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pacaur_neuron_install

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  1. :: Checking neuron integrity...
  2. ==> Making package: neuron 7.4-1 (Thu Jun  9 23:12:50 CDT 2016)
  3. ==> Retrieving sources...
  4.   -> Found nrn-7.4.tar.gz
  5. ==> Validating source files with md5sums...
  6.     nrn-7.4.tar.gz ... Passed
  7. :: Building neuron package(s)...
  8. ==> Making package: neuron 7.4-1 (Thu Jun  9 23:12:51 CDT 2016)
  9. ==> Checking runtime dependencies...
  10. ==> Checking buildtime dependencies...
  11. ==> Retrieving sources...
  12.   -> Found nrn-7.4.tar.gz
  13. ==> Validating source files with md5sums...
  14.     nrn-7.4.tar.gz ... Passed
  15. ==> Extracting sources...
  16.   -> Extracting nrn-7.4.tar.gz with bsdtar
  17. ==> Removing existing $pkgdir/ directory...
  18. ==> Starting build()...
  19. checking for a BSD-compatible install... /usr/bin/install -c
  20. checking whether build environment is sane... yes
  21. checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
  22. checking for gawk... gawk
  23. checking whether make sets $(MAKE)... yes
  24. checking whether make supports nested variables... yes
  25. checking build system type... x86_64-unknown-linux-gnu
  26. checking host system type... x86_64-unknown-linux-gnu
  27. CYGWIN=no
  28. MINGW=no
  29. checking for style of include used by make... GNU
  30. checking for g++... g++
  31. checking whether the C++ compiler works... yes
  32. checking for C++ compiler default output file name... a.out
  33. checking for suffix of executables...
  34. checking whether we are cross compiling... no
  35. checking for suffix of object files... o
  36. checking whether we are using the GNU C++ compiler... yes
  37. checking whether g++ accepts -g... yes
  38. checking dependency style of g++... gcc3
  39. Not trying to build rpms for your system (use --enable-rpm-rules to override)
  40. checking for gcc... gcc
  41. checking whether we are using the GNU C compiler... yes
  42. checking whether gcc accepts -g... yes
  43. checking for gcc option to accept ISO C89... none needed
  44. checking whether gcc understands -c and -o together... yes
  45. checking dependency style of gcc... gcc3
  46. checking how to run the C preprocessor... gcc -E
  47. checking for gawk... (cached) gawk
  48. checking for flex... flex
  49. checking lex output file root... lex.yy
  50. checking lex library... -lfl
  51. checking whether yytext is a pointer... yes
  52. checking for bison... bison -y
  53. checking whether ln -s works... yes
  54. checking for cos in -lm... yes
  55. Python binary found (/home/dan/.pyenv/shims/python)
  56. checking nrnpython configuration... get_python_version()  '3.5'
  57. sys.version_info[0]  '3'
  58. get_python_inc(0)  '/usr/include/python3.5m'
  59. get_config_var('LIBS')  '-lpthread -ldl  -lutil'
  60. get_config_var('LIBRARY')  'libpython3.5m.a'
  61. get_config_var('LIBDIR')  '/usr/lib'
  62. get_config_var('LIBS')  '-lpthread -ldl  -lutil'
  63. checking if python include files and libraries work... yes
  64. checking for python... python
  65. checking for cython... no
  66. checking for cython... cython
  67. checking for mpicc... mpicc
  68. checking for MPI_Init... yes
  69. checking for mpi.h... yes
  70. checking for mpic++... mpic++
  71. checking for mpi.h... yes
  72. checking how to print strings... printf
  73. checking for a sed that does not truncate output... /usr/bin/sed
  74. checking for grep that handles long lines and -e... /usr/bin/grep
  75. checking for egrep... /usr/bin/grep -E
  76. checking for fgrep... /usr/bin/grep -F
  77. checking for ld used by mpicc... /usr/lib/hardening-wrapper/bin/ld
  78. checking if the linker (/usr/lib/hardening-wrapper/bin/ld) is GNU ld... yes
  79. checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
  80. checking the name lister (/usr/bin/nm -B) interface... BSD nm
  81. checking the maximum length of command line arguments... 1572864
  82. checking whether the shell understands some XSI constructs... yes
  83. checking whether the shell understands "+="... yes
  84. checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
  85. checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
  86. checking for /usr/lib/hardening-wrapper/bin/ld option to reload object files... -r
  87. checking for objdump... objdump
  88. checking how to recognize dependent libraries... pass_all
  89. checking for dlltool... no
  90. checking how to associate runtime and link libraries... printf %s\n
  91. checking for ar... ar
  92. checking for archiver @FILE support... @
  93. checking for strip... strip
  94. checking for ranlib... ranlib
  95. checking command to parse /usr/bin/nm -B output from mpicc object... ok
  96. checking for sysroot... no
  97. checking for mt... no
  98. checking if : is a manifest tool... no
  99. checking for ANSI C header files... yes
  100. checking for sys/types.h... yes
  101. checking for sys/stat.h... yes
  102. checking for stdlib.h... yes
  103. checking for string.h... yes
  104. checking for memory.h... yes
  105. checking for strings.h... yes
  106. checking for inttypes.h... yes
  107. checking for stdint.h... yes
  108. checking for unistd.h... yes
  109. checking for dlfcn.h... yes
  110. checking for objdir... .libs
  111. checking if mpicc supports -fno-rtti -fno-exceptions... no
  112. checking for mpicc option to produce PIC... -fPIC -DPIC
  113. checking if mpicc PIC flag -fPIC -DPIC works... yes
  114. checking if mpicc static flag -static works... no
  115. checking if mpicc supports -c -o file.o... yes
  116. checking if mpicc supports -c -o file.o... (cached) yes
  117. checking whether the mpicc linker (/usr/lib/hardening-wrapper/bin/ld -m elf_x86_64) supports shared libraries... yes
  118. checking whether -lc should be explicitly linked in... no
  119. checking dynamic linker characteristics... GNU/Linux ld.so
  120. checking how to hardcode library paths into programs... immediate
  121. checking for shl_load... no
  122. checking for shl_load in -ldld... no
  123. checking for dlopen... no
  124. checking for dlopen in -ldl... yes
  125. checking whether a program can dlopen itself... yes
  126. checking whether a statically linked program can dlopen itself... yes
  127. checking whether stripping libraries is possible... yes
  128. checking if libtool supports shared libraries... yes
  129. checking whether to build shared libraries... yes
  130. checking whether to build static libraries... no
  131. checking how to run the C++ preprocessor... mpic++ -E
  132. checking for ld used by mpic++... /usr/lib/hardening-wrapper/bin/ld -m elf_x86_64
  133. checking if the linker (/usr/lib/hardening-wrapper/bin/ld -m elf_x86_64) is GNU ld... yes
  134. checking whether the mpic++ linker (/usr/lib/hardening-wrapper/bin/ld -m elf_x86_64) supports shared libraries... yes
  135. checking for mpic++ option to produce PIC... -fPIC -DPIC
  136. checking if mpic++ PIC flag -fPIC -DPIC works... yes
  137. checking if mpic++ static flag -static works... no
  138. checking if mpic++ supports -c -o file.o... yes
  139. checking if mpic++ supports -c -o file.o... (cached) yes
  140. checking whether the mpic++ linker (/usr/lib/hardening-wrapper/bin/ld -m elf_x86_64) supports shared libraries... yes
  141. checking dynamic linker characteristics... (cached) GNU/Linux ld.so
  142. checking how to hardcode library paths into programs... immediate
  143. configure: Use the NRNMECH_DLL_STYLE for "special"
  144. checking for tgetent in -lncurses... yes
  145. checking which library has the termcap functions... using libncurses
  146. checking checking compilation with -lreadline... ok
  147. Do not compile neosim specific code.
  148. Not building the nrnjava interface
  149. checking for X... libraries , headers
  150. checking for gethostbyname... yes
  151. checking for connect... yes
  152. checking for remove... yes
  153. checking for shmat... yes
  154. checking for IceConnectionNumber in -lICE... yes
  155. checking for dirent.h that defines DIR... yes
  156. checking for library containing opendir... none required
  157. checking for ANSI C header files... (cached) yes
  158. checking for sys/wait.h that is POSIX.1 compatible... yes
  159. checking fcntl.h usability... yes
  160. checking fcntl.h presence... yes
  161. checking for fcntl.h... yes
  162. checking limits.h usability... yes
  163. checking limits.h presence... yes
  164. checking for limits.h... yes
  165. checking malloc.h usability... yes
  166. checking malloc.h presence... yes
  167. checking for malloc.h... yes
  168. checking sgtty.h usability... yes
  169. checking sgtty.h presence... yes
  170. checking for sgtty.h... yes
  171. checking for strings.h... (cached) yes
  172. checking sys/file.h usability... yes
  173. checking sys/file.h presence... yes
  174. checking for sys/file.h... yes
  175. checking sys/ioctl.h usability... yes
  176. checking sys/ioctl.h presence... yes
  177. checking for sys/ioctl.h... yes
  178. checking sys/time.h usability... yes
  179. checking sys/time.h presence... yes
  180. checking for sys/time.h... yes
  181. checking termio.h usability... yes
  182. checking termio.h presence... yes
  183. checking for termio.h... yes
  184. checking for unistd.h... (cached) yes
  185. checking stdarg.h usability... yes
  186. checking stdarg.h presence... yes
  187. checking for stdarg.h... yes
  188. checking varargs.h usability... no
  189. checking varargs.h presence... no
  190. checking for varargs.h... no
  191. checking stropts.h usability... yes
  192. checking stropts.h presence... yes
  193. checking for stropts.h... yes
  194. checking sys/conf.h usability... no
  195. checking sys/conf.h presence... no
  196. checking for sys/conf.h... no
  197. checking locale.h usability... yes
  198. checking locale.h presence... yes
  199. checking for locale.h... yes
  200. checking fenv.h usability... yes
  201. checking fenv.h presence... yes
  202. checking for fenv.h... yes
  203. checking pthread.h usability... yes
  204. checking pthread.h presence... yes
  205. checking for pthread.h... yes
  206. configure: Using pthreads.
  207. checking for the pthreads library -lpthreads... no
  208. checking whether pthreads work without any flags... yes
  209. checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
  210. checking if more special flags are required for pthreads... no
  211. configure: successful.
  212. PTHREAD_LIBS=
  213. PTHREAD_CFLAGS=
  214. PTHREAD_CC=mpicc
  215. checking float.h usability... yes
  216. checking float.h presence... yes
  217. checking for float.h... yes
  218. checking math.h usability... yes
  219. checking math.h presence... yes
  220. checking for math.h... yes
  221. checking stream.h usability... no
  222. checking stream.h presence... no
  223. checking for stream.h... no
  224. checking for off_t... yes
  225. checking for pid_t... yes
  226. checking for size_t... yes
  227. checking for int64_t... yes
  228. checking whether byte ordering is bigendian... no
  229. checking whether time.h and sys/time.h may both be included... yes
  230. checking whether struct tm is in sys/time.h or time.h... time.h
  231. checking for working alloca.h... yes
  232. checking for alloca... yes
  233. checking for working memcmp... yes
  234. checking return type of signal handlers... void
  235. checking for vprintf... yes
  236. checking for _doprnt... no
  237. checking for ftime... yes
  238. checking for getcwd... yes
  239. checking for getpw... yes
  240. checking for gethostname... yes
  241. checking for gettimeofday... yes
  242. checking for mkdir... yes
  243. checking for putenv... yes
  244. checking for setenv... yes
  245. checking for select... yes
  246. checking for strdup... yes
  247. checking for strstr... yes
  248. checking for index... yes
  249. checking for bzero... yes
  250. checking for bcopy... yes
  251. checking for stty... no
  252. checking for lockf... yes
  253. checking for isatty... yes
  254. checking for mkstemp... yes
  255. checking for setitimer... yes
  256. checking for sigaction... yes
  257. checking for fesetround... yes
  258. checking for posix_memalign... yes
  259. checking for mallinfo... yes
  260. checking if SIGBUS defined in signal.h... yes
  261. checking if SIGSEGV defined in signal.h... yes
  262. checking whether we are using the GNU C++ compiler... (cached) yes
  263. checking whether mpic++ accepts -g... (cached) yes
  264. checking dependency style of mpic++... (cached) gcc3
  265. checking _G_config.h usability... yes
  266. checking _G_config.h presence... yes
  267. checking for _G_config.h... yes
  268. checking whether the compiler implements namespaces... yes
  269. checking whether the compiler has stringstream... yes
  270. Looking for InterViews in the usual places--
  271.  not in  
  272. Assuming InterViews in a standard? place.
  273. checking compilation with interviews... failed
  274. I can't compile and/or link an interviews program.  If InterViews is not
  275. installed in /usr or /usr/local or /usr/local/iv,
  276. specify the proper location of the interviews tree using
  277.  
  278.     configure --with-iv=/where/you/put/iv
  279.  
  280. The interviews headers should be in subdirectories of
  281. /where/you/put/iv/include, and the libraries should be in
  282. /where/you/put/iv/lib or /where/you/put/iv/x86_64/lib
  283. (not in /where/you/put/iv/lib/ALPHA or
  284. /where/you/put/iv/lib/LINUX or some other subdirectory of lib).
  285.  
  286. If you don't want interviews, but do want nrniv built with the non-gui
  287. c++ classes then specify configure --without-iv.
  288. ==> ERROR: A failure occurred in build().
  289.     Aborting...
  290. :: failed to build neuron package(s)
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