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  1. vagrant@precise64:~/freebayes/freebayes/debian$ bzr builddeb
  2. Building using working tree
  3. Building package in normal mode
  4. Looking for a way to retrieve the upstream tarball
  5. Upstream tarball already exists in build directory, using that
  6. Building the package in /home/vagrant/freebayes/build-area/freebayes-0.9.6, using debuild
  7. dpkg-buildpackage -rfakeroot -D -us -uc
  8. dpkg-buildpackage: export CFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security
  9. dpkg-buildpackage: export CPPFLAGS from dpkg-buildflags (origin: vendor): -D_FORTIFY_SOURCE=2
  10. dpkg-buildpackage: export CXXFLAGS from dpkg-buildflags (origin: vendor): -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security
  11. dpkg-buildpackage: export FFLAGS from dpkg-buildflags (origin: vendor): -g -O2
  12. dpkg-buildpackage: export LDFLAGS from dpkg-buildflags (origin: vendor): -Wl,-Bsymbolic-functions -Wl,-z,relro
  13. dpkg-buildpackage: source package freebayes
  14. dpkg-buildpackage: source version 0.9.6-0ubuntu4
  15. dpkg-buildpackage: source changed by Guillermo Carrasco <guillermo.carrasco@scilifelab.se>
  16. dpkg-source --before-build freebayes-0.9.6
  17. dpkg-buildpackage: host architecture amd64
  18. fakeroot debian/rules clean
  19. dh clean
  20. dh_testdir
  21. dh_clean
  22. dpkg-source -b freebayes-0.9.6
  23. dpkg-source: warning: no source format specified in debian/source/format, see dpkg-source(1)
  24. dpkg-source: warning: Version number suggests Ubuntu changes, but Maintainer: does not have Ubuntu address
  25. dpkg-source: warning: Version number suggests Ubuntu changes, but there is no XSBC-Original-Maintainer field
  26. dpkg-source: info: using source format `1.0'
  27. dpkg-source: info: building freebayes using existing freebayes_0.9.6.orig.tar.gz
  28. dpkg-source: info: building freebayes in freebayes_0.9.6-0ubuntu4.diff.gz
  29. dpkg-source: warning: newly created empty file '.pc/freebayes_fix_makefile_for_pbuild.diff/.timestamp' will not be represented in diff
  30. dpkg-source: warning: newly created empty file '.pc/freebayes_fix_compilation_error.diff/.timestamp' will not be represented in diff
  31. dpkg-source: warning: the diff modifies the following upstream files:
  32. .pc/applied-patches
  33. .pc/freebayes_fix_compilation_error.diff/vcflib/tabixpp/Makefile
  34. .pc/freebayes_fix_makefile_for_pbuild.diff/Makefile
  35. Makefile
  36. vcflib/tabixpp/Makefile
  37. dpkg-source: info: use the '3.0 (quilt)' format to have separate and documented changes to upstream files, see dpkg-source(1)
  38. dpkg-source: info: building freebayes in freebayes_0.9.6-0ubuntu4.dsc
  39. debian/rules build
  40. dh build
  41. dh_testdir
  42. dh_auto_configure
  43. dh_auto_build
  44. make[1]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6'
  45. cd src && make
  46. make[2]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/src'
  47. cd ../bamtools && mkdir -p build && cd build && cmake .. && make
  48. -- The C compiler identification is GNU
  49. -- The CXX compiler identification is GNU
  50. -- Check for working C compiler: /usr/bin/gcc
  51. -- Check for working C compiler: /usr/bin/gcc -- works
  52. -- Detecting C compiler ABI info
  53. -- Detecting C compiler ABI info - done
  54. -- Check for working CXX compiler: /usr/bin/c++
  55. -- Check for working CXX compiler: /usr/bin/c++ -- works
  56. -- Detecting CXX compiler ABI info
  57. -- Detecting CXX compiler ABI info - done
  58. -- Configuring done
  59. -- Generating done
  60. -- Build files have been written to: /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build
  61. make[3]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  62. make[4]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  63. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  64. Scanning dependencies of target SharedHeaders
  65. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  66. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  67. [ 1%] Exporting SharedHeaders
  68. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  69. [ 1%] Built target SharedHeaders
  70. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  71. Scanning dependencies of target APIHeaders
  72. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  73. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  74. [ 2%] Exporting APIHeaders
  75. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  76. [ 2%] Built target APIHeaders
  77. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  78. Scanning dependencies of target AlgorithmsHeaders
  79. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  80. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  81. [ 3%] Exporting AlgorithmsHeaders
  82. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  83. [ 3%] Built target AlgorithmsHeaders
  84. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  85. Scanning dependencies of target BamTools
  86. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  87. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  88. [ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o
  89. [ 5%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o
  90. [ 6%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o
  91. [ 7%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o
  92. [ 8%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o
  93. [ 9%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o
  94. [ 10%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o
  95. [ 11%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o
  96. [ 12%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o
  97. [ 13%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o
  98. [ 14%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o
  99. [ 15%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o
  100. [ 16%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o
  101. [ 17%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o
  102. [ 18%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o
  103. [ 19%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o
  104. [ 20%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o
  105. [ 21%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o
  106. [ 22%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o
  107. [ 23%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o
  108. [ 24%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o
  109. [ 25%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o
  110. [ 26%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o
  111. /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendRequest(size_t)’:
  112. /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  113. [ 27%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o
  114. [ 28%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o
  115. [ 29%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o
  116. [ 30%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o
  117. [ 31%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o
  118. [ 32%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o
  119. [ 33%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o
  120. [ 34%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o
  121. [ 35%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o
  122. /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/api/internal/io/TcpSocket_p.cpp: In member function ‘std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)’:
  123. /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/api/internal/io/TcpSocket_p.cpp:336:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  124. [ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o
  125. [ 37%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
  126. [ 38%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o
  127. [ 39%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o
  128. [ 40%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o
  129. [ 41%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o
  130. Linking CXX shared library ../../../lib/libbamtools.so
  131. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  132. [ 41%] Built target BamTools
  133. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  134. Scanning dependencies of target BamTools-static
  135. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  136. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  137. [ 42%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o
  138. [ 43%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o
  139. [ 44%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o
  140. [ 45%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o
  141. [ 46%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o
  142. [ 47%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o
  143. [ 48%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o
  144. [ 49%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o
  145. [ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o
  146. [ 51%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o
  147. [ 52%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o
  148. [ 53%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o
  149. [ 54%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o
  150. [ 55%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o
  151. [ 56%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o
  152. [ 57%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o
  153. [ 58%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o
  154. [ 59%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o
  155. [ 60%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o
  156. [ 61%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o
  157. [ 62%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o
  158. [ 63%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o
  159. [ 64%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o
  160. /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendRequest(size_t)’:
  161. /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/api/internal/io/BamHttp_p.cpp:396:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  162. [ 65%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o
  163. [ 66%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o
  164. [ 67%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o
  165. [ 68%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o
  166. [ 69%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o
  167. [ 70%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o
  168. [ 71%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o
  169. [ 72%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o
  170. [ 73%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o
  171. /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/api/internal/io/TcpSocket_p.cpp: In member function ‘std::string BamTools::Internal::TcpSocket::ReadLine(int64_t)’:
  172. /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/api/internal/io/TcpSocket_p.cpp:336:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  173. [ 74%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o
  174. [ 75%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o
  175. [ 76%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o
  176. [ 77%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o
  177. [ 78%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o
  178. [ 79%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o
  179. Linking CXX static library ../../../lib/libbamtools.a
  180. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  181. [ 79%] Built target BamTools-static
  182. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  183. Scanning dependencies of target jsoncpp
  184. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  185. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  186. [ 80%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o
  187. [ 81%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o
  188. [ 82%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_writer.cpp.o
  189. Linking CXX shared library ../../../../lib/libjsoncpp.so
  190. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  191. [ 82%] Built target jsoncpp
  192. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  193. Scanning dependencies of target BamTools-utils
  194. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  195. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  196. [ 83%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_fasta.cpp.o
  197. [ 84%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_options.cpp.o
  198. [ 85%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_pileup_engine.cpp.o
  199. [ 86%] Building CXX object src/utils/CMakeFiles/BamTools-utils.dir/bamtools_utilities.cpp.o
  200. Linking CXX shared library ../../../lib/libbamtools-utils.so
  201. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  202. [ 86%] Built target BamTools-utils
  203. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  204. Scanning dependencies of target bamtools_cmd
  205. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  206. make[5]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  207. [ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o
  208. [ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o
  209. [ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o
  210. [ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o
  211. In file included from /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/toolkit/bamtools_filter.cpp:14:0:
  212. /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/utils/bamtools_filter_engine.h: In member function ‘bool BamTools::FilterEngine<FilterChecker>::evaluateFilterRules(const T&) [with T = BamTools::BamAlignment, FilterChecker = BamTools::BamAlignmentChecker]’:
  213. /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/utils/bamtools_filter_engine.h:268:37: instantiated from ‘bool BamTools::FilterEngine<FilterChecker>::check(const T&) [with T = BamTools::BamAlignment, FilterChecker = BamTools::BamAlignmentChecker]’
  214. /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/toolkit/bamtools_filter.cpp:482:35: instantiated from here
  215. /home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/src/utils/bamtools_filter_engine.h:297:31: warning: variable ‘filterEnd’ set but not used [-Wunused-but-set-variable]
  216. [ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o
  217. [ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o
  218. [ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o
  219. [ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o
  220. [ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o
  221. [ 96%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o
  222. [ 97%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o
  223. [ 98%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o
  224. [ 99%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o
  225. [100%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o
  226. Linking CXX executable ../../../bin/bamtools
  227. make[5]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  228. [100%] Built target bamtools_cmd
  229. make[4]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  230. make[3]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/bamtools/build'
  231. g++ -O3 -I../bamtools/src -c freebayes.cpp
  232. g++ -O3 -I../bamtools/src -c BedReader.cpp
  233. g++ -O3 -I../bamtools/src -c CNV.cpp
  234. gcc -O3 -I../bamtools/src -c fastlz.c
  235. g++ -O3 -I../bamtools/src -c Fasta.cpp
  236. Fasta.cpp: In member function ‘std::string FastaReference::getSubSequence(std::string, int, int)’:
  237. Fasta.cpp:293:51: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  238. Fasta.cpp: In member function ‘std::string FastaReference::getSequence(std::string)’:
  239. Fasta.cpp:254:43: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  240. g++ -O3 -I../bamtools/src -c Parameters.cpp
  241. g++ -O3 -I../bamtools/src -c Allele.cpp
  242. g++ -O3 -I../bamtools/src -c Sample.cpp
  243. g++ -O3 -I../bamtools/src -c Result.cpp
  244. g++ -O3 -I../bamtools/src -c AlleleParser.cpp
  245. g++ -O3 -I../bamtools/src -c Utility.cpp
  246. g++ -O3 -I../bamtools/src -c Genotype.cpp
  247. g++ -O3 -I../bamtools/src -c DataLikelihood.cpp
  248. g++ -O3 -I../bamtools/src -c Multinomial.cpp
  249. g++ -O3 -I../bamtools/src -c Ewens.cpp
  250. g++ -O3 -I../bamtools/src -c ResultData.cpp
  251. g++ -O3 -I../bamtools/src -c Dirichlet.cpp
  252. g++ -O3 -I../bamtools/src -c Marginals.cpp
  253. g++ -O3 -I../bamtools/src -c split.cpp
  254. g++ -O3 -I../bamtools/src -c LeftAlign.cpp
  255. g++ -O3 -I../bamtools/src -c IndelAllele.cpp
  256. g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o ../vcflib/tabixpp/tabix.o ../vcflib/tabixpp/tabix.cpp
  257. cd ../vcflib/tabixpp && make
  258. make[3]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/vcflib/tabixpp'
  259. make[4]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/vcflib/tabixpp'
  260. gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzf.c -o bgzf.o
  261. bgzf.c: In function ‘bgzf_close’:
  262. bgzf.c:630:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
  263. gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE kstring.c -o kstring.o
  264. gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE knetfile.c -o knetfile.o
  265. knetfile.c: In function ‘khttp_connect_file’:
  266. knetfile.c:418:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  267. knetfile.c: In function ‘kftp_send_cmd’:
  268. knetfile.c:239:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  269. gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE index.c -o index.o
  270. gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bedidx.c -o bedidx.o
  271. ar -cru libtabix.a bgzf.o kstring.o knetfile.o index.o bedidx.o
  272. ranlib libtabix.a
  273. gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE main.c -o main.o
  274. gcc -g -Wall -O2 -fPIC -o tabix main.o -lm -L. -ltabix -lz
  275. gcc -c -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE bgzip.c -o bgzip.o
  276. bgzip.c: In function ‘main’:
  277. bgzip.c:198:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
  278. bgzip.c: In function ‘write_open’:
  279. bgzip.c:57:9: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  280. gcc -g -Wall -O2 -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz
  281. g++ -g -Wall -O2 -fPIC -o tabix++ main.cpp tabix.o bgzf.o -lm -L. -ltabix -lz
  282. make[4]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/vcflib/tabixpp'
  283. make[3]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/vcflib/tabixpp'
  284. cd ../vcflib/smithwaterman && make
  285. make[3]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/vcflib/smithwaterman'
  286. g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o smithwaterman.o smithwaterman.cpp
  287. g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o BandedSmithWaterman.o BandedSmithWaterman.cpp
  288. g++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security -D_FORTIFY_SOURCE=2 -c -o SmithWatermanGotoh.o SmithWatermanGotoh.cpp
  289. * linking smithwaterman
  290. make[3]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/vcflib/smithwaterman'
  291. g++ -O3 -I../bamtools/src -c ../vcflib/Variant.cpp
  292. g++ -O3 -I../bamtools/src freebayes.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o ../vcflib/tabixpp/tabix.o ../vcflib/tabixpp/bgzf.o ../vcflib/smithwaterman/SmithWatermanGotoh.o Variant.o ../bamtools/lib/libbamtools.a -o ../bin/freebayes -lz -lm -L./ -L../vcflib/tabixpp/ -L../bamtools/lib -ltabix
  293. g++ -O3 -I../bamtools/src -c bamleftalign.cpp
  294. g++ -O3 -I../bamtools/src bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o ../bamtools/lib/libbamtools.a -o ../bin/bamleftalign -lz -lm -L./ -L../vcflib/tabixpp/ -L../bamtools/lib -ltabix
  295. make[2]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6/src'
  296. make[1]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6'
  297. dh_auto_test
  298. fakeroot debian/rules binary
  299. dh binary
  300. dh_testroot
  301. dh_prep
  302. dh_installdirs
  303. dh_auto_install
  304. make[1]: Entering directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6'
  305. install -m 0755 bin/freebayes /home/vagrant/freebayes/build-area/freebayes-0.9.6/debian/freebayes
  306. install -m 0755 bin/bamleftalign /home/vagrant/freebayes/build-area/freebayes-0.9.6/debian/freebayes
  307. make[1]: Leaving directory `/home/vagrant/freebayes/build-area/freebayes-0.9.6'
  308. dh_install
  309. dh_installdocs
  310. dh_installchangelogs
  311. dh_installexamples
  312. dh_installman
  313. dh_installcatalogs
  314. dh_installcron
  315. dh_installdebconf
  316. dh_installemacsen
  317. dh_installifupdown
  318. dh_installinfo
  319. dh_pysupport
  320. dh_pysupport: This program is deprecated, you should use dh_python2 instead. Migration guide: http://deb.li/dhs2p
  321. dh_installinit
  322. dh_installmenu
  323. dh_installmime
  324. dh_installmodules
  325. dh_installlogcheck
  326. dh_installlogrotate
  327. dh_installpam
  328. dh_installppp
  329. dh_installudev
  330. dh_installwm
  331. dh_installxfonts
  332. dh_installgsettings
  333. dh_bugfiles
  334. dh_ucf
  335. dh_lintian
  336. dh_gconf
  337. dh_icons
  338. dh_perl
  339. dh_usrlocal
  340. dh_usrlocal: debian/freebayes/usr/local/bin/freebayes is not a directory
  341. dh_usrlocal: debian/freebayes/usr/local/bin/bamleftalign is not a directory
  342. rmdir: failed to remove `debian/freebayes/usr/local/bin': Directory not empty
  343. dh_usrlocal: rmdir debian/freebayes/usr/local/bin returned exit code 1
  344. make: *** [binary] Error 1
  345. dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit status 2
  346. debuild: fatal error at line 1350:
  347. dpkg-buildpackage -rfakeroot -D -us -uc failed
  348. bzr: ERROR: The build failed.
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