API tools faq
paste
Guest User

MaSuRCA output

a guest
Apr 27th, 2017
302
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 28.04 KB | None | 0 0
raw download clone embed print report
  1. [gc001@gc001 MaSuRCA-3.2.2_RC1]$ sudo ./install.sh
  2. ++ pwd
  3. + ROOT=/home/gc001/programs/MaSuRCA-3.2.2_RC1
  4. + '[' -z '' ']'
  5. + DEST=/home/gc001/programs/MaSuRCA-3.2.2_RC1
  6. + mkdir -p dist-bin
  7. + PATH=/sbin:/bin:/usr/sbin:/usr/bin:/home/gc001/programs/MaSuRCA-3.2.2_RC1/dist -bin
  8. ++ which make
  9. + ln -sf /bin/make /home/gc001/programs/MaSuRCA-3.2.2_RC1/dist-bin/gmake
  10. + ln -sf /home/gc001/programs/MaSuRCA-3.2.2_RC1/PkgConfig.pm /home/gc001/program s/MaSuRCA-3.2.2_RC1/dist-bin/pkg-config
  11. ++ grep -c '^processor' /proc/cpuinfo
  12. + export NUM_THREADS=2
  13. + NUM_THREADS=2
  14. + BINDIR=/home/gc001/programs/MaSuRCA-3.2.2_RC1/bin
  15. + LIBDIR=/home/gc001/programs/MaSuRCA-3.2.2_RC1/lib
  16. + export PKG_CONFIG_PATH=/home/gc001/programs/MaSuRCA-3.2.2_RC1/lib/pkgconfig:
  17. + PKG_CONFIG_PATH=/home/gc001/programs/MaSuRCA-3.2.2_RC1/lib/pkgconfig:
  18. + cd global-1
  19. + ./configure --prefix=/home/gc001/programs/MaSuRCA-3.2.2_RC1 --bindir=/home/gc0 01/programs/MaSuRCA-3.2.2_RC1/bin --libdir=/home/gc001/programs/MaSuRCA-3.2.2_RC 1/lib
  20. checking build system type... x86_64-unknown-linux-gnu
  21. checking host system type... x86_64-unknown-linux-gnu
  22. checking for a BSD-compatible install... /bin/install -c
  23. checking whether build environment is sane... yes
  24. checking for a thread-safe mkdir -p... /bin/mkdir -p
  25. checking for gawk... gawk
  26. checking whether make sets $(MAKE)... yes
  27. checking whether make supports nested variables... yes
  28. checking whether make supports nested variables... (cached) yes
  29. checking how to print strings... printf
  30. checking for style of include used by make... GNU
  31. checking for gcc... gcc
  32. checking whether the C compiler works... yes
  33. checking for C compiler default output file name... a.out
  34. checking for suffix of executables...
  35. checking whether we are cross compiling... no
  36. checking for suffix of object files... o
  37. checking whether we are using the GNU C compiler... yes
  38. checking whether gcc accepts -g... yes
  39. checking for gcc option to accept ISO C89... none needed
  40. checking whether gcc understands -c and -o together... yes
  41. checking dependency style of gcc... gcc3
  42. checking for a sed that does not truncate output... /bin/sed
  43. checking for grep that handles long lines and -e... /bin/grep
  44. checking for egrep... /bin/grep -E
  45. checking for fgrep... /bin/grep -F
  46. checking for ld used by gcc... /bin/ld
  47. checking if the linker (/bin/ld) is GNU ld... yes
  48. checking for BSD- or MS-compatible name lister (nm)... /bin/nm -B
  49. checking the name lister (/bin/nm -B) interface... BSD nm
  50. checking whether ln -s works... yes
  51. checking the maximum length of command line arguments... 1572864
  52. checking whether the shell understands some XSI constructs... yes
  53. checking whether the shell understands "+="... yes
  54. checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-li nux-gnu format... func_convert_file_noop
  55. checking how to convert x86_64-unknown-linux-gnu file names to toolchain format. .. func_convert_file_noop
  56. checking for /bin/ld option to reload object files... -r
  57. checking for objdump... objdump
  58. checking how to recognize dependent libraries... pass_all
  59. checking for dlltool... no
  60. checking how to associate runtime and link libraries... printf %s\n
  61. checking for ar... ar
  62. checking for archiver @FILE support... @
  63. checking for strip... strip
  64. checking for ranlib... ranlib
  65. checking command to parse /bin/nm -B output from gcc object... ok
  66. checking for sysroot... no
  67. checking for mt... no
  68. checking if : is a manifest tool... no
  69. checking how to run the C preprocessor... gcc -E
  70. checking for ANSI C header files... yes
  71. checking for sys/types.h... yes
  72. checking for sys/stat.h... yes
  73. checking for stdlib.h... yes
  74. checking for string.h... yes
  75. checking for memory.h... yes
  76. checking for strings.h... yes
  77. checking for inttypes.h... yes
  78. checking for stdint.h... yes
  79. checking for unistd.h... yes
  80. checking for dlfcn.h... yes
  81. checking for objdir... .libs
  82. checking if gcc supports -fno-rtti -fno-exceptions... no
  83. checking for gcc option to produce PIC... -fPIC -DPIC
  84. checking if gcc PIC flag -fPIC -DPIC works... yes
  85. checking if gcc static flag -static works... no
  86. checking if gcc supports -c -o file.o... yes
  87. checking if gcc supports -c -o file.o... (cached) yes
  88. checking whether the gcc linker (/bin/ld -m elf_x86_64) supports shared librarie s... yes
  89. checking whether -lc should be explicitly linked in... no
  90. checking dynamic linker characteristics... GNU/Linux ld.so
  91. checking how to hardcode library paths into programs... immediate
  92. checking whether stripping libraries is possible... yes
  93. checking if libtool supports shared libraries... yes
  94. checking whether to build shared libraries... yes
  95. checking whether to build static libraries... yes
  96. checking for gcc... (cached) gcc
  97. checking whether we are using the GNU C compiler... (cached) yes
  98. checking whether gcc accepts -g... (cached) yes
  99. checking for gcc option to accept ISO C89... (cached) none needed
  100. checking whether gcc understands -c and -o together... (cached) yes
  101. checking dependency style of gcc... (cached) gcc3
  102. checking for g++... g++
  103. checking whether we are using the GNU C++ compiler... yes
  104. checking whether g++ accepts -g... yes
  105. checking dependency style of g++... gcc3
  106. checking how to run the C++ preprocessor... g++ -E
  107. checking for ld used by g++... /bin/ld -m elf_x86_64
  108. checking if the linker (/bin/ld -m elf_x86_64) is GNU ld... yes
  109. checking whether the g++ linker (/bin/ld -m elf_x86_64) supports shared librarie s... yes
  110. checking for g++ option to produce PIC... -fPIC -DPIC
  111. checking if g++ PIC flag -fPIC -DPIC works... yes
  112. checking if g++ static flag -static works... no
  113. checking if g++ supports -c -o file.o... yes
  114. checking if g++ supports -c -o file.o... (cached) yes
  115. checking whether the g++ linker (/bin/ld -m elf_x86_64) supports shared librarie s... yes
  116. checking dynamic linker characteristics... (cached) GNU/Linux ld.so
  117. checking how to hardcode library paths into programs... immediate
  118. checking for pthread_create in -lpthread... yes
  119. checking for library containing clock_gettime... none required
  120. checking for __int128... yes
  121. checking for OpenMP flag of C++ compiler... -fopenmp
  122. checking for Boost headers version >= 1.46.0... yes
  123. checking for Boost's header version... 1_55
  124. checking boost/icl/interval_set.hpp usability... yes
  125. checking boost/icl/interval_set.hpp presence... yes
  126. checking for boost/icl/interval_set.hpp... yes
  127. checking for _NSGetExecutablePath... no
  128. checking if std::thread::sleep_for is supported... yes
  129. checking for stdlib.h... (cached) yes
  130. checking for unistd.h... (cached) yes
  131. checking for sys/param.h... yes
  132. checking for getpagesize... yes
  133. checking for working mmap... yes
  134. checking for mremap... yes
  135. checking zlib.h usability... yes
  136. checking zlib.h presence... yes
  137. checking for zlib.h... yes
  138. checking for zlibVersion in -lz... yes
  139. checking bzlib.h usability... yes
  140. checking bzlib.h presence... yes
  141. checking for bzlib.h... yes
  142. checking for BZ2_bzlibVersion in -lbz2... yes
  143. checking for pkg-config... /bin/pkg-config
  144. checking pkg-config is at least version 0.9.0... yes
  145. checking for __builtin_prefetch... yes
  146. checking for architecture... Linux-amd64
  147. checking for yaggo... false
  148. checking for perl... /bin/perl
  149. checking for Perl prefix... /usr
  150. checking for Perl extension include path... /usr/lib64/perl5/CORE
  151. checking for Perl extension target directory... $(libdir)/perl
  152. checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include
  153. checking for Perl extensions linker flags... -shared -O2 -g -pipe -Wall -Wp,-D_F ORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -Wl,-z,relro
  154. checking that generated files are newer than configure... done
  155. configure: creating ./config.status
  156. config.status: creating Makefile
  157. config.status: creating jellyfish/jellyfish-2.0.pc
  158. config.status: creating samtools/Makefile
  159. config.status: creating prepare/Makefile
  160. config.status: creating ufasta/Makefile
  161. config.status: creating quorum/Makefile
  162. config.status: creating SuperReads/Makefile
  163. config.status: creating SOAPdenovo2/Makefile
  164. config.status: creating PacBio/Makefile
  165. config.status: creating CA/Makefile
  166. config.status: creating CA8/Makefile
  167. config.status: creating jellyfish/Makefile
  168. config.status: creating MUMmer/Makefile
  169. config.status: creating config.h
  170. config.status: config.h is unchanged
  171. config.status: executing depfiles commands
  172. config.status: executing libtool commands
  173. + make -j 2 install-special
  174. Making install in jellyfish pwd /home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1
  175. make[1]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/jel lyfish'
  176. make install-am
  177. make[2]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/jel lyfish'
  178. CXX swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo
  179. CXX sub_commands/stats_main.o
  180. swig/perl5/swig_wrap.cpp:743:20: fatal error: EXTERN.h: No such file or director y
  181. #include "EXTERN.h"
  182. ^
  183. compilation terminated.
  184. make[2]: *** [swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo] Error 1
  185. make[2]: *** Waiting for unfinished jobs....
  186. make[2]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/jell yfish'
  187. make[1]: *** [install] Error 2
  188. make[1]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/jell yfish'
  189. Making install in samtools pwd /home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1
  190. make[1]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/sam tools'
  191. make[2]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/sam tools'
  192. /bin/mkdir -p '/home/gc001/programs/MaSuRCA-3.2.2_RC1/lib'
  193. /bin/mkdir -p '/home/gc001/programs/MaSuRCA-3.2.2_RC1/include/samtools/bcftools '
  194. /bin/sh ../libtool --mode=install /bin/install -c libbam.la bcftools/libbcf .la '/home/gc001/programs/MaSuRCA-3.2.2_RC1/lib'
  195. /bin/install -c -m 644 bcftools/bcf.h bcftools/kmin.h bcftools/prob1.h '/home/g c001/programs/MaSuRCA-3.2.2_RC1/include/samtools/bcftools'
  196. /bin/mkdir -p '/home/gc001/programs/MaSuRCA-3.2.2_RC1/include/samtools'
  197. /bin/install -c -m 644 bam.h bam2bcf.h bam_endian.h bgzf.h errmod.h faidx.h kal n.h khash.h klist.h knetfile.h kprobaln.h kseq.h ksort.h kstring.h razf.h sam.h sam_header.h sample.h bam_tview.h '/home/gc001/programs/MaSuRCA-3.2.2_RC1/includ e/samtools'
  198. libtool: install: /bin/install -c .libs/libbam.so.0.0.0 /home/gc001/programs/MaS uRCA-3.2.2_RC1/lib/libbam.so.0.0.0
  199. libtool: install: (cd /home/gc001/programs/MaSuRCA-3.2.2_RC1/lib && { ln -s -f l ibbam.so.0.0.0 libbam.so.0 || { rm -f libbam.so.0 && ln -s libbam.so.0.0.0 libba m.so.0; }; })
  200. libtool: install: (cd /home/gc001/programs/MaSuRCA-3.2.2_RC1/lib && { ln -s -f l ibbam.so.0.0.0 libbam.so || { rm -f libbam.so && ln -s libbam.so.0.0.0 libbam.so ; }; })
  201. libtool: install: /bin/install -c .libs/libbam.lai /home/gc001/programs/MaSuRCA- 3.2.2_RC1/lib/libbam.la
  202. libtool: install: /bin/install -c bcftools/.libs/libbcf.so.0.0.0 /home/gc001/pro grams/MaSuRCA-3.2.2_RC1/lib/libbcf.so.0.0.0
  203. libtool: install: (cd /home/gc001/programs/MaSuRCA-3.2.2_RC1/lib && { ln -s -f l ibbcf.so.0.0.0 libbcf.so.0 || { rm -f libbcf.so.0 && ln -s libbcf.so.0.0.0 libbc f.so.0; }; })
  204. libtool: install: (cd /home/gc001/programs/MaSuRCA-3.2.2_RC1/lib && { ln -s -f l ibbcf.so.0.0.0 libbcf.so || { rm -f libbcf.so && ln -s libbcf.so.0.0.0 libbcf.so ; }; })
  205. libtool: install: /bin/install -c bcftools/.libs/libbcf.lai /home/gc001/programs /MaSuRCA-3.2.2_RC1/lib/libbcf.la
  206. libtool: install: /bin/install -c .libs/libbam.a /home/gc001/programs/MaSuRCA-3. 2.2_RC1/lib/libbam.a
  207. libtool: install: chmod 644 /home/gc001/programs/MaSuRCA-3.2.2_RC1/lib/libbam.a
  208. libtool: install: ranlib /home/gc001/programs/MaSuRCA-3.2.2_RC1/lib/libbam.a
  209. libtool: install: /bin/install -c bcftools/.libs/libbcf.a /home/gc001/programs/M aSuRCA-3.2.2_RC1/lib/libbcf.a
  210. libtool: install: chmod 644 /home/gc001/programs/MaSuRCA-3.2.2_RC1/lib/libbcf.a
  211. libtool: install: ranlib /home/gc001/programs/MaSuRCA-3.2.2_RC1/lib/libbcf.a
  212. libtool: finish: PATH="/sbin:/bin:/usr/sbin:/usr/bin:/home/gc001/programs/MaSuRC A-3.2.2_RC1/dist-bin:/sbin" ldconfig -n /home/gc001/programs/MaSuRCA-3.2.2_RC1/l ib
  213. ----------------------------------------------------------------------
  214. Libraries have been installed in:
  215. /home/gc001/programs/MaSuRCA-3.2.2_RC1/lib
  216.  
  217. If you ever happen to want to link against installed libraries
  218. in a given directory, LIBDIR, you must either use libtool, and
  219. specify the full pathname of the library, or use the `-LLIBDIR'
  220. flag during linking and do at least one of the following:
  221. - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
  222. during execution
  223. - add LIBDIR to the `LD_RUN_PATH' environment variable
  224. during linking
  225. - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
  226. - have your system administrator add LIBDIR to `/etc/ld.so.conf'
  227.  
  228. See any operating system documentation about shared libraries for
  229. more information, such as the ld(1) and ld.so(8) manual pages.
  230. ----------------------------------------------------------------------
  231. /bin/mkdir -p '/home/gc001/programs/MaSuRCA-3.2.2_RC1/bin'
  232. /bin/sh ../libtool --mode=install /bin/install -c samtools '/home/gc001/prog rams/MaSuRCA-3.2.2_RC1/bin'
  233. libtool: install: /bin/install -c .libs/samtools /home/gc001/programs/MaSuRCA-3. 2.2_RC1/bin/samtools
  234. make[2]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/samt ools'
  235. make[1]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/samt ools'
  236. Making install in prepare pwd /home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1
  237. make[1]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/pre pare'
  238. make[2]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/pre pare'
  239. make[2]: Nothing to be done for `install-data-am'.
  240. /bin/mkdir -p '/home/gc001/programs/MaSuRCA-3.2.2_RC1/bin'
  241. /bin/sh ../libtool --mode=install /bin/install -c finalFusion '/home/gc001/p rograms/MaSuRCA-3.2.2_RC1/bin'
  242. libtool: install: /bin/install -c finalFusion /home/gc001/programs/MaSuRCA-3.2.2 _RC1/bin/finalFusion
  243. make[2]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/prep are'
  244. make[1]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/prep are'
  245. Making install in ufasta pwd /home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1
  246. make[1]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/ufa sta'
  247. make install-am
  248. make[2]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/ufa sta'
  249. make[3]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/ufa sta'
  250. make[3]: Nothing to be done for `install-data-am'.
  251. /bin/mkdir -p '/home/gc001/programs/MaSuRCA-3.2.2_RC1/bin'
  252. /bin/sh ../libtool --mode=install /bin/install -c ufasta '/home/gc001/progra ms/MaSuRCA-3.2.2_RC1/bin'
  253. libtool: install: /bin/install -c ufasta /home/gc001/programs/MaSuRCA-3.2.2_RC1/ bin/ufasta
  254. make[3]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/ufas ta'
  255. make[2]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/ufas ta'
  256. make[1]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/ufas ta'
  257. Making install in quorum pwd /home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1
  258. make[1]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/quo rum'
  259. make install-am
  260. make[2]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/quo rum'
  261. CXX src/error_correct_reads.o
  262. CXX src/create_database.o
  263. src/create_database.cc:23:33: fatal error: jellyfish/mer_dna.hpp: No such file o r directory
  264. #include <jellyfish/mer_dna.hpp>
  265. ^
  266. compilation terminated.
  267. src/error_correct_reads.cc:25:36: fatal error: jellyfish/atomic_gcc.hpp: No such file or directory
  268. #include <jellyfish/atomic_gcc.hpp>
  269. ^
  270. compilation terminated.
  271. make[2]: *** [src/create_database.o] Error 1
  272. make[2]: *** Waiting for unfinished jobs....
  273. make[2]: *** [src/error_correct_reads.o] Error 1
  274. make[2]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/quor um'
  275. make[1]: *** [install] Error 2
  276. make[1]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/quor um'
  277. Making install in SuperReads pwd /home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1
  278. make[1]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/Sup erReads'
  279. make install-am
  280. make[2]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/Sup erReads'
  281. CXX src/error_corrected2frg.o
  282. CXXLD reverse_complement
  283. src/error_corrected2frg.cc:24:29: fatal error: jellyfish/err.hpp: No such file o r directory
  284. #include <jellyfish/err.hpp>
  285. ^
  286. compilation terminated.
  287. /bin/ld: cannot find -ljellyfish-2.0
  288. collect2: error: ld returned 1 exit status
  289. make[2]: *** [reverse_complement] Error 1
  290. make[2]: *** Waiting for unfinished jobs....
  291. make[2]: *** [src/error_corrected2frg.o] Error 1
  292. make[2]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/Supe rReads'
  293. make[1]: *** [install] Error 2
  294. make[1]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/Supe rReads'
  295. Making install in SOAPdenovo2 pwd /home/gc001/programs/MaSuRCA-3.2.2_RC1/global- 1
  296. make[1]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/SOA Pdenovo2'
  297. CC standardPregraph/libstandard63_a-readseq1by1.o
  298. CXX sparsePregraph/libsparse63_a-build_preArc.o
  299. CXX sparsePregraph/libsparse63_a-io_func.o
  300. CC standardPregraph/libstandard127_a-readseq1by1.o
  301. CXX sparsePregraph/libsparse127_a-build_preArc.o
  302. CXX sparsePregraph/libsparse127_a-io_func.o
  303. AR libstandard63.a
  304. AR libsparse63.a
  305. AR libstandard127.a
  306. AR libsparse127.a
  307. GEN SOAPdenovo-63mer
  308. GEN SOAPdenovo-127mer
  309. make[2]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/SOA Pdenovo2'
  310. make[2]: Nothing to be done for `install-data-am'.
  311. /bin/mkdir -p '/home/gc001/programs/MaSuRCA-3.2.2_RC1/bin'
  312. /bin/sh ../libtool --mode=install /bin/install -c SOAPdenovo-63mer SOAPdenov o-127mer '/home/gc001/programs/MaSuRCA-3.2.2_RC1/bin'
  313. libtool: install: /bin/install -c SOAPdenovo-63mer /home/gc001/programs/MaSuRCA- 3.2.2_RC1/bin/SOAPdenovo-63mer
  314. libtool: install: /bin/install -c SOAPdenovo-127mer /home/gc001/programs/MaSuRCA -3.2.2_RC1/bin/SOAPdenovo-127mer
  315. make[2]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/SOAP denovo2'
  316. make[1]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/SOAP denovo2'
  317. Making install in PacBio pwd /home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1
  318. make[1]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/Pac Bio'
  319. make install-am
  320. make[2]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/Pac Bio'
  321. CXX src_jf_aligner/jf_aligner.o
  322. CXX src_jf_aligner/pb_aligner.o
  323. In file included from src_jf_aligner/jf_aligner.cc:8:0:
  324. ./src_jf_aligner/superread_parser.hpp:8:33: fatal error: jellyfish/mer_dna.hpp: No such file or directory
  325. #include <jellyfish/mer_dna.hpp>
  326. ^
  327. compilation terminated.
  328. In file included from ./src_jf_aligner/pb_aligner.hpp:12:0,
  329. from src_jf_aligner/pb_aligner.cc:8:
  330. ./src_jf_aligner/jf_aligner.hpp:14:33: fatal error: jellyfish/mer_dna.hpp: No su ch file or directory
  331. #include <jellyfish/mer_dna.hpp>
  332. ^
  333. compilation terminated.
  334. make[2]: *** [src_jf_aligner/jf_aligner.o] Error 1
  335. make[2]: *** Waiting for unfinished jobs....
  336. make[2]: *** [src_jf_aligner/pb_aligner.o] Error 1
  337. make[2]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/PacB io'
  338. make[1]: *** [install] Error 2
  339. make[1]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/PacB io'
  340. Making install in MUMmer pwd /home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1
  341. make[1]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/MUM mer'
  342. make install-am
  343. make[2]: Entering directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/MUM mer'
  344. CXX swig/perl5/swig_perl5_mummer_la-swig_wrap.lo
  345. CXXLD show-diff
  346. swig/perl5/swig_wrap.cpp:743:20: fatal error: EXTERN.h: No such file or director y
  347. #include "EXTERN.h"
  348. ^
  349. compilation terminated.
  350. make[2]: *** [swig/perl5/swig_perl5_mummer_la-swig_wrap.lo] Error 1
  351. make[2]: *** Waiting for unfinished jobs....
  352. make[2]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/MUMm er'
  353. make[1]: *** [install] Error 2
  354. make[1]: Leaving directory `/home/gc001/programs/MaSuRCA-3.2.2_RC1/global-1/MUMm er'
  355. make: *** [install-special] Error 2
Add Comment
Please, Sign In to add comment
Public Pastes
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!