API tools faq
paste
Advertisement
Guest User

Untitled

a guest
Mar 14th, 2015
215
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 45.72 KB | None | 0 0
raw download clone embed print report
  1. ==> Validating source files with md5sums...
  2. tophat-2.0.13.tar.gz ... Passed
  3. ==> Extracting sources...
  4. -> Extracting tophat-2.0.13.tar.gz with bsdtar
  5. ==> Starting prepare()...
  6. configure.ac:20: installing './ar-lib'
  7. configure.ac:20: installing './compile'
  8. ==> Starting build()...
  9. checking for a BSD-compatible install... /usr/bin/install -c
  10. checking whether build environment is sane... yes
  11. checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
  12. checking for gawk... gawk
  13. checking whether make sets $(MAKE)... yes
  14. checking whether make supports nested variables... yes
  15. checking whether the C++ compiler works... yes
  16. checking for C++ compiler default output file name... a.out
  17. checking for suffix of executables...
  18. checking whether we are cross compiling... no
  19. checking for suffix of object files... o
  20. checking whether we are using the GNU C++ compiler... yes
  21. checking whether clang++ accepts -g... yes
  22. checking for style of include used by make... GNU
  23. checking dependency style of clang++... gcc3
  24. checking for gcc... clang
  25. checking whether we are using the GNU C compiler... yes
  26. checking whether clang accepts -g... yes
  27. checking for clang option to accept ISO C89... none needed
  28. checking whether clang understands -c and -o together... yes
  29. checking dependency style of clang... gcc3
  30. checking for ar... ar
  31. checking the archiver (ar) interface... ar
  32. checking for gawk... (cached) gawk
  33. checking whether we are using the GNU C++ compiler... (cached) yes
  34. checking whether clang++ accepts -g... (cached) yes
  35. checking dependency style of clang++... (cached) gcc3
  36. checking for gcc... (cached) clang
  37. checking whether we are using the GNU C compiler... (cached) yes
  38. checking whether clang accepts -g... (cached) yes
  39. checking for clang option to accept ISO C89... (cached) none needed
  40. checking whether clang understands -c and -o together... (cached) yes
  41. checking dependency style of clang... (cached) gcc3
  42. checking whether make sets $(MAKE)... (cached) yes
  43. checking for ranlib... ranlib
  44. checking whether python2 version is >= 2.4... yes
  45. checking for python2 version... 2.7
  46. checking for python2 platform... linux2
  47. checking for python2 script directory... ${prefix}/lib/python2.7/site-packages
  48. checking for python2 extension module directory... ${exec_prefix}/lib/python2.7/site-packages
  49. checking for boostlib >= 1.38.0... yes
  50. checking whether the compiler implements namespaces... yes
  51. checking whether the Boost::Thread library is available... yes
  52. checking for main in -lboost_thread... yes
  53. checking whether Boost::Thread needs Boost::System library... yes
  54. checking how to run the C++ preprocessor... clang++ -E
  55. checking for grep that handles long lines and -e... /usr/bin/grep
  56. checking for egrep... /usr/bin/grep -E
  57. checking for ANSI C header files... yes
  58. checking for sys/types.h... yes
  59. checking for sys/stat.h... yes
  60. checking for stdlib.h... yes
  61. checking for string.h... yes
  62. checking for memory.h... yes
  63. checking for strings.h... yes
  64. checking for inttypes.h... yes
  65. checking for stdint.h... yes
  66. checking for unistd.h... yes
  67. checking for stdlib.h... (cached) yes
  68. checking for string.h... (cached) yes
  69. checking for unistd.h... (cached) yes
  70. checking for ANSI C header files... (cached) yes
  71. checking for stdbool.h that conforms to C99... yes
  72. checking for _Bool... no
  73. checking for inline... inline
  74. checking for pid_t... yes
  75. checking for size_t... yes
  76. checking for ptrdiff_t... yes
  77. checking for an ANSI C-conforming const... yes
  78. checking for special C compiler options needed for large files... no
  79. checking for _FILE_OFFSET_BITS value needed for large files... no
  80. checking for gzread in -lz... yes
  81. checking for stdlib.h... (cached) yes
  82. checking for GNU libc compatible malloc... yes
  83. checking for memset... yes
  84. checking for strdup... yes
  85. checking for strrchr... yes
  86. checking for strtol... yes
  87. checking for strsep... yes
  88. checking build system type... x86_64-unknown-linux-gnu
  89. checking host system type... x86_64-unknown-linux-gnu
  90. checking how to create a pax tar archive... gnutar
  91. checking dependency style of clang... (cached) gcc3
  92. checking dependency style of clang++... (cached) gcc3
  93. checking that generated files are newer than configure... done
  94. configure: creating ./config.status
  95. config.status: creating Makefile
  96. config.status: creating src/Makefile
  97. config.status: creating config.h
  98. config.status: executing depfiles commands
  99.  
  100. -- tophat 2.0.13 Configuration Results --
  101. C++ compiler: clang++ -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3
  102. Linker flags: -L/usr/lib -L./samtools-0.1.18 -Wl,-O1,--sort-common,--as-needed,-z,relro
  103. BOOST libraries: -lboost_thread -lboost_system
  104. GCC version: clang version 3.5.1 (tags/RELEASE_351/final)
  105. Host System type: x86_64-unknown-linux-gnu
  106. Install prefix: /usr
  107. Install eprefix: ${prefix}
  108.  
  109. See config.h for further configuration information.
  110. Email <tophat.cufflinks@gmail.com> with questions and bug reports.
  111.  
  112. WARNING! python was not found and is required to run tophat
  113. Please install python and point configure to the installed location
  114. make all-recursive
  115. make[1]: Entering directory '/tmp/yaourt-tmp-mgre/aur-tophat/src/tophat-2.0.13'
  116. Making all in src
  117. make[2]: Entering directory '/tmp/yaourt-tmp-mgre/aur-tophat/src/tophat-2.0.13/src'
  118. Makefile:1686: warning: overriding recipe for target 'libbam.a'
  119. Makefile:1213: warning: ignoring old recipe for target 'libbam.a'
  120. cd ./samtools-0.1.18 && make -e samtools_0.1.18 && cp libbam.a samtools_0.1.18 ..
  121. make[3]: Entering directory '/tmp/yaourt-tmp-mgre/aur-tophat/src/tophat-2.0.13/src/samtools-0.1.18'
  122. make[4]: Entering directory '/tmp/yaourt-tmp-mgre/aur-tophat/src/tophat-2.0.13/src/samtools-0.1.18'
  123. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o
  124. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o
  125. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o
  126. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam.c -o bam.o
  127. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o
  128. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam.c -o sam.o
  129. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o
  130. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o
  131. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o
  132. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o
  133. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. razf.c -o razf.o
  134. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o
  135. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o
  136. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. knetfile.c -o knetfile.o
  137. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o
  138. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o
  139. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o
  140. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o
  141. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o
  142. ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
  143. make[4]: Leaving directory '/tmp/yaourt-tmp-mgre/aur-tophat/src/tophat-2.0.13/src/samtools-0.1.18'
  144. make[4]: Entering directory '/tmp/yaourt-tmp-mgre/aur-tophat/src/tophat-2.0.13/src/samtools-0.1.18/bcftools'
  145. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf.c -o bcf.o
  146. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. vcf.c -o vcf.o
  147. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcfutils.c -o bcfutils.o
  148. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. prob1.c -o prob1.o
  149. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. em.c -o em.o
  150. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kfunc.c -o kfunc.o
  151. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kmin.c -o kmin.o
  152. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. index.c -o index.o
  153. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. fet.c -o fet.o
  154. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. mut.c -o mut.o
  155. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf2qcall.c -o bcf2qcall.o
  156. ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
  157. make[4]: Leaving directory '/tmp/yaourt-tmp-mgre/aur-tophat/src/tophat-2.0.13/src/samtools-0.1.18/bcftools'
  158. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_tview.c -o bam_tview.o
  159. bam_tview.c:434:2: warning:
  160. "No curses library is available; tview is disabled." [-W#warnings]
  161. #warning "No curses library is available; tview is disabled."
  162. ^
  163. 1 warning generated.
  164. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_plcmd.c -o bam_plcmd.o
  165. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_view.c -o sam_view.o
  166. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdup.c -o bam_rmdup.o
  167. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdupse.c -o bam_rmdupse.o
  168. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_mate.c -o bam_mate.o
  169. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_stat.c -o bam_stat.o
  170. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_color.c -o bam_color.o
  171. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bamtk.c -o bamtk.o
  172. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kaln.c -o kaln.o
  173. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2bcf.c -o bam2bcf.o
  174. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2bcf_indel.c -o bam2bcf_indel.o
  175. bam2bcf_indel.c:32:52: warning: for loop has empty body [-Wempty-body]
  176. ...for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
  177. ^
  178. bam2bcf_indel.c:32:52: note: put the semicolon on a separate line to silence
  179. this warning
  180. bam2bcf_indel.c:33:52: warning: for loop has empty body [-Wempty-body]
  181. ...for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
  182. ^
  183. bam2bcf_indel.c:33:52: note: put the semicolon on a separate line to silence
  184. this warning
  185. 2 warnings generated.
  186. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. errmod.c -o errmod.o
  187. errmod.c:79:8: warning: self-comparison always evaluates to false
  188. [-Wtautological-compare]
  189. if (m > m) return -1;
  190. ^
  191. 1 warning generated.
  192. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sample.c -o sample.o
  193. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. cut_target.c -o cut_target.o
  194. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. phase.c -o phase.o
  195. clang -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2depth.c -o bam2depth.o
  196. clang -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -o samtools_0.1.18 bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lm -lz #-lcurses
  197. make[3]: Leaving directory '/tmp/yaourt-tmp-mgre/aur-tophat/src/tophat-2.0.13/src/samtools-0.1.18'
  198. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT GBase.o -MD -MP -MF .deps/GBase.Tpo -c -o GBase.o GBase.cpp
  199. mv -f .deps/GBase.Tpo .deps/GBase.Po
  200. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT codons.o -MD -MP -MF .deps/codons.Tpo -c -o codons.o codons.cpp
  201. mv -f .deps/codons.Tpo .deps/codons.Po
  202. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT gdna.o -MD -MP -MF .deps/gdna.Tpo -c -o gdna.o gdna.cpp
  203. mv -f .deps/gdna.Tpo .deps/gdna.Po
  204. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT GStr.o -MD -MP -MF .deps/GStr.Tpo -c -o GStr.o GStr.cpp
  205. mv -f .deps/GStr.Tpo .deps/GStr.Po
  206. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT GFaSeqGet.o -MD -MP -MF .deps/GFaSeqGet.Tpo -c -o GFaSeqGet.o GFaSeqGet.cpp
  207. mv -f .deps/GFaSeqGet.Tpo .deps/GFaSeqGet.Po
  208. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT gff.o -MD -MP -MF .deps/gff.Tpo -c -o gff.o gff.cpp
  209. mv -f .deps/gff.Tpo .deps/gff.Po
  210. rm -f libgc.a
  211. ar cru libgc.a GBase.o codons.o gdna.o GStr.o GFaSeqGet.o gff.o
  212. ranlib libgc.a
  213. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp
  214. In file included from reads.cpp:21:
  215. In file included from ./SeqAn-1.3/seqan/find.h:43:
  216. In file included from ./SeqAn-1.3/seqan/sequence.h:50:
  217. In file included from ./SeqAn-1.3/seqan/basic.h:67:
  218. ./SeqAn-1.3/seqan/basic/basic_testing.h:259:5: warning: ignoring return value of
  219. function declared with warn_unused_result attribute [-Wunused-result]
  220. mkstemp(fileNameBuffer);
  221. ^~~~~~~ ~~~~~~~~~~~~~~
  222. In file included from reads.cpp:21:
  223. In file included from ./SeqAn-1.3/seqan/find.h:43:
  224. In file included from ./SeqAn-1.3/seqan/sequence.h:103:
  225. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning:
  226. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
  227. guard here, followed by #define of a different macro [-Wheader-guard]
  228. #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  229. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  230. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note:
  231. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
  232. mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  233. #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
  234. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  235. SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  236. 2 warnings generated.
  237. mv -f .deps/reads.Tpo .deps/reads.Po
  238. clang -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -MT alphabet.o -MD -MP -MF .deps/alphabet.Tpo -c -o alphabet.o alphabet.c
  239. mv -f .deps/alphabet.Tpo .deps/alphabet.Po
  240. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT bwt_map.o -MD -MP -MF .deps/bwt_map.Tpo -c -o bwt_map.o bwt_map.cpp
  241. In file included from bwt_map.cpp:21:
  242. In file included from ./SeqAn-1.3/seqan/sequence.h:50:
  243. In file included from ./SeqAn-1.3/seqan/basic.h:67:
  244. ./SeqAn-1.3/seqan/basic/basic_testing.h:259:5: warning: ignoring return value of
  245. function declared with warn_unused_result attribute [-Wunused-result]
  246. mkstemp(fileNameBuffer);
  247. ^~~~~~~ ~~~~~~~~~~~~~~
  248. In file included from bwt_map.cpp:21:
  249. In file included from ./SeqAn-1.3/seqan/sequence.h:103:
  250. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning:
  251. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
  252. guard here, followed by #define of a different macro [-Wheader-guard]
  253. #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  254. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  255. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note:
  256. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
  257. mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  258. #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
  259. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  260. SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  261. 2 warnings generated.
  262. mv -f .deps/bwt_map.Tpo .deps/bwt_map.Po
  263. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT common.o -MD -MP -MF .deps/common.Tpo -c -o common.o common.cpp
  264. mv -f .deps/common.Tpo .deps/common.Po
  265. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT junctions.o -MD -MP -MF .deps/junctions.Tpo -c -o junctions.o junctions.cpp
  266. In file included from junctions.cpp:16:
  267. In file included from ./junctions.h:19:
  268. In file included from ./SeqAn-1.3/seqan/sequence.h:50:
  269. In file included from ./SeqAn-1.3/seqan/basic.h:67:
  270. ./SeqAn-1.3/seqan/basic/basic_testing.h:259:5: warning: ignoring return value of
  271. function declared with warn_unused_result attribute [-Wunused-result]
  272. mkstemp(fileNameBuffer);
  273. ^~~~~~~ ~~~~~~~~~~~~~~
  274. In file included from junctions.cpp:16:
  275. In file included from ./junctions.h:19:
  276. In file included from ./SeqAn-1.3/seqan/sequence.h:103:
  277. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning:
  278. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
  279. guard here, followed by #define of a different macro [-Wheader-guard]
  280. #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  281. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  282. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note:
  283. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
  284. mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  285. #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
  286. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  287. SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  288. 2 warnings generated.
  289. mv -f .deps/junctions.Tpo .deps/junctions.Po
  290. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT insertions.o -MD -MP -MF .deps/insertions.Tpo -c -o insertions.o insertions.cpp
  291. In file included from insertions.cpp:28:
  292. In file included from ./SeqAn-1.3/seqan/sequence.h:50:
  293. In file included from ./SeqAn-1.3/seqan/basic.h:67:
  294. ./SeqAn-1.3/seqan/basic/basic_testing.h:259:5: warning: ignoring return value of
  295. function declared with warn_unused_result attribute [-Wunused-result]
  296. mkstemp(fileNameBuffer);
  297. ^~~~~~~ ~~~~~~~~~~~~~~
  298. In file included from insertions.cpp:28:
  299. In file included from ./SeqAn-1.3/seqan/sequence.h:103:
  300. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning:
  301. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
  302. guard here, followed by #define of a different macro [-Wheader-guard]
  303. #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  304. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  305. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note:
  306. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
  307. mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  308. #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
  309. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  310. SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  311. 2 warnings generated.
  312. mv -f .deps/insertions.Tpo .deps/insertions.Po
  313. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT deletions.o -MD -MP -MF .deps/deletions.Tpo -c -o deletions.o deletions.cpp
  314. In file included from deletions.cpp:15:
  315. In file included from ./deletions.h:18:
  316. In file included from ./SeqAn-1.3/seqan/sequence.h:50:
  317. In file included from ./SeqAn-1.3/seqan/basic.h:67:
  318. ./SeqAn-1.3/seqan/basic/basic_testing.h:259:5: warning: ignoring return value of
  319. function declared with warn_unused_result attribute [-Wunused-result]
  320. mkstemp(fileNameBuffer);
  321. ^~~~~~~ ~~~~~~~~~~~~~~
  322. In file included from deletions.cpp:15:
  323. In file included from ./deletions.h:18:
  324. In file included from ./SeqAn-1.3/seqan/sequence.h:103:
  325. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning:
  326. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
  327. guard here, followed by #define of a different macro [-Wheader-guard]
  328. #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  329. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  330. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note:
  331. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
  332. mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  333. #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
  334. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  335. SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  336. 2 warnings generated.
  337. mv -f .deps/deletions.Tpo .deps/deletions.Po
  338. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT fusions.o -MD -MP -MF .deps/fusions.Tpo -c -o fusions.o fusions.cpp
  339. In file included from fusions.cpp:25:
  340. In file included from ./SeqAn-1.3/seqan/sequence.h:50:
  341. In file included from ./SeqAn-1.3/seqan/basic.h:67:
  342. ./SeqAn-1.3/seqan/basic/basic_testing.h:259:5: warning: ignoring return value of
  343. function declared with warn_unused_result attribute [-Wunused-result]
  344. mkstemp(fileNameBuffer);
  345. ^~~~~~~ ~~~~~~~~~~~~~~
  346. In file included from fusions.cpp:25:
  347. In file included from ./SeqAn-1.3/seqan/sequence.h:103:
  348. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning:
  349. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
  350. guard here, followed by #define of a different macro [-Wheader-guard]
  351. #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  352. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  353. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note:
  354. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
  355. mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  356. #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
  357. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  358. SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  359. 2 warnings generated.
  360. mv -f .deps/fusions.Tpo .deps/fusions.Po
  361. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT align_status.o -MD -MP -MF .deps/align_status.Tpo -c -o align_status.o align_status.cpp
  362. In file included from align_status.cpp:20:
  363. In file included from ./bwt_map.h:17:
  364. In file included from ./SeqAn-1.3/seqan/sequence.h:50:
  365. In file included from ./SeqAn-1.3/seqan/basic.h:67:
  366. ./SeqAn-1.3/seqan/basic/basic_testing.h:259:5: warning: ignoring return value of
  367. function declared with warn_unused_result attribute [-Wunused-result]
  368. mkstemp(fileNameBuffer);
  369. ^~~~~~~ ~~~~~~~~~~~~~~
  370. In file included from align_status.cpp:20:
  371. In file included from ./bwt_map.h:17:
  372. In file included from ./SeqAn-1.3/seqan/sequence.h:103:
  373. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning:
  374. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
  375. guard here, followed by #define of a different macro [-Wheader-guard]
  376. #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  377. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  378. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note:
  379. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
  380. mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  381. #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
  382. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  383. SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  384. 2 warnings generated.
  385. mv -f .deps/align_status.Tpo .deps/align_status.Po
  386. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT fragments.o -MD -MP -MF .deps/fragments.Tpo -c -o fragments.o fragments.cpp
  387. In file included from fragments.cpp:15:
  388. In file included from ./bwt_map.h:17:
  389. In file included from ./SeqAn-1.3/seqan/sequence.h:50:
  390. In file included from ./SeqAn-1.3/seqan/basic.h:67:
  391. ./SeqAn-1.3/seqan/basic/basic_testing.h:259:5: warning: ignoring return value of
  392. function declared with warn_unused_result attribute [-Wunused-result]
  393. mkstemp(fileNameBuffer);
  394. ^~~~~~~ ~~~~~~~~~~~~~~
  395. In file included from fragments.cpp:15:
  396. In file included from ./bwt_map.h:17:
  397. In file included from ./SeqAn-1.3/seqan/sequence.h:103:
  398. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning:
  399. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
  400. guard here, followed by #define of a different macro [-Wheader-guard]
  401. #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  402. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  403. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note:
  404. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
  405. mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  406. #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
  407. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  408. SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  409. 2 warnings generated.
  410. mv -f .deps/fragments.Tpo .deps/fragments.Po
  411. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT tokenize.o -MD -MP -MF .deps/tokenize.Tpo -c -o tokenize.o tokenize.cpp
  412. mv -f .deps/tokenize.Tpo .deps/tokenize.Po
  413. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT inserts.o -MD -MP -MF .deps/inserts.Tpo -c -o inserts.o inserts.cpp
  414. In file included from inserts.cpp:17:
  415. In file included from ./bwt_map.h:17:
  416. In file included from ./SeqAn-1.3/seqan/sequence.h:50:
  417. In file included from ./SeqAn-1.3/seqan/basic.h:67:
  418. ./SeqAn-1.3/seqan/basic/basic_testing.h:259:5: warning: ignoring return value of
  419. function declared with warn_unused_result attribute [-Wunused-result]
  420. mkstemp(fileNameBuffer);
  421. ^~~~~~~ ~~~~~~~~~~~~~~
  422. In file included from inserts.cpp:17:
  423. In file included from ./bwt_map.h:17:
  424. In file included from ./SeqAn-1.3/seqan/sequence.h:103:
  425. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning:
  426. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
  427. guard here, followed by #define of a different macro [-Wheader-guard]
  428. #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  429. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  430. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note:
  431. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
  432. mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  433. #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
  434. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  435. SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  436. 2 warnings generated.
  437. mv -f .deps/inserts.Tpo .deps/inserts.Po
  438. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT qual.o -MD -MP -MF .deps/qual.Tpo -c -o qual.o qual.cpp
  439. mv -f .deps/qual.Tpo .deps/qual.Po
  440. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT bam_merge_impl.o -MD -MP -MF .deps/bam_merge_impl.Tpo -c -o bam_merge_impl.o bam_merge_impl.cpp
  441. mv -f .deps/bam_merge_impl.Tpo .deps/bam_merge_impl.Po
  442. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT utils.o -MD -MP -MF .deps/utils.Tpo -c -o utils.o utils.cpp
  443. mv -f .deps/utils.Tpo .deps/utils.Po
  444. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT coverage.o -MD -MP -MF .deps/coverage.Tpo -c -o coverage.o coverage.cpp
  445. In file included from coverage.cpp:15:
  446. In file included from ./coverage.h:17:
  447. In file included from ./bwt_map.h:17:
  448. In file included from ./SeqAn-1.3/seqan/sequence.h:50:
  449. In file included from ./SeqAn-1.3/seqan/basic.h:67:
  450. ./SeqAn-1.3/seqan/basic/basic_testing.h:259:5: warning: ignoring return value of
  451. function declared with warn_unused_result attribute [-Wunused-result]
  452. mkstemp(fileNameBuffer);
  453. ^~~~~~~ ~~~~~~~~~~~~~~
  454. In file included from coverage.cpp:15:
  455. In file included from ./coverage.h:17:
  456. In file included from ./bwt_map.h:17:
  457. In file included from ./SeqAn-1.3/seqan/sequence.h:103:
  458. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning:
  459. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
  460. guard here, followed by #define of a different macro [-Wheader-guard]
  461. #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  462. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  463. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note:
  464. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
  465. mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  466. #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
  467. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  468. SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  469. 2 warnings generated.
  470. mv -f .deps/coverage.Tpo .deps/coverage.Po
  471. rm -f libtophat.a
  472. ar cru libtophat.a reads.o alphabet.o bwt_map.o common.o junctions.o insertions.o deletions.o fusions.o align_status.o fragments.o tokenize.o inserts.o qual.o bam_merge_impl.o utils.o coverage.o
  473. ranlib libtophat.a
  474. clang++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -MT prep_reads.o -MD -MP -MF .deps/prep_reads.Tpo -c -o prep_reads.o prep_reads.cpp
  475. In file included from prep_reads.cpp:21:
  476. In file included from ./reads.h:16:
  477. In file included from ./SeqAn-1.3/seqan/sequence.h:50:
  478. In file included from ./SeqAn-1.3/seqan/basic.h:67:
  479. ./SeqAn-1.3/seqan/basic/basic_testing.h:259:5: warning: ignoring return value of
  480. function declared with warn_unused_result attribute [-Wunused-result]
  481. mkstemp(fileNameBuffer);
  482. ^~~~~~~ ~~~~~~~~~~~~~~
  483. In file included from prep_reads.cpp:21:
  484. In file included from ./reads.h:16:
  485. In file included from ./SeqAn-1.3/seqan/sequence.h:103:
  486. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:38:9: warning:
  487. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_' is used as a header
  488. guard here, followed by #define of a different macro [-Wheader-guard]
  489. #ifndef SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  490. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  491. ./SeqAn-1.3/seqan/sequence/string_set_dependent_generous.h:39:9: note:
  492. 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_' is defined here; did you
  493. mean 'SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_'?
  494. #define SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUSH_
  495. ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  496. SEQAN_SEQUENCE_STRING_SET_DEPENDENT_GENEROUS_H_
  497. 2 warnings generated.
  498. mv -f .deps/prep_reads.Tpo .deps/prep_reads.Po
  499. clang++ -O3 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4 -DNDEBUG -pthread -I/usr/include -I./samtools-0.1.18 -I./SeqAn-1.3 -L/usr/lib -L./samtools-0.1.18 -Wl,-O1,--sort-common,--as-needed,-z,relro -L./samtools-0.1.18 -L/usr/lib -L./samtools-0.1.18 -Wl,-O1,--sort-common,--as-needed,-z,relro -o prep_reads prep_reads.o ../src/libtophat.a -lbam -lz
  500. /usr/lib/libbam.a(sam.o): In function `samthreads':
  501. (.text+0x10): undefined reference to `hts_get_format'
  502. /usr/lib/libbam.a(sam.o): In function `samthreads':
  503. (.text+0x2f): undefined reference to `bgzf_mt'
  504. /usr/lib/libbam.a(sam.o): In function `samopen':
  505. (.text+0x51): undefined reference to `hts_open'
  506. /usr/lib/libbam.a(sam.o): In function `samopen':
  507. (.text+0x97): undefined reference to `hts_set_fai_filename'
  508. /usr/lib/libbam.a(sam.o): In function `samopen':
  509. (.text+0x9f): undefined reference to `sam_hdr_read'
  510. /usr/lib/libbam.a(sam.o): In function `samopen':
  511. (.text+0xb3): undefined reference to `hts_verbose'
  512. /usr/lib/libbam.a(sam.o): In function `samopen':
  513. (.text+0xf4): undefined reference to `hts_get_format'
  514. /usr/lib/libbam.a(sam.o): In function `samopen':
  515. (.text+0x106): undefined reference to `sam_hdr_write'
  516. /usr/lib/libbam.a(sam.o): In function `samclose':
  517. (.text+0x149): undefined reference to `bam_hdr_destroy'
  518. /usr/lib/libbam.a(sam.o): In function `samclose':
  519. (.text+0x151): undefined reference to `hts_close'
  520. /usr/lib/libbam.a(sam.o): In function `sampileup':
  521. (.text+0x185): undefined reference to `bam_init1'
  522. /usr/lib/libbam.a(sam.o): In function `sampileup':
  523. (.text+0x1d9): undefined reference to `sam_read1'
  524. /usr/lib/libbam.a(sam.o): In function `sampileup':
  525. (.text+0x1f7): undefined reference to `bam_destroy1'
  526. /usr/lib/libbam.a(sam.o): In function `samfaipath':
  527. (.text+0x28c): undefined reference to `hts_verbose'
  528. /usr/lib/libbam.a(sam.o): In function `samfaipath':
  529. (.text+0x29a): undefined reference to `fai_build'
  530. /usr/lib/libbam.a(bam_plbuf.o): In function `bam_plbuf_init':
  531. (.text+0x31): undefined reference to `bam_plp_init'
  532. /usr/lib/libbam.a(bam_plbuf.o): In function `bam_plbuf_destroy':
  533. (.text+0x58): undefined reference to `bam_plp_destroy'
  534. /usr/lib/libbam.a(bam_plbuf.o): In function `bam_plbuf_push':
  535. (.text+0x7f): undefined reference to `bam_plp_push'
  536. /usr/lib/libbam.a(bam_plbuf.o): In function `bam_plbuf_push':
  537. (.text+0xb9): undefined reference to `bam_plp_next'
  538. /usr/lib/libbam.a(bam_plbuf.o): In function `bam_plbuf_reset':
  539. (.text+0x4): undefined reference to `bam_plp_reset'
  540. prep_reads.o: In function `flt_reads_and_hits(std::vector<std::string, std::allocator<std::string> >&)':
  541. prep_reads.cpp:(.text+0x7c7): undefined reference to `samread'
  542. prep_reads.cpp:(.text+0x85e): undefined reference to `bam_header_destroy'
  543. prep_reads.cpp:(.text+0x8c1): undefined reference to `bam_header_destroy'
  544. prep_reads.cpp:(.text+0xf5c): undefined reference to `bam_header_destroy'
  545. prep_reads.o: In function `process_reads(std::vector<std::string, std::allocator<std::string> >&, std::vector<FZPipe, std::allocator<FZPipe> >&, std::vector<std::string, std::allocator<std::string> >&, std::vector<FZPipe, std::allocator<FZPipe> >&)':
  546. prep_reads.cpp:(.text+0x35d4): undefined reference to `bam_header_destroy'
  547. prep_reads.cpp:(.text+0x360c): undefined reference to `bam_header_destroy'
  548. prep_reads.o: In function `GBamWriter::write(bam1_t*, long)':
  549. prep_reads.cpp:(.text._ZN10GBamWriter5writeEP6bam1_tl[_ZN10GBamWriter5writeEP6bam1_tl]+0x98): undefined reference to `samwrite'
  550. prep_reads.o: In function `GBamWriter::GBamWriter(char const*, char const*, std::string)':
  551. prep_reads.cpp:(.text._ZN10GBamWriterC2EPKcS1_Ss[_ZN10GBamWriterC2EPKcS1_Ss]+0x19): undefined reference to `sam_open'
  552. prep_reads.cpp:(.text._ZN10GBamWriterC2EPKcS1_Ss[_ZN10GBamWriterC2EPKcS1_Ss]+0x38): undefined reference to `sam_header_read'
  553. prep_reads.cpp:(.text._ZN10GBamWriterC2EPKcS1_Ss[_ZN10GBamWriterC2EPKcS1_Ss]+0x58): undefined reference to `sam_close'
  554. ../src/libtophat.a(reads.o): In function `ReadStream::get_direct(Read&)':
  555. reads.cpp:(.text+0x2609): undefined reference to `samread'
  556. ../src/libtophat.a(common.o): In function `GBamRecord::set_cigar(char const*)':
  557. common.cpp:(.text+0x27e1): undefined reference to `bam_calend'
  558. ../src/libtophat.a(common.o): In function `GBamRecord::add_sequence(char const*, int)':
  559. common.cpp:(.text+0x294c): undefined reference to `bam_cigar2qlen'
  560. common.cpp:(.text+0x2a18): undefined reference to `bam_nt16_table'
  561. ../src/libtophat.a(common.o): In function `GBamRecord::find_tag(char const*)':
  562. common.cpp:(.text+0x2fe4): undefined reference to `bam_aux_get'
  563. ../src/libtophat.a(common.o): In function `GBamRecord::tag_char(char const*)':
  564. common.cpp:(.text+0x2ff5): undefined reference to `bam_aux_get'
  565. common.cpp:(.text+0x3002): undefined reference to `bam_aux2A'
  566. ../src/libtophat.a(common.o): In function `GBamRecord::tag_int(char const*)':
  567. common.cpp:(.text+0x3015): undefined reference to `bam_aux_get'
  568. common.cpp:(.text+0x3023): undefined reference to `bam_aux2i'
  569. ../src/libtophat.a(common.o): In function `GBamRecord::tag_str(char const*)':
  570. common.cpp:(.text+0x3066): undefined reference to `bam_aux_get'
  571. common.cpp:(.text+0x3073): undefined reference to `bam_aux2Z'
  572. ../src/libtophat.a(common.o): In function `GBamRecord::spliceStrand()':
  573. common.cpp:(.text+0x312a): undefined reference to `bam_aux_get'
  574. common.cpp:(.text+0x3137): undefined reference to `bam_aux2A'
  575. ../src/libtophat.a(common.o): In function `GBamRecord::sequence()':
  576. common.cpp:(.text+0x31e0): undefined reference to `bam_nt16_rev_table'
  577. ../src/libtophat.a(common.o): In function `GBamRecord::seqData(std::string*)':
  578. common.cpp:(.text+0x35f8): undefined reference to `bam_nt16_rev_table'
  579. common.cpp:(.text+0x3642): undefined reference to `bam_nt16_rev_table'
  580. common.cpp:(.text+0x3672): undefined reference to `bam_nt16_rev_table'
  581. clang: error: linker command failed with exit code 1 (use -v to see invocation)
  582. Makefile:1302: recipe for target 'prep_reads' failed
  583. make[2]: *** [prep_reads] Error 1
  584. make[2]: Leaving directory '/tmp/yaourt-tmp-mgre/aur-tophat/src/tophat-2.0.13/src'
  585. Makefile:386: recipe for target 'all-recursive' failed
  586. make[1]: *** [all-recursive] Error 1
  587. make[1]: Leaving directory '/tmp/yaourt-tmp-mgre/aur-tophat/src/tophat-2.0.13'
  588. Makefile:327: recipe for target 'all' failed
  589. make: *** [all] Error 2
  590. ==> ERROR: A failure occurred in build().
  591. Aborting...
  592. ==> ERROR: Makepkg was unable to build tophat.
  593. ==> Restart building tophat ? [y/N]
Advertisement
Add Comment
Please, Sign In to add comment
Advertisement
Public Pastes
Advertisement
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy.  OK, I Understand
Not a member of Pastebin yet?
Sign Up, it unlocks many cool features!