1. * Package: sci-biology/maq-0.7.1-r1
2. * Repository: gentoo
3. * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
4. * USE: amd64 elibc_glibc kernel_linux multilib test userland_GNU
5. * FEATURES: sandbox test userpriv usersandbox
6. >>> Unpacking source...
7. >>> Unpacking maq-0.7.1.tar.bz2 to /tmp/portage/sci-biology/maq-0.7.1-r1/work
8. >>> Unpacking calib-36.dat.gz to /tmp/portage/sci-biology/maq-0.7.1-r1/work
9. >>> Source unpacked in /tmp/portage/sci-biology/maq-0.7.1-r1/work
10. >>> Preparing source in /tmp/portage/sci-biology/maq-0.7.1-r1/work/maq-0.7.1 ...
11. * Applying maq-0.7.1-flags.patch ...
12. [ ok ]
13. * Applying maq-0.7.1-bfr-overfl.patch ...
14. [ ok ]
15. * Running eautoreconf in '/tmp/portage/sci-biology/maq-0.7.1-r1/work/maq-0.7.1' ...
16. * Running aclocal ...
17. [ ok ]
18. * Running autoconf ...
19. [ ok ]
20. * Running autoheader ...
21. [ ok ]
22. * Running automake --add-missing --copy ...
23. [ ok ]
24. >>> Source prepared.
25. >>> Configuring source in /tmp/portage/sci-biology/maq-0.7.1-r1/work/maq-0.7.1 ...
26. * econf: updating maq-0.7.1/config.sub with /usr/share/gnuconfig/config.sub
27. * econf: updating maq-0.7.1/config.guess with /usr/share/gnuconfig/config.guess
28. ./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
29. configure: loading site script /usr/share/config.site
30. configure: loading site script /usr/share/crossdev/include/site/linux
31. configure: loading site script /usr/share/crossdev/include/site/linux-gnu
32. configure: loading site script /usr/share/crossdev/include/site/x86_64-linux-gnu
33. checking for a BSD-compatible install... /usr/bin/install -c
34. checking whether build environment is sane... yes
35. checking for a thread-safe mkdir -p... /bin/mkdir -p
36. checking for gawk... gawk
37. checking whether make sets $(MAKE)... yes
38. checking build system type... x86_64-pc-linux-gnu
39. checking host system type... x86_64-pc-linux-gnu
40. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
41. checking whether the C compiler works... yes
42. checking for C compiler default output file name... a.out
43. checking for suffix of executables...
44. checking whether we are cross compiling... no
45. checking for suffix of object files... o
46. checking whether we are using the GNU C compiler... yes
47. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
48. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
49. checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
50. checking whether we are using the GNU C++ compiler... yes
51. checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
52. checking if gcc accepts -m64... yes
53. checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
54. checking for grep that handles long lines and -e... /bin/grep
55. checking for egrep... /bin/grep -E
56. checking for ANSI C header files... yes
57. checking for sys/types.h... yes
58. checking for sys/stat.h... yes
59. checking for stdlib.h... yes
60. checking for string.h... yes
61. checking for memory.h... yes
62. checking for strings.h... yes
63. checking for inttypes.h... yes
64. checking for stdint.h... yes
65. checking for unistd.h... yes
66. checking zlib.h usability... yes
67. checking zlib.h presence... yes
68. checking for zlib.h... yes
69. checking that generated files are newer than configure... done
70. configure: creating ./config.status
71. config.status: creating Makefile
72. config.status: creating config.h
73. >>> Source configured.
74. >>> Compiling source in /tmp/portage/sci-biology/maq-0.7.1-r1/work/maq-0.7.1 ...
75. make -j24
76. make all-am
77. make[1]: Entering directory `/tmp/portage/sci-biology/maq-0.7.1-r1/work/maq-0.7.1'
78. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c main.c
79. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c const.c
80. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c seq.c
81. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c bfa.c
82. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o read.o read.cc
83. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c fasta2bfa.c
84. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c fastq2bfq.c
85. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o merge.o merge.cc
86. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o match_aux.o match_aux.cc
87. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o match.o match.cc
88. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o sort_mapping.o sort_mapping.cc
89. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o assemble.o assemble.cc
90. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o pileup.o pileup.cc
91. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o mapcheck.o mapcheck.cc
92. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c get_pos.c
93. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c assopt.c
94. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c aux_utils.c
95. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o rbcc.o rbcc.cc
96. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o subsnp.o subsnp.cc
97. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o pair_stat.o pair_stat.cc
98. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o indel_soa.o indel_soa.cc
99. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c maqmap.c
100. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c maqmap_conv.c
101. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o altchr.o altchr.cc
102. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c submap.c
103. bfa.c: In function 'nst_bfa_len':
104. bfa.c:46:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
105. bfa.c:48:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
106. bfa.c: In function 'nst_load_bfa1':
107. bfa.c:31:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
108. bfa.c:32:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
109. bfa.c:33:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
110. bfa.c:35:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
111. bfa.c:37:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
112. fasta2bfa.c: In function 'nst_fasta2bfa1':
113. fasta2bfa.c:148:8: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result]
114. fasta2bfa.c:149:8: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result]
115. fasta2bfa.c:150:8: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result]
116. fasta2bfa.c:151:8: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result]
117. fasta2bfa.c:152:8: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result]
118. fasta2bfa.c:153:8: warning: ignoring return value of 'fwrite', declared with attribute warn_unused_result [-Wunused-result]
119. fastq2bfq.c: In function 'fastq2bfq':
120. fastq2bfq.c:30:5: warning: assignment from incompatible pointer type [enabled by default]
121. fastq2bfq.c:36:7: warning: assignment from incompatible pointer type [enabled by default]
122. fastq2bfq.c:47:3: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [enabled by default]
123. In file included from fastq2bfq.c:1:0:
124. /usr/include/zlib.h:1324:21: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
125. fastq2bfq.c:48:3: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [enabled by default]
126. In file included from fastq2bfq.c:1:0:
127. /usr/include/zlib.h:1324:21: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
128. fastq2bfq.c:49:3: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [enabled by default]
129. In file included from fastq2bfq.c:1:0:
130. /usr/include/zlib.h:1324:21: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
131. fastq2bfq.c:50:3: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [enabled by default]
132. In file included from fastq2bfq.c:1:0:
133. /usr/include/zlib.h:1324:21: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
134. fastq2bfq.c:53:4: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
135. In file included from fastq2bfq.c:1:0:
136. /usr/include/zlib.h:1494:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
137. fastq2bfq.c:62:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
138. In file included from fastq2bfq.c:1:0:
139. /usr/include/zlib.h:1494:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
140. altchr.cc: In function 'int ma_altchr(int, char**)':
141. altchr.cc:101:39: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
142. altchr.cc:102:45: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
143. altchr.cc:103:46: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
144. altchr.cc:104:42: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
145. altchr.cc:105:54: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
146. altchr.cc:106:55: warning: ignoring return value of 'size_t fwrite(const void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
147. sort_mapping.cc: In function 'int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)':
148. sort_mapping.cc:59:62: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses]
149. indel_soa.cc: In function 'void fill_counter(bit32_t*, int, nst_bfa1_t*, gzFile)':
150. indel_soa.cc:42:44: warning: suggest parentheses around '-' inside '<<' [-Wparentheses]
151. indel_soa.cc:56:44: warning: suggest parentheses around '-' inside '<<' [-Wparentheses]x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c -o rmdup.o rmdup.cc
153. mapcheck.cc: In function 'int ma_mapcheck(int, char**)':
154. mapcheck.cc:60:17: warning: variable 'fpout' set but not used [-Wunused-but-set-variable]
155. match.cc: In function 'int alt_cal_mm(bit64_t)':
156. match.cc:58:21: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
157. match.cc:61:22: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
158. match.cc: In function 'int alt_cal_err(bit64_t, bit64_t)':
159. match.cc:67:21: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
160. match.cc:70:22: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses]
161. In file included from mapcheck.cc:11:0:
162. stdhash.hh: In instantiation of 'bool hash_set_misc<keytype_t>::insert(const keytype_t&) [with keytype_t = long long unsigned int]':
163. mapcheck.cc:24:45: required from here
164. stdhash.hh:415:81: error: 'direct_insert_aux' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
165. stdhash.hh:415:81: note: declarations in dependent base '__lh3_hash_base_class<long long unsigned int>' are not found by unqualified lookup
166. stdhash.hh:415:81: note: use 'this->direct_insert_aux' instead
167. assemble.cc: In function 'base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*)':
168. assemble.cc:106:64: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses]
169. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -Wall -D_FASTMAP -DMAQ_LONGREADS -O2 -pipe -ggdb -march=native -ftracer -c simulate.c
170. match.cc: In function 'void match_search(const match_aux_t*, match_data_t*, const nst_bfa1_t*, int, ref_canlist_t*)':
171. match.cc:292:10: warning: variable 'n_reads' set but not used [-Wunused-but-set-variable]
172. make[1]: *** [mapcheck.o] Error 1
173. make[1]: *** Waiting for unfinished jobs....
174. match.cc: In function 'int ma_match(int, char**)':
175. match.cc:525:32: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
176. simulate.c: In function 'maq_simutrain':
177. simulate.c:83:8: warning: assignment from incompatible pointer type [enabled by default]
178. simulate.c:86:2: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [enabled by default]
179. In file included from simulate.c:6:0:
180. /usr/include/zlib.h:1324:21: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
181. simulate.c:87:2: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
182. In file included from simulate.c:6:0:
183. /usr/include/zlib.h:1494:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
184. In file included from rmdup.cc:7:0:
185. stdhash.hh: In instantiation of 'bool hash_map_misc<keytype_t, valtype_t>::insert(const keytype_t&, const valtype_t&) [with keytype_t = long long unsigned int; valtype_t = maqmap1_t*]':
186. rmdup.cc:98:29: required from here
187. stdhash.hh:496:81: error: 'direct_insert_aux' was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
188. stdhash.hh:496:81: note: declarations in dependent base '__lh3_hash_base_class<long long unsigned int>' are not found by unqualified lookup
189. stdhash.hh:496:81: note: use 'this->direct_insert_aux' instead
190. make[1]: *** [rmdup.o] Error 1
191. make[1]: Leaving directory `/tmp/portage/sci-biology/maq-0.7.1-r1/work/maq-0.7.1'
192. make: *** [all] Error 2
193. * ERROR: sci-biology/maq-0.7.1-r1 failed (compile phase):
194. * emake failed
195. *
196. * If you need support, post the output of `emerge --info '=sci-biology/maq-0.7.1-r1'`,
197. * the complete build log and the output of `emerge -pqv '=sci-biology/maq-0.7.1-r1'`.
198. * The complete build log is located at '/var/log/portage/sci-biology:maq-0.7.1-r1:20120621-153519.log'.
199. * For convenience, a symlink to the build log is located at '/tmp/portage/sci-biology/maq-0.7.1-r1/temp/build.log'.
200. * The ebuild environment file is located at '/tmp/portage/sci-biology/maq-0.7.1-r1/temp/environment'.
201. * Working directory: '/tmp/portage/sci-biology/maq-0.7.1-r1/work/maq-0.7.1'
202. * S: '/tmp/portage/sci-biology/maq-0.7.1-r1/work/maq-0.7.1'