1. * Package: sci-biology/abyss-1.3.3
  2. * Repository: gentoo
  3. * Maintainer: weaver@gentoo.org sci-biology@gentoo.org
  4. * USE: amd64 elibc_glibc kernel_linux mpi multilib openmp test userland_GNU
  5. * FEATURES: sandbox test userpriv usersandbox
  6. >>> Unpacking source...
  7. >>> Unpacking abyss-1.3.3.tar.gz to /tmp/portage/sci-biology/abyss-1.3.3/work
  8. >>> Source unpacked in /tmp/portage/sci-biology/abyss-1.3.3/work
  9. >>> Preparing source in /tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3 ...
  10. * Running eautoreconf in '/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3' ...
  11. * Running aclocal ...
  12. [ ok ]
  13. * Running autoconf ...
  14. [ ok ]
  15. * Running autoheader ...
  16. [ ok ]
  17. * Running automake --add-missing --copy --foreign ...
  18. [ ok ]
  19. >>> Source prepared.
  20. >>> Configuring source in /tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3 ...
  21. ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --libdir=/usr/lib64 --disable-dependency-tracking --enable-openmp
  22. configure: loading site script /usr/share/config.site
  23. configure: loading site script /usr/share/crossdev/include/site/linux
  24. configure: loading site script /usr/share/crossdev/include/site/linux-gnu
  25. configure: loading site script /usr/share/crossdev/include/site/x86_64-linux-gnu
  26. checking for a BSD-compatible install... /usr/bin/install -c
  27. checking whether build environment is sane... yes
  28. checking for a thread-safe mkdir -p... /bin/mkdir -p
  29. checking for gawk... gawk
  30. checking whether make sets $(MAKE)... yes
  31. checking for gawk... (cached) gawk
  32. checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
  33. checking whether the C compiler works... yes
  34. checking for C compiler default output file name... a.out
  35. checking for suffix of executables...
  36. checking whether we are cross compiling... no
  37. checking for suffix of object files... o
  38. checking whether we are using the GNU C compiler... yes
  39. checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
  40. checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
  41. checking for style of include used by make... GNU
  42. checking dependency style of x86_64-pc-linux-gnu-gcc... none
  43. checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
  44. checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
  45. checking whether we are using the GNU C++ compiler... yes
  46. checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
  47. checking dependency style of x86_64-pc-linux-gnu-g++... none
  48. checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
  49. checking for grep that handles long lines and -e... /bin/grep
  50. checking for egrep... /bin/grep -E
  51. checking for ANSI C header files... yes
  52. checking for sys/types.h... yes
  53. checking for sys/stat.h... yes
  54. checking for stdlib.h... yes
  55. checking for string.h... yes
  56. checking for memory.h... yes
  57. checking for strings.h... yes
  58. checking for inttypes.h... yes
  59. checking for stdint.h... yes
  60. checking for unistd.h... yes
  61. checking dlfcn.h usability... yes
  62. checking dlfcn.h presence... yes
  63. checking for dlfcn.h... yes
  64. checking fcntl.h usability... yes
  65. checking fcntl.h presence... yes
  66. checking for fcntl.h... yes
  67. checking float.h usability... yes
  68. checking float.h presence... yes
  69. checking for float.h... yes
  70. checking limits.h usability... yes
  71. checking limits.h presence... yes
  72. checking for limits.h... yes
  73. checking stddef.h usability... yes
  74. checking stddef.h presence... yes
  75. checking for stddef.h... yes
  76. checking for stdint.h... (cached) yes
  77. checking for stdlib.h... (cached) yes
  78. checking sys/param.h usability... yes
  79. checking sys/param.h presence... yes
  80. checking for sys/param.h... yes
  81. checking for stdbool.h that conforms to C99... yes
  82. checking for _Bool... yes
  83. checking for ANSI C header files... (cached) yes
  84. checking whether byte ordering is bigendian... no
  85. checking for an ANSI C-conforming const... yes
  86. checking for inline... inline
  87. checking for ptrdiff_t... yes
  88. checking for mode_t... yes
  89. checking for pid_t... yes
  90. checking for size_t... yes
  91. checking for ssize_t... yes
  92. checking for int64_t... yes
  93. checking for uint8_t... yes
  94. checking for uint16_t... yes
  95. checking for uint32_t... yes
  96. checking for uint64_t... yes
  97. checking for dup2... yes
  98. checking for gethostname... yes
  99. checking for getopt_long... yes
  100. checking for getpagesize... yes
  101. checking for memset... yes
  102. checking for strdup... yes
  103. checking for strerror... yes
  104. checking for strtoul... yes
  105. checking vfork.h usability... no
  106. checking vfork.h presence... no
  107. checking for vfork.h... no
  108. checking for fork... yes
  109. checking for vfork... yes
  110. checking for working fork... yes
  111. checking for working vfork... (cached) yes
  112. checking for stdlib.h... (cached) yes
  113. checking for GNU libc compatible malloc... (cached) yes
  114. checking for working memcmp... yes
  115. checking for stdlib.h... (cached) yes
  116. checking for GNU libc compatible realloc... (cached) yes
  117. checking for vprintf... yes
  118. checking for _doprnt... no
  119. checking whether HOST_NAME_MAX is declared... yes
  120. checking mpi.h usability... yes
  121. checking mpi.h presence... yes
  122. checking for mpi.h... yes
  123. checking for MPI_Init in -lmpi... yes
  124. checking for sqrt in -lm... yes
  125. checking for pow... yes
  126. checking for sqrt... yes
  127. checking for ceilf... yes
  128. checking for dlsym in -ldl... yes
  129. checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
  130. checking boost/property_map/property_map.hpp usability... yes
  131. checking boost/property_map/property_map.hpp presence... yes
  132. checking for boost/property_map/property_map.hpp... yes
  133. checking google/sparse_hash_map usability... yes
  134. checking google/sparse_hash_map presence... yes
  135. checking for google/sparse_hash_map... yes
  136. checking unordered_map usability... no
  137. checking unordered_map presence... no
  138. checking for unordered_map... no
  139. checking tr1/unordered_map usability... yes
  140. checking tr1/unordered_map presence... yes
  141. checking for tr1/unordered_map... yes
  142. checking for x86_64-pc-linux-gnu-g++ option to support OpenMP... -fopenmp
  143. checking that generated files are newer than configure... done
  144. configure: creating ./config.status
  145. config.status: creating Makefile
  146. config.status: creating ABYSS/Makefile
  147. config.status: creating Align/Makefile
  148. config.status: creating Assembly/Makefile
  149. config.status: creating Common/Makefile
  150. config.status: creating DataLayer/Makefile
  151. config.status: creating FMIndex/Makefile
  152. config.status: creating Graph/Makefile
  153. config.status: creating Parallel/Makefile
  154. config.status: creating bin/Makefile
  155. config.status: creating doc/Makefile
  156. config.status: creating dialign/Makefile
  157. config.status: creating kmerprint/Makefile
  158. config.status: creating AdjList/Makefile
  159. config.status: creating DAssembler/Makefile
  160. config.status: creating DistanceEst/Makefile
  161. config.status: creating Map/Makefile
  162. config.status: creating Overlap/Makefile
  163. config.status: creating PopBubbles/Makefile
  164. config.status: creating Scaffold/Makefile
  165. config.status: creating SimpleGraph/Makefile
  166. config.status: creating MergePaths/Makefile
  167. config.status: creating KAligner/Makefile
  168. config.status: creating ParseAligns/Makefile
  169. config.status: creating PathOverlap/Makefile
  170. config.status: creating Consensus/Makefile
  171. config.status: creating FilterGraph/Makefile
  172. config.status: creating config.h
  173. config.status: executing depfiles commands
  174. >>> Source configured.
  175. >>> Compiling source in /tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3 ...
  176. make -j24
  177. (CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/missing --run autoheader)
  178. rm -f stamp-h1
  179. touch config.h.in
  180. cd . && /bin/sh ./config.status config.h
  181. config.status: creating config.h
  182. config.status: config.h is unchanged
  183. make all-recursive
  184. make[1]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3'
  185. Making all in bin
  186. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/bin'
  187. make[2]: Nothing to be done for `all'.
  188. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/bin'
  189. Making all in doc
  190. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/doc'
  191. make[2]: Nothing to be done for `all'.
  192. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/doc'
  193. Making all in Assembly
  194. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Assembly'
  195. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libassembly_a-AssemblyAlgorithms.o `test -f 'AssemblyAlgorithms.cpp' || echo './'`AssemblyAlgorithms.cpp
  196. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libassembly_a-BranchGroup.o `test -f 'BranchGroup.cpp' || echo './'`BranchGroup.cpp
  197. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libassembly_a-BranchRecord.o `test -f 'BranchRecord.cpp' || echo './'`BranchRecord.cpp
  198. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libassembly_a-DotWriter.o `test -f 'DotWriter.cpp' || echo './'`DotWriter.cpp
  199. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libassembly_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
  200. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libassembly_a-SequenceCollection.o `test -f 'SequenceCollection.cpp' || echo './'`SequenceCollection.cpp
  201. rm -f libassembly.a
  202. ar cru libassembly.a libassembly_a-AssemblyAlgorithms.o libassembly_a-BranchGroup.o libassembly_a-BranchRecord.o libassembly_a-DotWriter.o libassembly_a-Options.o libassembly_a-SequenceCollection.o
  203. x86_64-pc-linux-gnu-ranlib libassembly.a
  204. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Assembly'
  205. Making all in Common
  206. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Common'
  207. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-ContigID.o `test -f 'ContigID.cpp' || echo './'`ContigID.cpp
  208. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Fcontrol.o `test -f 'Fcontrol.cpp' || echo './'`Fcontrol.cpp
  209. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-HashFunction.o `test -f 'HashFunction.cpp' || echo './'`HashFunction.cpp
  210. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Histogram.o `test -f 'Histogram.cpp' || echo './'`Histogram.cpp
  211. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Kmer.o `test -f 'Kmer.cpp' || echo './'`Kmer.cpp
  212. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Log.o `test -f 'Log.cpp' || echo './'`Log.cpp
  213. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Options.o `test -f 'Options.cpp' || echo './'`Options.cpp
  214. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-SeqExt.o `test -f 'SeqExt.cpp' || echo './'`SeqExt.cpp
  215. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Sequence.o `test -f 'Sequence.cpp' || echo './'`Sequence.cpp
  216. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-SignalHandler.o `test -f 'SignalHandler.cpp' || echo './'`SignalHandler.cpp
  217. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Timer.o `test -f 'Timer.cpp' || echo './'`Timer.cpp
  218. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libcommon_a-Uncompress.o `test -f 'Uncompress.cpp' || echo './'`Uncompress.cpp
  219. Uncompress.cpp: In function 'int uncompress(const char*)':
  220. Uncompress.cpp:69:6: warning: variable 'n' might be clobbered by 'longjmp' or 'vfork' [-Wclobbered]
  221. rm -f libcommon.a
  222. ar cru libcommon.a libcommon_a-ContigID.o libcommon_a-Fcontrol.o libcommon_a-HashFunction.o libcommon_a-Histogram.o libcommon_a-Kmer.o libcommon_a-Log.o libcommon_a-Options.o libcommon_a-SeqExt.o libcommon_a-Sequence.o libcommon_a-SignalHandler.o libcommon_a-Timer.o libcommon_a-Uncompress.o
  223. x86_64-pc-linux-gnu-ranlib libcommon.a
  224. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Common'
  225. Making all in DataLayer
  226. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/DataLayer'
  227. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libdatalayer_a-FastaReader.o `test -f 'FastaReader.cpp' || echo './'`FastaReader.cpp
  228. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libdatalayer_a-FastaWriter.o `test -f 'FastaWriter.cpp' || echo './'`FastaWriter.cpp
  229. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_fac-fac.o `test -f 'fac.cc' || echo './'`fac.cc
  230. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_tofastq-abyss-tofastq.o `test -f 'abyss-tofastq.cc' || echo './'`abyss-tofastq.cc
  231. rm -f libdatalayer.a
  232. ar cru libdatalayer.a libdatalayer_a-FastaReader.o libdatalayer_a-FastaWriter.o
  233. x86_64-pc-linux-gnu-ranlib libdatalayer.a
  234. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-tofastq abyss_tofastq-abyss-tofastq.o libdatalayer.a ../Common/libcommon.a -ldl -lm
  235. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-fac abyss_fac-fac.o libdatalayer.a ../Common/libcommon.a -ldl -lm
  236. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/DataLayer'
  237. Making all in FMIndex
  238. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/FMIndex'
  239. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libfmindex_a-bit_array.o `test -f 'bit_array.cc' || echo './'`bit_array.cc
  240. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_count-count.o `test -f 'count.cc' || echo './'`count.cc
  241. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_dawg-abyss-dawg.o `test -f 'abyss-dawg.cc' || echo './'`abyss-dawg.cc
  242. rm -f libfmindex.a
  243. ar cru libfmindex.a libfmindex_a-bit_array.o
  244. x86_64-pc-linux-gnu-ranlib libfmindex.a
  245. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-count abyss_count-count.o libfmindex.a ../Common/libcommon.a -ldl -lm
  246. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-dawg abyss_dawg-abyss-dawg.o libfmindex.a ../Common/libcommon.a -ldl -lm
  247. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/FMIndex'
  248. Making all in Graph
  249. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Graph'
  250. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libgraph_a-ConstrainedSearch.o `test -f 'ConstrainedSearch.cpp' || echo './'`ConstrainedSearch.cpp
  251. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_gc-gc.o `test -f 'gc.cc' || echo './'`gc.cc
  252. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_todot-todot.o `test -f 'todot.cc' || echo './'`todot.cc
  253. rm -f libgraph.a
  254. ar cru libgraph.a libgraph_a-ConstrainedSearch.o
  255. x86_64-pc-linux-gnu-ranlib libgraph.a
  256. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-gc abyss_gc-gc.o ../Common/libcommon.a -ldl -lm
  257. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -L. -Wl,-O1 -Wl,--as-needed -o abyss-todot abyss_todot-todot.o libgraph.a ../Common/libcommon.a -ldl -lm
  258. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Graph'
  259. Making all in dialign
  260. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/dialign'
  261. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c alig.c
  262. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c assemble.c
  263. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c diag.c
  264. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c io.c
  265. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c orf.c
  266. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c parameters.c
  267. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c prob.c
  268. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c translate.c
  269. x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I. -O2 -pipe -ggdb -march=native -ftracer -c museq.c
  270. io.c: In function 'read_diag_prob_dist':
  271. io.c:371:13: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
  272. io.c: In function 'read_scr_matrix':
  273. io.c:270:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
  274. io.c:282:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
  275. rm -f libdialign.a
  276. ar cru libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o
  277. x86_64-pc-linux-gnu-ranlib libdialign.a
  278. x86_64-pc-linux-gnu-gcc -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o dialign museq.o libdialign.a -ldl -lm
  279. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/dialign'
  280. Making all in Align
  281. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Align'
  282. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libalign_a-alignGlobal.o `test -f 'alignGlobal.cc' || echo './'`alignGlobal.cc
  283. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libalign_a-dialign.o `test -f 'dialign.cpp' || echo './'`dialign.cpp
  284. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libalign_a-dna_diag_prob.o `test -f 'dna_diag_prob.cc' || echo './'`dna_diag_prob.cc
  285. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o libalign_a-smith_waterman.o `test -f 'smith_waterman.cpp' || echo './'`smith_waterman.cpp
  286. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_align-align.o `test -f 'align.cc' || echo './'`align.cc
  287. rm -f libalign.a
  288. ar cru libalign.a libalign_a-alignGlobal.o libalign_a-dialign.o libalign_a-dna_diag_prob.o libalign_a-smith_waterman.o
  289. x86_64-pc-linux-gnu-ranlib libalign.a
  290. x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-align abyss_align-align.o ./libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
  291. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Align'
  292. Making all in ABYSS
  293. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/ABYSS'
  294. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ABYSS-Abyss.o `test -f 'Abyss.cpp' || echo './'`Abyss.cpp
  295. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o ABYSS ABYSS-Abyss.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
  296. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/ABYSS'
  297. Making all in Parallel
  298. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Parallel'
  299. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ABYSS_P-parallelAbyss.o `test -f 'parallelAbyss.cpp' || echo './'`parallelAbyss.cpp
  300. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ABYSS_P-CommLayer.o `test -f 'CommLayer.cpp' || echo './'`CommLayer.cpp
  301. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ABYSS_P-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
  302. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ABYSS_P-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
  303. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ABYSS_P-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
  304. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a -lmpi -ldl -lm
  305. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Parallel'
  306. Making all in AdjList
  307. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/AdjList'
  308. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o AdjList-AdjList.o `test -f 'AdjList.cpp' || echo './'`AdjList.cpp
  309. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o AdjList AdjList-AdjList.o ../Graph/libgraph.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
  310. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/AdjList'
  311. Making all in Consensus
  312. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Consensus'
  313. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp
  314. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
  315. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Consensus'
  316. Making all in DAssembler
  317. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/DAssembler'
  318. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp
  319. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp
  320. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
  321. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/DAssembler'
  322. Making all in DistanceEst
  323. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/DistanceEst'
  324. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp
  325. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp
  326. x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../Common/libcommon.a -ldl -lm
  327. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/DistanceEst'
  328. Making all in KAligner
  329. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/KAligner'
  330. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -pthread -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp
  331. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -pthread -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp
  332. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -pthread -Wl,-O1 -Wl,--as-needed -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
  333. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/KAligner'
  334. Making all in Map
  335. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Map'
  336. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc
  337. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I. -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc
  338. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I. -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc
  339. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
  340. x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
  341. x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
  342. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Map'
  343. Making all in MergePaths
  344. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/MergePaths'
  345. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp
  346. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp
  347. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp
  348. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o MergeContigs MergeContigs-MergeContigs.o ../DataLayer/libdatalayer.a ../Graph/libgraph.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm
  349. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o PathConsensus PathConsensus-PathConsensus.o ../DataLayer/libdatalayer.a ../Graph/libgraph.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm
  350. x86_64-pc-linux-gnu-g++ -Wall -Wextra -fopenmp -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o MergePaths MergePaths-MergePaths.o ../DataLayer/libdatalayer.a ../Common/libcommon.a ../Graph/libgraph.a -ldl -lm
  351. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/MergePaths'
  352. Making all in Overlap
  353. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Overlap'
  354. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp
  355. x86_64-pc-linux-gnu-g++ -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -Wl,-O1 -Wl,--as-needed -o Overlap Overlap-Overlap.o ../Graph/libgraph.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
  356. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/Overlap'
  357. Making all in ParseAligns
  358. make[2]: Entering directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/ParseAligns'
  359. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc
  360. x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I. -Wall -Wextra -O2 -pipe -ggdb -march=native -ftracer -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp
  361. abyss-fixmate.cc:129:8: error: 'intptr_t' does not name a type
  362. abyss-fixmate.cc: In function 'void printProgress(const Alignments&)':
  363. abyss-fixmate.cc:142:38: error: expected type-specifier before 'intptr_t'
  364. abyss-fixmate.cc:142:38: error: expected '>' before 'intptr_t'
  365. abyss-fixmate.cc:142:38: error: expected '(' before 'intptr_t'
  366. abyss-fixmate.cc:142:38: error: 'intptr_t' was not declared in this scope
  367. abyss-fixmate.cc:142:54: error: 'sbrk' was not declared in this scope
  368. abyss-fixmate.cc:142:59: error: 'sbrk0' was not declared in this scope
  369. abyss-fixmate.cc:142:64: error: expected ')' before ';' token
  370. make[2]: *** [abyss_fixmate-abyss-fixmate.o] Error 1
  371. make[2]: *** Waiting for unfinished jobs....
  372. make[2]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3/ParseAligns'
  373. make[1]: *** [all-recursive] Error 1
  374. make[1]: Leaving directory `/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3'
  375. make: *** [all] Error 2
  376. * ERROR: sci-biology/abyss-1.3.3 failed (compile phase):
  377. * emake failed
  378. *
  379. * If you need support, post the output of `emerge --info '=sci-biology/abyss-1.3.3'`,
  380. * the complete build log and the output of `emerge -pqv '=sci-biology/abyss-1.3.3'`.
  381. * The complete build log is located at '/var/log/portage/sci-biology:abyss-1.3.3:20120620-063015.log'.
  382. * For convenience, a symlink to the build log is located at '/tmp/portage/sci-biology/abyss-1.3.3/temp/build.log'.
  383. * The ebuild environment file is located at '/tmp/portage/sci-biology/abyss-1.3.3/temp/environment'.
  384. * Working directory: '/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3'
  385. * S: '/tmp/portage/sci-biology/abyss-1.3.3/work/abyss-1.3.3'