm
1165. make[3]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
1166. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
1167. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Perl'
1168. Making install in Cluster
1169. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Cluster'
1170. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Cluster'
1171. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/bin'
1172. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/man/man1'
1173. /usr/bin/install -c AnalyseDists AnalyseSeqs '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/bin'
1174. /usr/bin/install -c -m 644 AnalyseDists.1 AnalyseSeqs.1 '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/man/man1'
1175. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Cluster'
1176. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Cluster'
1177. Making install in RNAforester
1178. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
1179. Making install in g2-0.70
1180. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70'
1181. test -d /tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/lib64 || mkdir -p /tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/lib64
1182. test -d /tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/include || mkdir -p /tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/include
1183. /usr/bin/install -c -m 644 libg2.a /tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/lib64
1184. for IFILE in ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ; do \
1185. /usr/bin/install -c -m 644 $IFILE /tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/include; \
1186. done
1187. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/g2-0.70'
1188. Making install in src
1189. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/src'
1190. make[3]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/src'
1191. make[3]: Nothing to be done for `install-data-am'.
1192. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/bin'
1193. /usr/bin/install -c RNAforester '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/bin'
1194. make[3]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/src'
1195. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/src'
1196. Making install in man
1197. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/man'
1198. make[3]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/man'
1199. make[3]: Nothing to be done for `install-exec-am'.
1200. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/man/man1'
1201. /usr/bin/install -c -m 644 RNAforester.1 '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/man/man1'
1202. make[3]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/man'
1203. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester/man'
1204. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
1205. make[3]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
1206. make[3]: Nothing to be done for `install-exec-am'.
1207. make[3]: Nothing to be done for `install-data-am'.
1208. make[3]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
1209. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
1210. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/RNAforester'
1211. Making install in Kinfold
1212. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
1213. Making install in Example
1214. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold/Example'
1215. make[3]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold/Example'
1216. make[3]: Nothing to be done for `install-exec-am'.
1217. make[3]: Nothing to be done for `install-data-am'.
1218. make[3]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold/Example'
1219. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold/Example'
1220. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
1221. make[3]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
1222. make[3]: Nothing to be done for `install-data-am'.
1223. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/bin'
1224. /usr/bin/install -c Kinfold '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/bin'
1225. make[3]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
1226. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
1227. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5/Kinfold'
1228. make[1]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
1229. make[2]: Entering directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
1230. make[2]: Nothing to be done for `install-exec-am'.
1231. /bin/mkdir -p '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/ViennaRNA'
1232. /usr/bin/install -c -m 644 vienna13.par default.par '/tmp/portage/sci-biology/vienna-rna-1.8.5/image//usr/share/ViennaRNA'
1233. make[2]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
1234. make[1]: Leaving directory `/tmp/portage/sci-biology/vienna-rna-1.8.5/work/ViennaRNA-1.8.5'
1235. >>> Completed installing vienna-rna-1.8.5 into /tmp/portage/sci-biology/vienna-rna-1.8.5/image/
1237. * Tinderbox QA Notice! Insecure functions used
1238. tmpnam@@GLIBC_2.2.5 /tmp/portage/sci-biology/vienna-rna-1.8.5/image/usr/bin/readseq-vienna
1239. * Tinderbox QA Notice (end)! Insecure functions used
1240. strip: x86_64-pc-linux-gnu-strip --strip-unneeded -R .comment -R .GCC.command.line
1241. usr/bin/readseq-vienna
1242. usr/bin/Kinfold
1243. usr/bin/RNAforester
1244. usr/bin/AnalyseSeqs
1245. usr/bin/AnalyseDists
1246. usr/bin/b2ct
1247. usr/bin/popt
1248. usr/bin/RNAaliduplex
1249. usr/bin/RNAup
1250. usr/bin/RNAplfold
1251. usr/bin/RNAcofold
1252. usr/bin/RNAalifold
1253. usr/bin/RNApaln
1254. usr/bin/RNAduplex
1255. usr/bin/RNALfold
1256. usr/bin/RNAsubopt
1257. usr/bin/RNAplot
1258. usr/bin/RNAinverse
1259. usr/bin/RNAdistance
1260. usr/bin/RNApdist
1261. usr/bin/RNAfold
1262. usr/bin/RNAeval
1263. usr/bin/RNAheat
1264. usr/lib64/perl5/vendor_perl/5.16.0/x86_64-linux/auto/RNA/RNA.so
1265. ecompressdir: bzip2 -9 /usr/share/info
1266. ecompressdir: bzip2 -9 /usr/share/man
1267. * ERROR: sci-biology/vienna-rna-1.8.5 failed (postinst phase):
1268. * distutils_pkg_postinst() called illegally
1269. *
1270. * Call stack:
1271. * ebuild.sh, line 85: Called pkg_postinst
1272. * environment, line 4166: Called distutils_pkg_postinst
1273. * environment, line 1616: Called die
1274. * The specific snippet of code:
1275. * die "${FUNCNAME}() called illegally";
1276. *
1277. * If you need support, post the output of `emerge --info '=sci-biology/vienna-rna-1.8.5'`,
1278. * the complete build log and the output of `emerge -pqv '=sci-biology/vienna-rna-1.8.5'`.