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16-coot.txt

erpannec
May 19th, 2020
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  1. ./build-it: line 3877: exported: command not found
  2. From tar file: /home/erwinp/autobuild/building/sources/coot-0.9.tar.gz
  3. building in: /home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9
  4. CFLAGS:
  5. CXXFLAGS: -g -O
  6. CPPFLAGS:
  7. LDFLAGS:
  8. PATH: /home/erwinp/autobuild/Linux-cn1200-gtk2-python/bin:/home/erwinp/autobuild/Linux-cn1200-gtk2-python/bin:/home/erwinp/autobuild/Linux-cn1200-pre-release-gtk2/bin:/mnt/d/WSL/usr/local/bin/phenix-1.17.1-3660/build/bin:/usr/local/bin/CCP4/ccp4-7.0/etc:/usr/local/bin/CCP4/ccp4-7.0/bin:/home/erwinp/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files (x86)/Intel/iCLS Client/:/mnt/c/Program Files/Intel/iCLS Client/:/mnt/c/Program Files (x86)/Common Files/ArcSoft/Bin:/mnt/c/ProgramData/Oracle/Java/javapath:/mnt/c/Program Files/PHP/v5.3:/mnt/c/Program Files/Common Files/Microsoft Shared/Windows Live:/mnt/c/Program Files (x86)/Common Files/Microsoft Shared/Windows Live:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0/:/mnt/c/Program Files (x86)/ATI Technologies/ATI.ACE/Core-Static:/mnt/c/Program Files (x86)/Windows Live/Shared:/mnt/c/Program Files/Dell/Dell Data Protection/TSS/bin/:/mnt/c/CCP4/6.4/bin:/mnt/c/adb/platform-tools-latest-windows/platform-tools:/mnt/c/UNICORN/Dll:/mnt/c/Program Files/cURL/bin:/mnt/c/Program Files (x86)/Microsoft SQL Server/100/Tools/Binn/:/mnt/c/Program Files/Microsoft SQL Server/100/Tools/Binn/:/mnt/c/Program Files/Microsoft SQL Server/100/DTS/Binn/:/mnt/c/Windows/system32/tools:/mnt/c/Program Files (x86)/WinSCP/:/mnt/c/Program Files (x86)/pscp/:/mnt/c/Program Files/PyMOL:/mnt/c/Program Files/PyMOL/Scripts:/mnt/c/Program Files/PuTTY/:/mnt/c/Windows/System32/OpenSSH/:/mnt/d/atsas/bin:/mnt/c/Windows/System32/cmd.exe:/mnt/d/Projects/LxRunOffline-v3.3.3:/mnt/c/Program Files (x86)/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Program Files/Intel/Intel(R) Management Engine Components/DAL:/mnt/c/Program Files (x86)/Intel/Intel(R) Management Engine Components/IPT:/mnt/c/Program Files/Intel/Intel(R) Management Engine Components/IPT:/mnt/c/Program Files (x86)/GnuWin32/bin:/mnt/c/Users/Erwin Pannecoucke/AppData/Local/Programs/Python/Launcher/:/mnt/c/Users/Erwin Pannecoucke/AppData/Local/Microsoft/WindowsApps:/usr/local/bin/XDS:/usr/local/bin/XDS_tools:/snap/bin:/usr/local/bin/XDS:/usr/local/bin/XDS_tools:/usr/local/bin:/usr/sbin:/usr/bsd:/sbin:/usr/bin:/bin::/etc:/usr/etc
  9. using this guile:
  10. /home/erwinp/autobuild/Linux-cn1200-gtk2-python/bin/guile
  11. ./configure --prefix=/home/erwinp/autobuild/Linux-cn1200-gtk2-python --with-fftw-prefix=/home/erwinp/autobuild/Linux-cn1200-gtk2-python --with-goocanvas-prefix=/home/erwinp/autobuild/Linux-cn1200-gtk2-python --with-glut-prefix=/home/erwinp/autobuild/Linux-cn1200-gtk2-python COOT_BUILD_INFO_STRING= --with-guile --with-guile-gtk --with-guile-gtk-prefix=/home/erwinp/autobuild/Linux-cn1200-gtk2-python --with-python --with-pygtk --disable-shared
  12. checking for a BSD-compatible install... /usr/bin/install -c
  13. checking whether build environment is sane... yes
  14. checking for a thread-safe mkdir -p... /bin/mkdir -p
  15. checking for gawk... gawk
  16. checking whether make sets $(MAKE)... yes
  17. checking whether make supports nested variables... yes
  18. checking for style of include used by make... GNU
  19. checking for gcc... gcc
  20. checking whether the C compiler works... yes
  21. checking for C compiler default output file name... a.out
  22. checking for suffix of executables...
  23. checking whether we are cross compiling... no
  24. checking for suffix of object files... o
  25. checking whether we are using the GNU C compiler... yes
  26. checking whether gcc accepts -g... yes
  27. checking for gcc option to accept ISO C89... none needed
  28. checking dependency style of gcc... gcc3
  29. checking for library containing strerror... none required
  30. checking for gcc... (cached) gcc
  31. checking whether we are using the GNU C compiler... (cached) yes
  32. checking whether gcc accepts -g... (cached) yes
  33. checking for gcc option to accept ISO C89... (cached) none needed
  34. checking dependency style of gcc... (cached) gcc3
  35. checking how to run the C preprocessor... gcc -E
  36. checking for grep that handles long lines and -e... /bin/grep
  37. checking for egrep... /bin/grep -E
  38. checking for ANSI C header files... yes
  39. checking for g++... g++
  40. checking whether we are using the GNU C++ compiler... yes
  41. checking whether g++ accepts -g... yes
  42. checking dependency style of g++... gcc3
  43. checking build system type... x86_64-unknown-linux-gnu
  44. checking host system type... x86_64-unknown-linux-gnu
  45. checking how to print strings... printf
  46. checking for a sed that does not truncate output... /bin/sed
  47. checking for fgrep... /bin/grep -F
  48. checking for ld used by gcc... /usr/bin/ld
  49. checking if the linker (/usr/bin/ld) is GNU ld... yes
  50. checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
  51. checking the name lister (/usr/bin/nm -B) interface... BSD nm
  52. checking whether ln -s works... yes
  53. checking the maximum length of command line arguments... 1572864
  54. checking whether the shell understands some XSI constructs... yes
  55. checking whether the shell understands "+="... yes
  56. checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
  57. checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
  58. checking for /usr/bin/ld option to reload object files... -r
  59. checking for objdump... objdump
  60. checking how to recognize dependent libraries... pass_all
  61. checking for dlltool... no
  62. checking how to associate runtime and link libraries... printf %s\n
  63. checking for ar... ar
  64. checking for archiver @FILE support... @
  65. checking for strip... strip
  66. checking for ranlib... ranlib
  67. checking command to parse /usr/bin/nm -B output from gcc object... ok
  68. checking for sysroot... no
  69. checking for mt... mt
  70. checking if mt is a manifest tool... no
  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... yes
  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 (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
  89. checking dynamic linker characteristics... GNU/Linux ld.so
  90. checking how to hardcode library paths into programs... immediate
  91. checking whether stripping libraries is possible... yes
  92. checking if libtool supports shared libraries... yes
  93. checking whether to build shared libraries... no
  94. checking whether to build static libraries... yes
  95. checking how to run the C++ preprocessor... g++ -E
  96. checking for ld used by g++... /usr/bin/ld -m elf_x86_64
  97. checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
  98. checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
  99. checking for g++ option to produce PIC... -fPIC -DPIC
  100. checking if g++ PIC flag -fPIC -DPIC works... yes
  101. checking if g++ static flag -static works... yes
  102. checking if g++ supports -c -o file.o... yes
  103. checking if g++ supports -c -o file.o... (cached) yes
  104. checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
  105. checking dynamic linker characteristics... (cached) GNU/Linux ld.so
  106. checking how to hardcode library paths into programs... immediate
  107. checking which libtool initialization strategy to adopt... AC-PROG-LIBTOOL
  108. checking what warning flags to pass to the C compiler... -Wall -Wunused
  109. checking what language compliance flags to pass to the C compiler...
  110. checking what warning flags to pass to the C++ compiler... -Wall -Wno-unused
  111. checking what language compliance flags to pass to the C++ compiler...
  112. checking sys/stdtypes.h usability... no
  113. checking sys/stdtypes.h presence... no
  114. checking for sys/stdtypes.h... no
  115. checking for OpenMP flag of C compiler... -fopenmp
  116. checking for pkg-config... /usr/bin/pkg-config
  117. checking pkg-config is at least version 0.9.0... yes
  118. checking for GLIB... yes
  119. checking if this is MINGW on Windows... no
  120. checking for LIBPNG... yes
  121. checking for CAIRO... yes
  122. checking for SQLite3... no
  123. checking for mmdb2... yes
  124. checking for ssm... yes
  125. no
  126. checking for non-prefixed single-precision FFTW2 (fftw.h)... yes
  127. checking for Clipper... yes
  128. Congratulations, you are using Guile
  129. checking for guile... /home/erwinp/autobuild/Linux-cn1200-gtk2-python/bin/guile
  130. checking for guile-config... /home/erwinp/autobuild/Linux-cn1200-gtk2-python/bin/guile-config
  131. checking for guile-tools... /home/erwinp/autobuild/Linux-cn1200-gtk2-python/bin/guile-tools
  132. checking libguile compile flags... -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -P -pthread
  133. checking libguile link flags... -P -pthread -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lguile -lltdl -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lgmp -lcrypt -lm -lltdl
  134. checking for Guile-Lib... yes
  135. checking for guile-gui... yes
  136. checking GUILE_VERSION: 1.8
  137. checking for gsl-config... /home/erwinp/autobuild/Linux-cn1200-gtk2-python/bin/gsl-config
  138. checking for GSL - version >= 1.3... yes
  139. checking for GTK... yes
  140. checking for GNOME_CANVAS... yes
  141. checking for pkg-config... /usr/bin/pkg-config
  142. checking for GtkGLExt - version >= 1.0.0... yes (version 1.2.0)
  143. checking for glLineWidth in -lGL... yes
  144. checking for GLUT... yes
  145. checking for Python... checking Python.h usability... yes
  146. checking Python.h presence... yes
  147. checking for Python.h... yes
  148. Cool, using Python
  149. checking for PYGTK... yes
  150. Good we have pygtk
  151. checking for python version... 2.7
  152. checking for python platform... linux2
  153. checking for python script directory... ${prefix}/lib/python2.7/site-packages
  154. checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages
  155. checking for guile-gtk... /home/erwinp/autobuild/Linux-cn1200-gtk2-python
  156. checking for boostlib >=  (102000)... yes
  157. checking for python2.7... /home/erwinp/autobuild/Linux-cn1200-gtk2-python/bin/python2.7
  158. checking for a version of Python >= '2.1.0'... yes
  159. checking for the distutils Python package... yes
  160. checking for Python include path... -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include/python2.7
  161. checking for Python library path... -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lpython2.7
  162. checking for Python site-packages path... /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/python2.7/site-packages
  163. checking python extra libraries... -lpthread -ldl  -lutil -lm
  164. checking python extra linking flags... -Xlinker -export-dynamic
  165. checking consistency of all components of python development environment... yes
  166. checking whether the Boost::Python library is available... yes
  167. checking whether boost_python is the correct library... yes
  168. checking for Goocanvas... yes
  169. Not using MySQL database
  170. checking for curl >= 7.9.7... 7.65.3
  171. checking build type... Linux-x86_64-ubuntu-18.04.4-python-gtk2
  172. checking that generated files are newer than configure... done
  173. configure: creating ./config.status
  174. config.status: creating Makefile
  175. config.status: creating macros/Makefile
  176. config.status: creating pdb-templates/Makefile
  177. config.status: creating scheme/Makefile
  178. config.status: creating python/Makefile
  179. config.status: creating compat/Makefile
  180. config.status: creating utils/Makefile
  181. config.status: creating coot-utils/Makefile
  182. config.status: creating protein_db/Makefile
  183. config.status: creating ccp4mg-utils/Makefile
  184. config.status: creating coords/Makefile
  185. config.status: creating db-main/Makefile
  186. config.status: creating density-contour/Makefile
  187. config.status: creating surface/Makefile
  188. config.status: creating coot-surface/Makefile
  189. config.status: creating angles/Makefile
  190. config.status: creating mini-mol/Makefile
  191. config.status: creating skeleton/Makefile
  192. config.status: creating ligand/Makefile
  193. config.status: creating geometry/Makefile
  194. config.status: creating ideal/Makefile
  195. config.status: creating build/Makefile
  196. config.status: creating analysis/Makefile
  197. config.status: creating high-res/Makefile
  198. config.status: creating tw/Makefile
  199. config.status: creating cootaneer/Makefile
  200. config.status: creating cootilus/Makefile
  201. config.status: creating greg-tests/Makefile
  202. config.status: creating python-tests/Makefile
  203. config.status: creating lidia-core/Makefile
  204. config.status: creating libgtkgraph/Makefile
  205. config.status: creating goograph/Makefile
  206. config.status: creating lbg/Makefile
  207. config.status: creating doc/Makefile
  208. config.status: creating src/Makefile
  209. config.status: creating src/coot
  210. config.status: creating python/coot_load_modules.py
  211. config.status: creating data/Makefile
  212. config.status: creating data/rama-coeffs/Makefile
  213. config.status: creating data/metal/Makefile
  214. config.status: creating data/cho-models/Makefile
  215. config.status: creating data/cho-acedrg/Makefile
  216. config.status: creating pixmaps/Makefile
  217. config.status: creating pixmaps/icons/Makefile
  218. config.status: creating rama-data/Makefile
  219. config.status: creating man/Makefile
  220. config.status: creating pli/Makefile
  221. config.status: creating fonts/Makefile
  222. config.status: creating pyrogen/Makefile
  223. config.status: creating pyrogen/pyrogen
  224. config.status: creating auxil/Makefile
  225. config.status: creating auxil/catcheck/Makefile
  226. config.status: creating auxil/rama/Makefile
  227. config.status: creating auxil/sec-str/Makefile
  228. config.status: creating auxil/strand-analysis/Makefile
  229. config.status: creating auxil/vectors/Makefile
  230. config.status: creating rcrane/Makefile
  231. config.status: executing depfiles commands
  232. config.status: executing libtool commands
  233. Making all in auxil
  234. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil'
  235. Making all in catcheck
  236. make[2]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil/catcheck'
  237. make[2]: Nothing to be done for 'all'.
  238. make[2]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil/catcheck'
  239. Making all in rama
  240. make[2]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil/rama'
  241. make[2]: Nothing to be done for 'all'.
  242. make[2]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil/rama'
  243. Making all in sec-str
  244. make[2]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil/sec-str'
  245. make[2]: Nothing to be done for 'all'.
  246. make[2]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil/sec-str'
  247. Making all in strand-analysis
  248. make[2]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil/strand-analysis'
  249. make[2]: Nothing to be done for 'all'.
  250. make[2]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil/strand-analysis'
  251. Making all in vectors
  252. make[2]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil/vectors'
  253. make[2]: Nothing to be done for 'all'.
  254. make[2]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil/vectors'
  255. make[2]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil'
  256. make[2]: Nothing to be done for 'all-am'.
  257. make[2]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil'
  258. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/auxil'
  259. Making all in scheme
  260. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/scheme'
  261. make[1]: Nothing to be done for 'all'.
  262. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/scheme'
  263. Making all in python
  264. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/python'
  265. make[1]: Nothing to be done for 'all'.
  266. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/python'
  267. Making all in pdb-templates
  268. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/pdb-templates'
  269. make[1]: Nothing to be done for 'all'.
  270. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/pdb-templates'
  271. Making all in macros
  272. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/macros'
  273. make[1]: Nothing to be done for 'all'.
  274. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/macros'
  275. Making all in compat
  276. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/compat'
  277. /bin/bash ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.   -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O2 -Wall -Wunused  -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c -o getopt.lo getopt.c
  278. /bin/bash ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.   -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O2 -Wall -Wunused  -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c -o getopt1.lo getopt1.c
  279. libtool: compile:  gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O2 -Wall -Wunused -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -o getopt.o
  280. libtool: compile:  gcc -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O2 -Wall -Wunused -MT getopt1.lo -MD -MP -MF .deps/getopt1.Tpo -c getopt1.c -o getopt1.o
  281. mv -f .deps/getopt1.Tpo .deps/getopt1.Plo
  282. mv -f .deps/getopt.Tpo .deps/getopt.Plo
  283. /bin/bash ../libtool  --tag=CC   --mode=link gcc  -g -O2 -Wall -Wunused    -o libcoot-compat.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib getopt.lo getopt1.lo  
  284. libtool: link: ar cru .libs/libcoot-compat.a  getopt.o getopt1.o
  285. ar: `u' modifier ignored since `D' is the default (see `U')
  286. libtool: link: ranlib .libs/libcoot-compat.a
  287. libtool: link: ( cd ".libs" && rm -f "libcoot-compat.la" && ln -s "../libcoot-compat.la" "libcoot-compat.la" )
  288. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/compat'
  289. Making all in utils
  290. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/utils'
  291. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c -o coot-utils.lo coot-utils.cc
  292. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-fasta.lo -MD -MP -MF .deps/coot-fasta.Tpo -c -o coot-fasta.lo coot-fasta.cc
  293. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT atomic-numbers.lo -MD -MP -MF .deps/atomic-numbers.Tpo -c -o atomic-numbers.lo atomic-numbers.cc
  294. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT gdk-keysyms.lo -MD -MP -MF .deps/gdk-keysyms.Tpo -c -o gdk-keysyms.lo gdk-keysyms.cc
  295. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT hsv-rgb.lo -MD -MP -MF .deps/hsv-rgb.Tpo -c -o hsv-rgb.lo hsv-rgb.cc
  296. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT dodec.lo -MD -MP -MF .deps/dodec.Tpo -c -o dodec.lo dodec.cc
  297. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT win-compat.lo -MD -MP -MF .deps/win-compat.Tpo -c -o win-compat.lo win-compat.cc
  298. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT threads.lo -MD -MP -MF .deps/threads.Tpo -c -o threads.lo threads.cc
  299. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT gdk-keysyms.lo -MD -MP -MF .deps/gdk-keysyms.Tpo -c gdk-keysyms.cc -o gdk-keysyms.o
  300. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-utils.lo -MD -MP -MF .deps/coot-utils.Tpo -c coot-utils.cc -o coot-utils.o
  301. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT dodec.lo -MD -MP -MF .deps/dodec.Tpo -c dodec.cc -o dodec.o
  302. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT threads.lo -MD -MP -MF .deps/threads.Tpo -c threads.cc -o threads.o
  303. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT atomic-numbers.lo -MD -MP -MF .deps/atomic-numbers.Tpo -c atomic-numbers.cc -o atomic-numbers.o
  304. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT hsv-rgb.lo -MD -MP -MF .deps/hsv-rgb.Tpo -c hsv-rgb.cc -o hsv-rgb.o
  305. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT win-compat.lo -MD -MP -MF .deps/win-compat.Tpo -c win-compat.cc -o win-compat.o
  306. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-fasta.lo -MD -MP -MF .deps/coot-fasta.Tpo -c coot-fasta.cc -o coot-fasta.o
  307. mv -f .deps/win-compat.Tpo .deps/win-compat.Plo
  308. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT align-utils.lo -MD -MP -MF .deps/align-utils.Tpo -c -o align-utils.lo align-utils.cc
  309. mv -f .deps/threads.Tpo .deps/threads.Plo
  310. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT pir-alignment.lo -MD -MP -MF .deps/pir-alignment.Tpo -c -o pir-alignment.lo pir-alignment.cc
  311. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT align-utils.lo -MD -MP -MF .deps/align-utils.Tpo -c align-utils.cc -o align-utils.o
  312. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT pir-alignment.lo -MD -MP -MF .deps/pir-alignment.Tpo -c pir-alignment.cc -o pir-alignment.o
  313. mv -f .deps/hsv-rgb.Tpo .deps/hsv-rgb.Plo
  314. mv -f .deps/atomic-numbers.Tpo .deps/atomic-numbers.Plo
  315. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT split-indices.lo -MD -MP -MF .deps/split-indices.Tpo -c -o split-indices.lo split-indices.cc
  316. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT radix.lo -MD -MP -MF .deps/radix.Tpo -c -o radix.lo radix.cc
  317. mv -f .deps/coot-fasta.Tpo .deps/coot-fasta.Plo
  318. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include    -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT logging.lo -MD -MP -MF .deps/logging.Tpo -c -o logging.lo logging.cc
  319. mv -f .deps/dodec.Tpo .deps/dodec.Plo
  320. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT split-indices.lo -MD -MP -MF .deps/split-indices.Tpo -c split-indices.cc -o split-indices.o
  321. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT radix.lo -MD -MP -MF .deps/radix.Tpo -c radix.cc -o radix.o
  322. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT logging.lo -MD -MP -MF .deps/logging.Tpo -c logging.cc -o logging.o
  323. mv -f .deps/align-utils.Tpo .deps/align-utils.Plo
  324. mv -f .deps/radix.Tpo .deps/radix.Plo
  325. mv -f .deps/coot-utils.Tpo .deps/coot-utils.Plo
  326. mv -f .deps/pir-alignment.Tpo .deps/pir-alignment.Plo
  327. mv -f .deps/logging.Tpo .deps/logging.Plo
  328. mv -f .deps/split-indices.Tpo .deps/split-indices.Plo
  329. mv -f .deps/gdk-keysyms.Tpo .deps/gdk-keysyms.Plo
  330. /bin/bash ../libtool  --tag=CXX   --mode=link g++   -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused    -o libcoot-utils.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib coot-utils.lo coot-fasta.lo atomic-numbers.lo gdk-keysyms.lo hsv-rgb.lo dodec.lo win-compat.lo threads.lo align-utils.lo pir-alignment.lo split-indices.lo radix.lo logging.lo  
  331. libtool: link: ar cru .libs/libcoot-utils.a  coot-utils.o coot-fasta.o atomic-numbers.o gdk-keysyms.o hsv-rgb.o dodec.o win-compat.o threads.o align-utils.o pir-alignment.o split-indices.o radix.o logging.o
  332. ar: `u' modifier ignored since `D' is the default (see `U')
  333. libtool: link: ranlib .libs/libcoot-utils.a
  334. libtool: link: ( cd ".libs" && rm -f "libcoot-utils.la" && ln -s "../libcoot-utils.la" "libcoot-utils.la" )
  335. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/utils'
  336. Making all in protein_db
  337. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/protein_db'
  338. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT protein_db.lo -MD -MP -MF .deps/protein_db.Tpo -c -o protein_db.lo protein_db.cpp
  339. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT protein_db_utils.lo -MD -MP -MF .deps/protein_db_utils.Tpo -c -o protein_db_utils.lo protein_db_utils.cpp
  340. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT rna_db.lo -MD -MP -MF .deps/rna_db.Tpo -c -o rna_db.lo rna_db.cpp
  341. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT rna_db.lo -MD -MP -MF .deps/rna_db.Tpo -c rna_db.cpp -o rna_db.o
  342. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT protein_db.lo -MD -MP -MF .deps/protein_db.Tpo -c protein_db.cpp -o protein_db.o
  343. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT protein_db_utils.lo -MD -MP -MF .deps/protein_db_utils.Tpo -c protein_db_utils.cpp -o protein_db_utils.o
  344. mv -f .deps/rna_db.Tpo .deps/rna_db.Plo
  345. mv -f .deps/protein_db_utils.Tpo .deps/protein_db_utils.Plo
  346. mv -f .deps/protein_db.Tpo .deps/protein_db.Plo
  347. /bin/bash ../libtool  --tag=CXX   --mode=link g++  -g -O -Wall -Wno-unused    -o libcoot-protein-db.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib protein_db.lo protein_db_utils.lo rna_db.lo -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lmmdb2
  348. libtool: link: ar cru .libs/libcoot-protein-db.a  protein_db.o protein_db_utils.o rna_db.o
  349. ar: `u' modifier ignored since `D' is the default (see `U')
  350. libtool: link: ranlib .libs/libcoot-protein-db.a
  351. libtool: link: ( cd ".libs" && rm -f "libcoot-protein-db.la" && ln -s "../libcoot-protein-db.la" "libcoot-protein-db.la" )
  352. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/protein_db'
  353. Making all in mini-mol
  354. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/mini-mol'
  355. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c -o mini-mol.lo mini-mol.cc
  356. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c -o mini-mol-utils.lo mini-mol-utils.cc
  357. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c -o atom-quads.lo atom-quads.cc
  358. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT mini-mol.lo -MD -MP -MF .deps/mini-mol.Tpo -c mini-mol.cc -o mini-mol.o
  359. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT atom-quads.lo -MD -MP -MF .deps/atom-quads.Tpo -c atom-quads.cc -o atom-quads.o
  360. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT mini-mol-utils.lo -MD -MP -MF .deps/mini-mol-utils.Tpo -c mini-mol-utils.cc -o mini-mol-utils.o
  361. mv -f .deps/mini-mol-utils.Tpo .deps/mini-mol-utils.Plo
  362. mv -f .deps/atom-quads.Tpo .deps/atom-quads.Plo
  363. mv -f .deps/mini-mol.Tpo .deps/mini-mol.Plo
  364. /bin/bash ../libtool  --tag=CXX   --mode=link g++  -g -O -Wall -Wno-unused    -o libcoot-mini-mol.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib mini-mol.lo mini-mol-utils.lo atom-quads.lo ../utils/libcoot-utils.la -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lmmdb2 -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2  
  365. libtool: link: ar cru .libs/libcoot-mini-mol.a  mini-mol.o mini-mol-utils.o atom-quads.o
  366. ar: `u' modifier ignored since `D' is the default (see `U')
  367. libtool: link: ranlib .libs/libcoot-mini-mol.a
  368. libtool: link: ( cd ".libs" && rm -f "libcoot-mini-mol.la" && ln -s "../libcoot-mini-mol.la" "libcoot-mini-mol.la" )
  369. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/mini-mol'
  370. Making all in geometry
  371. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/geometry'
  372. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT protein-geometry.lo -MD -MP -MF .deps/protein-geometry.Tpo -c -o protein-geometry.lo protein-geometry.cc
  373. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT protein-geometry-mmdb.lo -MD -MP -MF .deps/protein-geometry-mmdb.Tpo -c -o protein-geometry-mmdb.lo protein-geometry-mmdb.cc
  374. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT read-sbase.lo -MD -MP -MF .deps/read-sbase.Tpo -c -o read-sbase.lo read-sbase.cc
  375. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT energy-lib.lo -MD -MP -MF .deps/energy-lib.Tpo -c -o energy-lib.lo energy-lib.cc
  376. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT mol-utils.lo -MD -MP -MF .deps/mol-utils.Tpo -c -o mol-utils.lo mol-utils.cc
  377. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT chem_mods.lo -MD -MP -MF .deps/chem_mods.Tpo -c -o chem_mods.lo chem_mods.cc
  378. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT srs-interface.lo -MD -MP -MF .deps/srs-interface.Tpo -c -o srs-interface.lo srs-interface.cc
  379. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT protein-donor-acceptors.lo -MD -MP -MF .deps/protein-donor-acceptors.Tpo -c -o protein-donor-acceptors.lo protein-donor-acceptors.cc
  380. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT protein-geometry.lo -MD -MP -MF .deps/protein-geometry.Tpo -c protein-geometry.cc -o protein-geometry.o
  381. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT energy-lib.lo -MD -MP -MF .deps/energy-lib.Tpo -c energy-lib.cc -o energy-lib.o
  382. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT mol-utils.lo -MD -MP -MF .deps/mol-utils.Tpo -c mol-utils.cc -o mol-utils.o
  383. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT protein-geometry-mmdb.lo -MD -MP -MF .deps/protein-geometry-mmdb.Tpo -c protein-geometry-mmdb.cc -o protein-geometry-mmdb.o
  384. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT read-sbase.lo -MD -MP -MF .deps/read-sbase.Tpo -c read-sbase.cc -o read-sbase.o
  385. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT chem_mods.lo -MD -MP -MF .deps/chem_mods.Tpo -c chem_mods.cc -o chem_mods.o
  386. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT protein-donor-acceptors.lo -MD -MP -MF .deps/protein-donor-acceptors.Tpo -c protein-donor-acceptors.cc -o protein-donor-acceptors.o
  387. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT srs-interface.lo -MD -MP -MF .deps/srs-interface.Tpo -c srs-interface.cc -o srs-interface.o
  388. mv -f .deps/srs-interface.Tpo .deps/srs-interface.Plo
  389. mv -f .deps/mol-utils.Tpo .deps/mol-utils.Plo
  390. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT lbg-graph.lo -MD -MP -MF .deps/lbg-graph.Tpo -c -o lbg-graph.lo lbg-graph.cc
  391. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT dreiding.lo -MD -MP -MF .deps/dreiding.Tpo -c -o dreiding.lo dreiding.cc
  392. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT lbg-graph.lo -MD -MP -MF .deps/lbg-graph.Tpo -c lbg-graph.cc -o lbg-graph.o
  393. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT dreiding.lo -MD -MP -MF .deps/dreiding.Tpo -c dreiding.cc -o dreiding.o
  394. mv -f .deps/read-sbase.Tpo .deps/read-sbase.Plo
  395. mv -f .deps/protein-donor-acceptors.Tpo .deps/protein-donor-acceptors.Plo
  396. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT dict-utils.lo -MD -MP -MF .deps/dict-utils.Tpo -c -o dict-utils.lo dict-utils.cc
  397. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT cif-parse.lo -MD -MP -MF .deps/cif-parse.Tpo -c -o cif-parse.lo cif-parse.cc
  398. mv -f .deps/protein-geometry-mmdb.Tpo .deps/protein-geometry-mmdb.Plo
  399. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT main-chain.lo -MD -MP -MF .deps/main-chain.Tpo -c -o main-chain.lo main-chain.cc
  400. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT dict-utils.lo -MD -MP -MF .deps/dict-utils.Tpo -c dict-utils.cc -o dict-utils.o
  401. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT cif-parse.lo -MD -MP -MF .deps/cif-parse.Tpo -c cif-parse.cc -o cif-parse.o
  402. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT main-chain.lo -MD -MP -MF .deps/main-chain.Tpo -c main-chain.cc -o main-chain.o
  403. mv -f .deps/lbg-graph.Tpo .deps/lbg-graph.Plo
  404. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT residue-and-atom-specs.lo -MD -MP -MF .deps/residue-and-atom-specs.Tpo -c -o residue-and-atom-specs.lo residue-and-atom-specs.cc
  405. mv -f .deps/main-chain.Tpo .deps/main-chain.Plo
  406. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT mol-utils-2.lo -MD -MP -MF .deps/mol-utils-2.Tpo -c -o mol-utils-2.lo mol-utils-2.cc
  407. mv -f .deps/dreiding.Tpo .deps/dreiding.Plo
  408. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT residue-and-atom-specs.lo -MD -MP -MF .deps/residue-and-atom-specs.Tpo -c residue-and-atom-specs.cc -o residue-and-atom-specs.o
  409. g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT compare-dictionaries.o -MD -MP -MF .deps/compare-dictionaries.Tpo -c -o compare-dictionaries.o compare-dictionaries.cc
  410. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT mol-utils-2.lo -MD -MP -MF .deps/mol-utils-2.Tpo -c mol-utils-2.cc -o mol-utils-2.o
  411. mv -f .deps/energy-lib.Tpo .deps/energy-lib.Plo
  412. g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT make-shelx-restraints.o -MD -MP -MF .deps/make-shelx-restraints.Tpo -c -o make-shelx-restraints.o make-shelx-restraints.cc
  413. mv -f .deps/mol-utils-2.Tpo .deps/mol-utils-2.Plo
  414. mv -f .deps/chem_mods.Tpo .deps/chem_mods.Plo
  415. g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused  -MT available-comp-id.o -MD -MP -MF .deps/available-comp-id.Tpo -c -o available-comp-id.o available-comp-id.cc
  416. mv -f .deps/residue-and-atom-specs.Tpo .deps/residue-and-atom-specs.Plo
  417. mv -f .deps/available-comp-id.Tpo .deps/available-comp-id.Po
  418. mv -f .deps/compare-dictionaries.Tpo .deps/compare-dictionaries.Po
  419. mv -f .deps/make-shelx-restraints.Tpo .deps/make-shelx-restraints.Po
  420. mv -f .deps/dict-utils.Tpo .deps/dict-utils.Plo
  421. mv -f .deps/cif-parse.Tpo .deps/cif-parse.Plo
  422. mv -f .deps/protein-geometry.Tpo .deps/protein-geometry.Plo
  423. /bin/bash ../libtool  --tag=CXX   --mode=link g++ -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused    -o libcoot-geometry.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib protein-geometry.lo protein-geometry-mmdb.lo read-sbase.lo energy-lib.lo mol-utils.lo chem_mods.lo srs-interface.lo protein-donor-acceptors.lo lbg-graph.lo dreiding.lo dict-utils.lo cif-parse.lo main-chain.lo residue-and-atom-specs.lo mol-utils-2.lo ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2  -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lmmdb2
  424. libtool: link: ar cru .libs/libcoot-geometry.a  protein-geometry.o protein-geometry-mmdb.o read-sbase.o energy-lib.o mol-utils.o chem_mods.o srs-interface.o protein-donor-acceptors.o lbg-graph.o dreiding.o dict-utils.o cif-parse.o main-chain.o residue-and-atom-specs.o mol-utils-2.o
  425. ar: `u' modifier ignored since `D' is the default (see `U')
  426. libtool: link: ranlib .libs/libcoot-geometry.a
  427. libtool: link: ( cd ".libs" && rm -f "libcoot-geometry.la" && ln -s "../libcoot-geometry.la" "libcoot-geometry.la" )
  428. /bin/bash ../libtool  --tag=CXX   --mode=link g++ -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused    -o coot-compare-dictionaries compare-dictionaries.o ./libcoot-geometry.la ../utils/libcoot-utils.la ../compat/libcoot-compat.la -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lmmdb2
  429. /bin/bash ../libtool  --tag=CXX   --mode=link g++ -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused    -o coot-make-shelx-restraints make-shelx-restraints.o ./libcoot-geometry.la ../utils/libcoot-utils.la -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2
  430. /bin/bash ../libtool  --tag=CXX   --mode=link g++ -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"'  -g -O -Wall -Wno-unused    -o coot-available-comp-id available-comp-id.o ./libcoot-geometry.la  
  431. libtool: link: g++ -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -o coot-available-comp-id available-comp-id.o  ./.libs/libcoot-geometry.a -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -L=/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib:-L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib: /home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/mini-mol/.libs/libcoot-mini-mol.a /home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/utils/.libs/libcoot-utils.a /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-ccp4.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-cif.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-minimol.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-mmdb.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-cns.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-phs.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-contrib.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-core.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/librfftw.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libfftw.so -lm -lpthread /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libccp4c.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libmmdb2.so -Wl,-rpath -Wl,/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -Wl,-rpath -Wl,/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib
  432. libtool: link: g++ -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -o coot-compare-dictionaries compare-dictionaries.o  ./.libs/libcoot-geometry.a -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -L=/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib:-L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib: /home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/mini-mol/.libs/libcoot-mini-mol.a /home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/utils/.libs/libcoot-utils.a /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-ccp4.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-cif.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-minimol.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-mmdb.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-cns.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-phs.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-contrib.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-core.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/librfftw.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libfftw.so -lm -lpthread /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libccp4c.so ../utils/.libs/libcoot-utils.a ../compat/.libs/libcoot-compat.a /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libmmdb2.so -Wl,-rpath -Wl,/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -Wl,-rpath -Wl,/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib
  433. libtool: link: g++ -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -o coot-make-shelx-restraints make-shelx-restraints.o  ./.libs/libcoot-geometry.a -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -L=/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib:-L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib: /home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/mini-mol/.libs/libcoot-mini-mol.a /home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/utils/.libs/libcoot-utils.a ../utils/.libs/libcoot-utils.a /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-ccp4.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-cif.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-minimol.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-mmdb.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-cns.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-phs.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-contrib.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-core.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/librfftw.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libfftw.so -lm -lpthread /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libccp4c.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libmmdb2.so -Wl,-rpath -Wl,/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -Wl,-rpath -Wl,/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib
  434. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/geometry'
  435. Making all in lidia-core
  436. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/lidia-core'
  437. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..   -I/usr/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT lbg-shared.lo -MD -MP -MF .deps/lbg-shared.Tpo -c -o lbg-shared.lo lbg-shared.cc
  438. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..   -I/usr/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT lbg-molfile.lo -MD -MP -MF .deps/lbg-molfile.Tpo -c -o lbg-molfile.lo lbg-molfile.cc
  439. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..   -I/usr/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT lig-build.lo -MD -MP -MF .deps/lig-build.Tpo -c -o lig-build.lo lig-build.cc
  440. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..   -I/usr/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT rdkit-interface.lo -MD -MP -MF .deps/rdkit-interface.Tpo -c -o rdkit-interface.lo rdkit-interface.cc
  441. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..   -I/usr/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT cod-types.lo -MD -MP -MF .deps/cod-types.Tpo -c -o cod-types.lo cod-types.cc
  442. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..   -I/usr/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT bond-record-container-t.lo -MD -MP -MF .deps/bond-record-container-t.Tpo -c -o bond-record-container-t.lo bond-record-container-t.cc
  443. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..   -I/usr/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT cod-atom-type-t.lo -MD -MP -MF .deps/cod-atom-type-t.Tpo -c -o cod-atom-type-t.lo cod-atom-type-t.cc
  444. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..   -I/usr/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT cod-atom-types.lo -MD -MP -MF .deps/cod-atom-types.Tpo -c -o cod-atom-types.lo cod-atom-types.cc
  445. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT lbg-shared.lo -MD -MP -MF .deps/lbg-shared.Tpo -c lbg-shared.cc -o lbg-shared.o
  446. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT lbg-molfile.lo -MD -MP -MF .deps/lbg-molfile.Tpo -c lbg-molfile.cc -o lbg-molfile.o
  447. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT lig-build.lo -MD -MP -MF .deps/lig-build.Tpo -c lig-build.cc -o lig-build.o
  448. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT bond-record-container-t.lo -MD -MP -MF .deps/bond-record-container-t.Tpo -c bond-record-container-t.cc -o bond-record-container-t.o
  449. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT rdkit-interface.lo -MD -MP -MF .deps/rdkit-interface.Tpo -c rdkit-interface.cc -o rdkit-interface.o
  450. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT cod-types.lo -MD -MP -MF .deps/cod-types.Tpo -c cod-types.cc -o cod-types.o
  451. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT cod-atom-type-t.lo -MD -MP -MF .deps/cod-atom-type-t.Tpo -c cod-atom-type-t.cc -o cod-atom-type-t.o
  452. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT cod-atom-types.lo -MD -MP -MF .deps/cod-atom-types.Tpo -c cod-atom-types.cc -o cod-atom-types.o
  453. mv -f .deps/bond-record-container-t.Tpo .deps/bond-record-container-t.Plo
  454. mv -f .deps/cod-atom-type-t.Tpo .deps/cod-atom-type-t.Plo
  455. mv -f .deps/cod-types.Tpo .deps/cod-types.Plo
  456. mv -f .deps/rdkit-interface.Tpo .deps/rdkit-interface.Plo
  457. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..   -I/usr/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT bond-table-record-t.lo -MD -MP -MF .deps/bond-table-record-t.Tpo -c -o bond-table-record-t.lo bond-table-record-t.cc
  458. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..   -I/usr/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT chemical-feature-clusters.lo -MD -MP -MF .deps/chemical-feature-clusters.Tpo -c -o chemical-feature-clusters.lo chemical-feature-clusters.cc
  459. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..   -I/usr/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT atom-types.lo -MD -MP -MF .deps/atom-types.Tpo -c -o atom-types.lo atom-types.cc
  460. mv -f .deps/cod-atom-types.Tpo .deps/cod-atom-types.Plo
  461. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..   -I/usr/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT get-residue.lo -MD -MP -MF .deps/get-residue.Tpo -c -o get-residue.lo get-residue.cc
  462. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT bond-table-record-t.lo -MD -MP -MF .deps/bond-table-record-t.Tpo -c bond-table-record-t.cc -o bond-table-record-t.o
  463. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT atom-types.lo -MD -MP -MF .deps/atom-types.Tpo -c atom-types.cc -o atom-types.o
  464. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT chemical-feature-clusters.lo -MD -MP -MF .deps/chemical-feature-clusters.Tpo -c chemical-feature-clusters.cc -o chemical-feature-clusters.o
  465. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/usr/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT get-residue.lo -MD -MP -MF .deps/get-residue.Tpo -c get-residue.cc -o get-residue.o
  466. mv -f .deps/lbg-shared.Tpo .deps/lbg-shared.Plo
  467. mv -f .deps/bond-table-record-t.Tpo .deps/bond-table-record-t.Plo
  468. mv -f .deps/chemical-feature-clusters.Tpo .deps/chemical-feature-clusters.Plo
  469. mv -f .deps/atom-types.Tpo .deps/atom-types.Plo
  470. mv -f .deps/get-residue.Tpo .deps/get-residue.Plo
  471. mv -f .deps/lig-build.Tpo .deps/lig-build.Plo
  472. mv -f .deps/lbg-molfile.Tpo .deps/lbg-molfile.Plo
  473. /bin/bash ../libtool  --tag=CXX   --mode=link g++  -g -O -Wall -Wno-unused    -o libcoot-lidia-core.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib lbg-shared.lo lbg-molfile.lo lig-build.lo rdkit-interface.lo cod-types.lo bond-record-container-t.lo cod-atom-type-t.lo cod-atom-types.lo bond-table-record-t.lo chemical-feature-clusters.lo atom-types.lo get-residue.lo ../geometry/libcoot-geometry.la  
  474. libtool: link: ar cru .libs/libcoot-lidia-core.a  lbg-shared.o lbg-molfile.o lig-build.o rdkit-interface.o cod-types.o bond-record-container-t.o cod-atom-type-t.o cod-atom-types.o bond-table-record-t.o chemical-feature-clusters.o atom-types.o get-residue.o
  475. ar: `u' modifier ignored since `D' is the default (see `U')
  476. libtool: link: ranlib .libs/libcoot-lidia-core.a
  477. libtool: link: ( cd ".libs" && rm -f "libcoot-lidia-core.la" && ln -s "../libcoot-lidia-core.la" "libcoot-lidia-core.la" )
  478. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/lidia-core'
  479. Making all in coot-utils
  480. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/coot-utils'
  481. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-coord-utils.lo -MD -MP -MF .deps/coot-coord-utils.Tpo -c -o coot-coord-utils.lo coot-coord-utils.cc
  482. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-coord-utils-nucleotides.lo -MD -MP -MF .deps/coot-coord-utils-nucleotides.Tpo -c -o coot-coord-utils-nucleotides.lo coot-coord-utils-nucleotides.cc
  483. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-rama.lo -MD -MP -MF .deps/coot-rama.Tpo -c -o coot-rama.lo coot-rama.cc
  484. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-h-bonds.lo -MD -MP -MF .deps/coot-h-bonds.Tpo -c -o coot-h-bonds.lo coot-h-bonds.cc
  485. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT hole.lo -MD -MP -MF .deps/hole.Tpo -c -o hole.lo hole.cc
  486. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT read-sm-cif.lo -MD -MP -MF .deps/read-sm-cif.Tpo -c -o read-sm-cif.lo read-sm-cif.cc
  487. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT bonded-pairs.lo -MD -MP -MF .deps/bonded-pairs.Tpo -c -o bonded-pairs.lo bonded-pairs.cc
  488. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT helix-analysis.lo -MD -MP -MF .deps/helix-analysis.Tpo -c -o helix-analysis.lo helix-analysis.cc
  489. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-rama.lo -MD -MP -MF .deps/coot-rama.Tpo -c coot-rama.cc -o coot-rama.o
  490. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT hole.lo -MD -MP -MF .deps/hole.Tpo -c hole.cc -o hole.o
  491. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-h-bonds.lo -MD -MP -MF .deps/coot-h-bonds.Tpo -c coot-h-bonds.cc -o coot-h-bonds.o
  492. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT bonded-pairs.lo -MD -MP -MF .deps/bonded-pairs.Tpo -c bonded-pairs.cc -o bonded-pairs.o
  493. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT read-sm-cif.lo -MD -MP -MF .deps/read-sm-cif.Tpo -c read-sm-cif.cc -o read-sm-cif.o
  494. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-coord-utils-nucleotides.lo -MD -MP -MF .deps/coot-coord-utils-nucleotides.Tpo -c coot-coord-utils-nucleotides.cc -o coot-coord-utils-nucleotides.o
  495. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-coord-utils.lo -MD -MP -MF .deps/coot-coord-utils.Tpo -c coot-coord-utils.cc -o coot-coord-utils.o
  496. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT helix-analysis.lo -MD -MP -MF .deps/helix-analysis.Tpo -c helix-analysis.cc -o helix-analysis.o
  497. mv -f .deps/helix-analysis.Tpo .deps/helix-analysis.Plo
  498. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT elastic.lo -MD -MP -MF .deps/elastic.Tpo -c -o elastic.lo elastic.cc
  499. mv -f .deps/coot-rama.Tpo .deps/coot-rama.Plo
  500. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT glyco-torsions.lo -MD -MP -MF .deps/glyco-torsions.Tpo -c -o glyco-torsions.lo glyco-torsions.cc
  501. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT elastic.lo -MD -MP -MF .deps/elastic.Tpo -c elastic.cc -o elastic.o
  502. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT glyco-torsions.lo -MD -MP -MF .deps/glyco-torsions.Tpo -c glyco-torsions.cc -o glyco-torsions.o
  503. mv -f .deps/coot-coord-utils-nucleotides.Tpo .deps/coot-coord-utils-nucleotides.Plo
  504. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-least-squares.lo -MD -MP -MF .deps/coot-least-squares.Tpo -c -o coot-least-squares.lo coot-least-squares.cc
  505. mv -f .deps/elastic.Tpo .deps/elastic.Plo
  506. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT atom-overlaps.lo -MD -MP -MF .deps/atom-overlaps.Tpo -c -o atom-overlaps.lo atom-overlaps.cc
  507. mv -f .deps/bonded-pairs.Tpo .deps/bonded-pairs.Plo
  508. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-least-squares.lo -MD -MP -MF .deps/coot-least-squares.Tpo -c coot-least-squares.cc -o coot-least-squares.o
  509. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT reduce.lo -MD -MP -MF .deps/reduce.Tpo -c -o reduce.lo reduce.cc
  510. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT atom-overlaps.lo -MD -MP -MF .deps/atom-overlaps.Tpo -c atom-overlaps.cc -o atom-overlaps.o
  511. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT reduce.lo -MD -MP -MF .deps/reduce.Tpo -c reduce.cc -o reduce.o
  512. mv -f .deps/coot-least-squares.Tpo .deps/coot-least-squares.Plo
  513. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT atom-selection-container.lo -MD -MP -MF .deps/atom-selection-container.Tpo -c -o atom-selection-container.lo atom-selection-container.cc
  514. mv -f .deps/hole.Tpo .deps/hole.Plo
  515. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT contact-info.lo -MD -MP -MF .deps/contact-info.Tpo -c -o contact-info.lo contact-info.cc
  516. mv -f .deps/read-sm-cif.Tpo .deps/read-sm-cif.Plo
  517. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-shelx-ins.lo -MD -MP -MF .deps/coot-shelx-ins.Tpo -c -o coot-shelx-ins.lo coot-shelx-ins.cc
  518. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT atom-selection-container.lo -MD -MP -MF .deps/atom-selection-container.Tpo -c atom-selection-container.cc -o atom-selection-container.o
  519. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT contact-info.lo -MD -MP -MF .deps/contact-info.Tpo -c contact-info.cc -o contact-info.o
  520. mv -f .deps/coot-h-bonds.Tpo .deps/coot-h-bonds.Plo
  521. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-shelx-ins.lo -MD -MP -MF .deps/coot-shelx-ins.Tpo -c coot-shelx-ins.cc -o coot-shelx-ins.o
  522. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT secondary-structure-headers.lo -MD -MP -MF .deps/secondary-structure-headers.Tpo -c -o secondary-structure-headers.lo secondary-structure-headers.cc
  523. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT secondary-structure-headers.lo -MD -MP -MF .deps/secondary-structure-headers.Tpo -c secondary-structure-headers.cc -o secondary-structure-headers.o
  524. mv -f .deps/glyco-torsions.Tpo .deps/glyco-torsions.Plo
  525. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT plane-utils.lo -MD -MP -MF .deps/plane-utils.Tpo -c -o plane-utils.lo plane-utils.cc
  526. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT plane-utils.lo -MD -MP -MF .deps/plane-utils.Tpo -c plane-utils.cc -o plane-utils.o
  527. mv -f .deps/secondary-structure-headers.Tpo .deps/secondary-structure-headers.Plo
  528. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT c-beta-deviations.lo -MD -MP -MF .deps/c-beta-deviations.Tpo -c -o c-beta-deviations.lo c-beta-deviations.cc
  529. mv -f .deps/atom-selection-container.Tpo .deps/atom-selection-container.Plo
  530. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT lidia-core-functions.lo -MD -MP -MF .deps/lidia-core-functions.Tpo -c -o lidia-core-functions.lo lidia-core-functions.cc
  531. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT c-beta-deviations.lo -MD -MP -MF .deps/c-beta-deviations.Tpo -c c-beta-deviations.cc -o c-beta-deviations.o
  532. mv -f .deps/plane-utils.Tpo .deps/plane-utils.Plo
  533. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT atom-tools.lo -MD -MP -MF .deps/atom-tools.Tpo -c -o atom-tools.lo atom-tools.cc
  534. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT lidia-core-functions.lo -MD -MP -MF .deps/lidia-core-functions.Tpo -c lidia-core-functions.cc -o lidia-core-functions.o
  535. mv -f .deps/lidia-core-functions.Tpo .deps/lidia-core-functions.Plo
  536. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT bonded-atoms.lo -MD -MP -MF .deps/bonded-atoms.Tpo -c -o bonded-atoms.lo bonded-atoms.cc
  537. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT atom-tools.lo -MD -MP -MF .deps/atom-tools.Tpo -c atom-tools.cc -o atom-tools.o
  538. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT bonded-atoms.lo -MD -MP -MF .deps/bonded-atoms.Tpo -c bonded-atoms.cc -o bonded-atoms.o
  539. mv -f .deps/coot-shelx-ins.Tpo .deps/coot-shelx-ins.Plo
  540. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT bricks.lo -MD -MP -MF .deps/bricks.Tpo -c -o bricks.lo bricks.cc
  541. mv -f .deps/c-beta-deviations.Tpo .deps/c-beta-deviations.Plo
  542. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT helix-like.lo -MD -MP -MF .deps/helix-like.Tpo -c -o helix-like.lo helix-like.cc
  543. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT bricks.lo -MD -MP -MF .deps/bricks.Tpo -c bricks.cc -o bricks.o
  544. mv -f .deps/contact-info.Tpo .deps/contact-info.Plo
  545. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT merge-atom-selections.lo -MD -MP -MF .deps/merge-atom-selections.Tpo -c -o merge-atom-selections.lo merge-atom-selections.cc
  546. mv -f .deps/reduce.Tpo .deps/reduce.Plo
  547. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT contacts-by-bricks.lo -MD -MP -MF .deps/contacts-by-bricks.Tpo -c -o contacts-by-bricks.lo contacts-by-bricks.cc
  548. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT helix-like.lo -MD -MP -MF .deps/helix-like.Tpo -c helix-like.cc -o helix-like.o
  549. mv -f .deps/bonded-atoms.Tpo .deps/bonded-atoms.Plo
  550. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT stack-and-pair.lo -MD -MP -MF .deps/stack-and-pair.Tpo -c -o stack-and-pair.lo stack-and-pair.cc
  551. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT merge-atom-selections.lo -MD -MP -MF .deps/merge-atom-selections.Tpo -c merge-atom-selections.cc -o merge-atom-selections.o
  552. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT contacts-by-bricks.lo -MD -MP -MF .deps/contacts-by-bricks.Tpo -c contacts-by-bricks.cc -o contacts-by-bricks.o
  553. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT stack-and-pair.lo -MD -MP -MF .deps/stack-and-pair.Tpo -c stack-and-pair.cc -o stack-and-pair.o
  554. mv -f .deps/atom-tools.Tpo .deps/atom-tools.Plo
  555. mv -f .deps/bricks.Tpo .deps/bricks.Plo
  556. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT fast-eigens.lo -MD -MP -MF .deps/fast-eigens.Tpo -c -o fast-eigens.lo fast-eigens.cc
  557. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT strand-fragments.lo -MD -MP -MF .deps/strand-fragments.Tpo -c -o strand-fragments.lo strand-fragments.cc
  558. mv -f .deps/helix-like.Tpo .deps/helix-like.Plo
  559. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT sfcalc-genmap.lo -MD -MP -MF .deps/sfcalc-genmap.Tpo -c -o sfcalc-genmap.lo sfcalc-genmap.cc
  560. mv -f .deps/atom-overlaps.Tpo .deps/atom-overlaps.Plo
  561. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT cablam-markup.lo -MD -MP -MF .deps/cablam-markup.Tpo -c -o cablam-markup.lo cablam-markup.cc
  562. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT strand-fragments.lo -MD -MP -MF .deps/strand-fragments.Tpo -c strand-fragments.cc -o strand-fragments.o
  563. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT fast-eigens.lo -MD -MP -MF .deps/fast-eigens.Tpo -c fast-eigens.cc -o fast-eigens.o
  564. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT sfcalc-genmap.lo -MD -MP -MF .deps/sfcalc-genmap.Tpo -c sfcalc-genmap.cc -o sfcalc-genmap.o
  565. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT cablam-markup.lo -MD -MP -MF .deps/cablam-markup.Tpo -c cablam-markup.cc -o cablam-markup.o
  566. mv -f .deps/contacts-by-bricks.Tpo .deps/contacts-by-bricks.Plo
  567. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot_shiftfield.lo -MD -MP -MF .deps/coot_shiftfield.Tpo -c -o coot_shiftfield.lo coot_shiftfield.cpp
  568. mv -f .deps/coot-coord-utils.Tpo .deps/coot-coord-utils.Plo
  569. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT shiftfield.lo -MD -MP -MF .deps/shiftfield.Tpo -c -o shiftfield.lo shiftfield.cpp
  570. mv -f .deps/fast-eigens.Tpo .deps/fast-eigens.Plo
  571. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT slurp-map.lo -MD -MP -MF .deps/slurp-map.Tpo -c -o slurp-map.lo slurp-map.cc
  572. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot_shiftfield.lo -MD -MP -MF .deps/coot_shiftfield.Tpo -c coot_shiftfield.cpp -o coot_shiftfield.o
  573. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT shiftfield.lo -MD -MP -MF .deps/shiftfield.Tpo -c shiftfield.cpp -o shiftfield.o
  574. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT slurp-map.lo -MD -MP -MF .deps/slurp-map.Tpo -c slurp-map.cc -o slurp-map.o
  575. mv -f .deps/strand-fragments.Tpo .deps/strand-fragments.Plo
  576. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-coord-extras.lo -MD -MP -MF .deps/coot-coord-extras.Tpo -c -o coot-coord-extras.lo coot-coord-extras.cc
  577. mv -f .deps/merge-atom-selections.Tpo .deps/merge-atom-selections.Plo
  578. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-coord-lsq.lo -MD -MP -MF .deps/coot-coord-lsq.Tpo -c -o coot-coord-lsq.lo coot-coord-lsq.cc
  579. In file included from /home/erwinp/autobuild/Linux-cn1200-gtk2-python/include/clipper/core/cell.h:50:0,
  580.                 from /home/erwinp/autobuild/Linux-cn1200-gtk2-python/include/clipper/core/coords.h:49,
  581.                 from /home/erwinp/autobuild/Linux-cn1200-gtk2-python/include/clipper/core/container.h:49,
  582.                 from /home/erwinp/autobuild/Linux-cn1200-gtk2-python/include/clipper/core/container_types.h:49,
  583.                 from /home/erwinp/autobuild/Linux-cn1200-gtk2-python/include/clipper/core/container_hkl.h:49,
  584.                 from /home/erwinp/autobuild/Linux-cn1200-gtk2-python/include/clipper/clipper.h:7,
  585.                 from shiftfield.h:8,
  586.                 from shiftfield.cpp:5:
  587. /home/erwinp/autobuild/Linux-cn1200-gtk2-python/include/clipper/core/clipper_types.h: In instantiation of 'std::vector<T> clipper::Matrix<T>::solve(const std::vector<T>&) const [with T = float]':
  588. shiftfield.cpp:139:18:   required from here
  589. /home/erwinp/autobuild/Linux-cn1200-gtk2-python/include/clipper/core/clipper_types.h:565:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  590.   if ( Array2d<T>::rows() != b.size() )
  591. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-coord-extras.lo -MD -MP -MF .deps/coot-coord-extras.Tpo -c coot-coord-extras.cc -o coot-coord-extras.o
  592. mv -f .deps/cablam-markup.Tpo .deps/cablam-markup.Plo
  593. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-coord-lsq.lo -MD -MP -MF .deps/coot-coord-lsq.Tpo -c coot-coord-lsq.cc -o coot-coord-lsq.o
  594. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-tree-extras.lo -MD -MP -MF .deps/coot-tree-extras.Tpo -c -o coot-tree-extras.lo coot-tree-extras.cc
  595. mv -f .deps/stack-and-pair.Tpo .deps/stack-and-pair.Plo
  596. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT water-coordination.lo -MD -MP -MF .deps/water-coordination.Tpo -c -o water-coordination.lo water-coordination.cc
  597. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-tree-extras.lo -MD -MP -MF .deps/coot-tree-extras.Tpo -c coot-tree-extras.cc -o coot-tree-extras.o
  598. mv -f .deps/sfcalc-genmap.Tpo .deps/sfcalc-genmap.Plo
  599. mv -f .deps/slurp-map.Tpo .deps/slurp-map.Plo
  600. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT lsq-improve.lo -MD -MP -MF .deps/lsq-improve.Tpo -c -o lsq-improve.lo lsq-improve.cc
  601. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-coord-utils-glyco.lo -MD -MP -MF .deps/coot-coord-utils-glyco.Tpo -c -o coot-coord-utils-glyco.lo coot-coord-utils-glyco.cc
  602. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT water-coordination.lo -MD -MP -MF .deps/water-coordination.Tpo -c water-coordination.cc -o water-coordination.o
  603. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT lsq-improve.lo -MD -MP -MF .deps/lsq-improve.Tpo -c lsq-improve.cc -o lsq-improve.o
  604. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-coord-utils-glyco.lo -MD -MP -MF .deps/coot-coord-utils-glyco.Tpo -c coot-coord-utils-glyco.cc -o coot-coord-utils-glyco.o
  605. mv -f .deps/coot_shiftfield.Tpo .deps/coot_shiftfield.Plo
  606. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT jed-flip.lo -MD -MP -MF .deps/jed-flip.Tpo -c -o jed-flip.lo jed-flip.cc
  607. mv -f .deps/coot-coord-lsq.Tpo .deps/coot-coord-lsq.Plo
  608. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-map-utils.lo -MD -MP -MF .deps/coot-map-utils.Tpo -c -o coot-map-utils.lo coot-map-utils.cc
  609. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT jed-flip.lo -MD -MP -MF .deps/jed-flip.Tpo -c jed-flip.cc -o jed-flip.o
  610. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-map-utils.lo -MD -MP -MF .deps/coot-map-utils.Tpo -c coot-map-utils.cc -o coot-map-utils.o
  611. mv -f .deps/water-coordination.Tpo .deps/water-coordination.Plo
  612. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT peak-search.lo -MD -MP -MF .deps/peak-search.Tpo -c -o peak-search.lo peak-search.cc
  613. mv -f .deps/shiftfield.Tpo .deps/shiftfield.Plo
  614. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT peak-search-from-list.lo -MD -MP -MF .deps/peak-search-from-list.Tpo -c -o peak-search-from-list.lo peak-search-from-list.cc
  615. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT peak-search.lo -MD -MP -MF .deps/peak-search.Tpo -c peak-search.cc -o peak-search.o
  616. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT peak-search-from-list.lo -MD -MP -MF .deps/peak-search-from-list.Tpo -c peak-search-from-list.cc -o peak-search-from-list.o
  617. mv -f .deps/lsq-improve.Tpo .deps/lsq-improve.Plo
  618. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT trim.lo -MD -MP -MF .deps/trim.Tpo -c -o trim.lo trim.cc
  619. mv -f .deps/peak-search-from-list.Tpo .deps/peak-search-from-list.Plo
  620. mv -f .deps/coot-tree-extras.Tpo .deps/coot-tree-extras.Plo
  621. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT xmap-stats.lo -MD -MP -MF .deps/xmap-stats.Tpo -c -o xmap-stats.lo xmap-stats.cc
  622. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT maps-spherical.lo -MD -MP -MF .deps/maps-spherical.Tpo -c -o maps-spherical.lo maps-spherical.cc
  623. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT trim.lo -MD -MP -MF .deps/trim.Tpo -c trim.cc -o trim.o
  624. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT xmap-stats.lo -MD -MP -MF .deps/xmap-stats.Tpo -c xmap-stats.cc -o xmap-stats.o
  625. mv -f .deps/jed-flip.Tpo .deps/jed-flip.Plo
  626. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-map-heavy.lo -MD -MP -MF .deps/coot-map-heavy.Tpo -c -o coot-map-heavy.lo coot-map-heavy.cc
  627. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT maps-spherical.lo -MD -MP -MF .deps/maps-spherical.Tpo -c maps-spherical.cc -o maps-spherical.o
  628. mv -f .deps/peak-search.Tpo .deps/peak-search.Plo
  629. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT coot-fffear.lo -MD -MP -MF .deps/coot-fffear.Tpo -c -o coot-fffear.lo coot-fffear.cc
  630. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-map-heavy.lo -MD -MP -MF .deps/coot-map-heavy.Tpo -c coot-map-heavy.cc -o coot-map-heavy.o
  631. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT coot-fffear.lo -MD -MP -MF .deps/coot-fffear.Tpo -c coot-fffear.cc -o coot-fffear.o
  632. mv -f .deps/trim.Tpo .deps/trim.Plo
  633. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT spherical-harmonics.lo -MD -MP -MF .deps/spherical-harmonics.Tpo -c -o spherical-harmonics.lo spherical-harmonics.cc
  634. mv -f .deps/xmap-stats.Tpo .deps/xmap-stats.Plo
  635. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I..  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE  -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused  -MT segmap.lo -MD -MP -MF .deps/segmap.Tpo -c -o segmap.lo segmap.cc
  636. mv -f .deps/coot-coord-extras.Tpo .deps/coot-coord-extras.Plo
  637. /bin/bash ../libtool  --tag=CXX   --mode=link g++ -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused    -o libcoot-coord-utils.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib coot-coord-utils.lo coot-coord-utils-nucleotides.lo coot-rama.lo coot-h-bonds.lo hole.lo read-sm-cif.lo bonded-pairs.lo helix-analysis.lo elastic.lo glyco-torsions.lo coot-least-squares.lo atom-overlaps.lo reduce.lo atom-selection-container.lo contact-info.lo coot-shelx-ins.lo secondary-structure-headers.lo plane-utils.lo c-beta-deviations.lo lidia-core-functions.lo atom-tools.lo bonded-atoms.lo bricks.lo helix-like.lo merge-atom-selections.lo contacts-by-bricks.lo stack-and-pair.lo fast-eigens.lo strand-fragments.lo sfcalc-genmap.lo cablam-markup.lo coot_shiftfield.lo shiftfield.lo slurp-map.lo ../lidia-core/libcoot-lidia-core.la ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lmmdb2 -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lgsl -lgslcblas -lm  -L/usr/lib/x86_64-linux-gnu  -lpython2.7 -lpthread -ldl -lutil -lm -Xlinker -export-dynamic -lutil
  638. mv -f .deps/coot-coord-utils-glyco.Tpo .deps/coot-coord-utils-glyco.Plo
  639. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT spherical-harmonics.lo -MD -MP -MF .deps/spherical-harmonics.Tpo -c spherical-harmonics.cc -o spherical-harmonics.o
  640. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DUSE_GUILE -DUSE_PYTHON -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -g -O -Wall -Wno-unused -MT segmap.lo -MD -MP -MF .deps/segmap.Tpo -c segmap.cc -o segmap.o
  641. mv -f .deps/spherical-harmonics.Tpo .deps/spherical-harmonics.Plo
  642. mv -f .deps/segmap.Tpo .deps/segmap.Plo
  643. mv -f .deps/maps-spherical.Tpo .deps/maps-spherical.Plo
  644. libtool: link: ar cru .libs/libcoot-coord-utils.a  coot-coord-utils.o coot-coord-utils-nucleotides.o coot-rama.o coot-h-bonds.o hole.o read-sm-cif.o bonded-pairs.o helix-analysis.o elastic.o glyco-torsions.o coot-least-squares.o atom-overlaps.o reduce.o atom-selection-container.o contact-info.o coot-shelx-ins.o secondary-structure-headers.o plane-utils.o c-beta-deviations.o lidia-core-functions.o atom-tools.o bonded-atoms.o bricks.o helix-like.o merge-atom-selections.o contacts-by-bricks.o stack-and-pair.o fast-eigens.o strand-fragments.o sfcalc-genmap.o cablam-markup.o coot_shiftfield.o shiftfield.o slurp-map.o
  645. ar: `u' modifier ignored since `D' is the default (see `U')
  646. mv -f .deps/coot-map-heavy.Tpo .deps/coot-map-heavy.Plo
  647. libtool: link: ranlib .libs/libcoot-coord-utils.a
  648. libtool: link: ( cd ".libs" && rm -f "libcoot-coord-utils.la" && ln -s "../libcoot-coord-utils.la" "libcoot-coord-utils.la" )
  649. /bin/bash ../libtool  --tag=CXX   --mode=link g++ -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused    -o libcoot-coord-extras.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib coot-coord-extras.lo coot-coord-lsq.lo coot-tree-extras.lo water-coordination.lo lsq-improve.lo coot-coord-utils-glyco.lo jed-flip.lo libcoot-coord-utils.la -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2
  650. mv -f .deps/coot-fffear.Tpo .deps/coot-fffear.Plo
  651. mv -f .deps/coot-map-utils.Tpo .deps/coot-map-utils.Plo
  652. /bin/bash ../libtool  --tag=CXX   --mode=link g++ -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused    -o libcoot-map-utils.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib coot-map-utils.lo peak-search.lo peak-search-from-list.lo trim.lo xmap-stats.lo maps-spherical.lo libcoot-coord-utils.la -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2
  653. libtool: link: ar cru .libs/libcoot-coord-extras.a  coot-coord-extras.o coot-coord-lsq.o coot-tree-extras.o water-coordination.o lsq-improve.o coot-coord-utils-glyco.o jed-flip.o
  654. ar: `u' modifier ignored since `D' is the default (see `U')
  655. libtool: link: ranlib .libs/libcoot-coord-extras.a
  656. libtool: link: ar cru .libs/libcoot-map-utils.a  coot-map-utils.o peak-search.o peak-search-from-list.o trim.o xmap-stats.o maps-spherical.o
  657. ar: `u' modifier ignored since `D' is the default (see `U')
  658. libtool: link: ( cd ".libs" && rm -f "libcoot-coord-extras.la" && ln -s "../libcoot-coord-extras.la" "libcoot-coord-extras.la" )
  659. libtool: link: ranlib .libs/libcoot-map-utils.a
  660. libtool: link: ( cd ".libs" && rm -f "libcoot-map-utils.la" && ln -s "../libcoot-map-utils.la" "libcoot-map-utils.la" )
  661. /bin/bash ../libtool  --tag=CXX   --mode=link g++ -DHAVE_GSL  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -g -O -Wall -Wno-unused    -o libcoot-map-heavy.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib coot-map-heavy.lo coot-fffear.lo spherical-harmonics.lo segmap.lo libcoot-map-utils.la libcoot-coord-utils.la -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lgsl -lgslcblas -lm
  662. libtool: link: ar cru .libs/libcoot-map-heavy.a  coot-map-heavy.o coot-fffear.o spherical-harmonics.o segmap.o
  663. ar: `u' modifier ignored since `D' is the default (see `U')
  664. libtool: link: ranlib .libs/libcoot-map-heavy.a
  665. libtool: link: ( cd ".libs" && rm -f "libcoot-map-heavy.la" && ln -s "../libcoot-map-heavy.la" "libcoot-map-heavy.la" )
  666. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/coot-utils'
  667. Making all in angles
  668. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/angles'
  669. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -g -O1 -g -O -Wall -Wno-unused  -MT libcoot_AngleInfo_la-AngleInfo.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo.Tpo -c -o libcoot_AngleInfo_la-AngleInfo.lo `test -f 'AngleInfo.cc' || echo './'`AngleInfo.cc
  670. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -g -O1 -g -O -Wall -Wno-unused  -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c -o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo `test -f 'AngleInfo-angle-torsions-autogen.cc' || echo './'`AngleInfo-angle-torsions-autogen.cc
  671. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -g -O1 -g -O -Wall -Wno-unused  -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c -o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo `test -f 'AngleInfo-theta_2-autogen.cc' || echo './'`AngleInfo-theta_2-autogen.cc
  672. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O1 -g -O -Wall -Wno-unused -MT libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo -c AngleInfo-theta_2-autogen.cc -o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o
  673. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O1 -g -O -Wall -Wno-unused -MT libcoot_AngleInfo_la-AngleInfo.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo.Tpo -c AngleInfo.cc -o libcoot_AngleInfo_la-AngleInfo.o
  674. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O1 -g -O -Wall -Wno-unused -MT libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo -MD -MP -MF .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo -c AngleInfo-angle-torsions-autogen.cc -o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o
  675. mv -f .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Tpo .deps/libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.Plo
  676. mv -f .deps/libcoot_AngleInfo_la-AngleInfo.Tpo .deps/libcoot_AngleInfo_la-AngleInfo.Plo
  677. mv -f .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Tpo .deps/libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.Plo
  678. /bin/bash ../libtool  --tag=CXX   --mode=link g++ -g -O1 -g -O -Wall -Wno-unused    -o libcoot-AngleInfo.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib libcoot_AngleInfo_la-AngleInfo.lo libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.lo libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.lo  
  679. libtool: link: ar cru .libs/libcoot-AngleInfo.a  libcoot_AngleInfo_la-AngleInfo.o libcoot_AngleInfo_la-AngleInfo-angle-torsions-autogen.o libcoot_AngleInfo_la-AngleInfo-theta_2-autogen.o
  680. ar: `u' modifier ignored since `D' is the default (see `U')
  681. libtool: link: ranlib .libs/libcoot-AngleInfo.a
  682. libtool: link: ( cd ".libs" && rm -f "libcoot-AngleInfo.la" && ln -s "../libcoot-AngleInfo.la" "libcoot-AngleInfo.la" )
  683. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/angles'
  684. Making all in ccp4mg-utils
  685. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/ccp4mg-utils'
  686. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/usr/include/libpng16 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c -o geomutil.lo geomutil.cc
  687. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/usr/include/libpng16 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c -o mgtree.lo mgtree.cc
  688. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/usr/include/libpng16 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c -o cartesian.lo cartesian.cc
  689. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/usr/include/libpng16 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c -o matrix.lo matrix.cc
  690. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/usr/include/libpng16 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c -o quat.lo quat.cc
  691. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/usr/include/libpng16 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c -o ppmutil.lo ppmutil.cc
  692. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/usr/include/libpng16 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT mgtree.lo -MD -MP -MF .deps/mgtree.Tpo -c mgtree.cc -o mgtree.o
  693. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/usr/include/libpng16 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT geomutil.lo -MD -MP -MF .deps/geomutil.Tpo -c geomutil.cc -o geomutil.o
  694. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/usr/include/libpng16 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.cc -o matrix.o
  695. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/usr/include/libpng16 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT quat.lo -MD -MP -MF .deps/quat.Tpo -c quat.cc -o quat.o
  696. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/usr/include/libpng16 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT ppmutil.lo -MD -MP -MF .deps/ppmutil.Tpo -c ppmutil.cc -o ppmutil.o
  697. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/usr/include/libpng16 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT cartesian.lo -MD -MP -MF .deps/cartesian.Tpo -c cartesian.cc -o cartesian.o
  698. mv -f .deps/quat.Tpo .deps/quat.Plo
  699. mv -f .deps/geomutil.Tpo .deps/geomutil.Plo
  700. mv -f .deps/cartesian.Tpo .deps/cartesian.Plo
  701. mv -f .deps/matrix.Tpo .deps/matrix.Plo
  702. mv -f .deps/ppmutil.Tpo .deps/ppmutil.Plo
  703. mv -f .deps/mgtree.Tpo .deps/mgtree.Plo
  704. /bin/bash ../libtool  --tag=CXX   --mode=link g++  -g -O -Wall -Wno-unused    -o libccp4mg-utils.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib geomutil.lo mgtree.lo cartesian.lo matrix.lo quat.lo ppmutil.lo -lpng16 -lz
  705. libtool: link: ar cru .libs/libccp4mg-utils.a  geomutil.o mgtree.o cartesian.o matrix.o quat.o ppmutil.o
  706. ar: `u' modifier ignored since `D' is the default (see `U')
  707. libtool: link: ranlib .libs/libccp4mg-utils.a
  708. libtool: link: ( cd ".libs" && rm -f "libccp4mg-utils.la" && ln -s "../libccp4mg-utils.la" "libccp4mg-utils.la" )
  709. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/ccp4mg-utils'
  710. Making all in db-main
  711. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/db-main'
  712. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -g -O -Wall -Wno-unused  -MT db-main.lo -MD -MP -MF .deps/db-main.Tpo -c -o db-main.lo db-main.cc
  713. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -g -O -Wall -Wno-unused  -MT db-strands.lo -MD -MP -MF .deps/db-strands.Tpo -c -o db-strands.lo db-strands.cc
  714. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -g -O -Wall -Wno-unused -MT db-main.lo -MD -MP -MF .deps/db-main.Tpo -c db-main.cc -o db-main.o
  715. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DPKGDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot\" -DDATADIR=\"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share\" -g -O -Wall -Wno-unused -MT db-strands.lo -MD -MP -MF .deps/db-strands.Tpo -c db-strands.cc -o db-strands.o
  716. mv -f .deps/db-strands.Tpo .deps/db-strands.Plo
  717. mv -f .deps/db-main.Tpo .deps/db-main.Plo
  718. /bin/bash ../libtool  --tag=CXX   --mode=link g++ -DPKGDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share/coot"' -DDATADIR='"/home/erwinp/autobuild/Linux-cn1200-gtk2-python/share"' -g -O -Wall -Wno-unused    -o libcoot-db-main.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib db-main.lo db-strands.lo ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../utils/libcoot-utils.la -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lmmdb2
  719. libtool: link: ar cru .libs/libcoot-db-main.a  db-main.o db-strands.o
  720. ar: `u' modifier ignored since `D' is the default (see `U')
  721. libtool: link: ranlib .libs/libcoot-db-main.a
  722. libtool: link: ( cd ".libs" && rm -f "libcoot-db-main.la" && ln -s "../libcoot-db-main.la" "libcoot-db-main.la" )
  723. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/db-main'
  724. Making all in analysis
  725. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/analysis'
  726. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT bfkurt.lo -MD -MP -MF .deps/bfkurt.Tpo -c -o bfkurt.lo bfkurt.cc
  727. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT mogul.lo -MD -MP -MF .deps/mogul.Tpo -c -o mogul.lo mogul.cc
  728. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT kolmogorov.lo -MD -MP -MF .deps/kolmogorov.Tpo -c -o kolmogorov.lo kolmogorov.cc
  729. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT stats.lo -MD -MP -MF .deps/stats.Tpo -c -o stats.lo stats.cc
  730. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT cablam.lo -MD -MP -MF .deps/cablam.Tpo -c -o cablam.lo cablam.cc
  731. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT typed-distances.lo -MD -MP -MF .deps/typed-distances.Tpo -c -o typed-distances.lo typed-distances.cc
  732. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT b-factor-histogram.lo -MD -MP -MF .deps/b-factor-histogram.Tpo -c -o b-factor-histogram.lo b-factor-histogram.cc
  733. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT daca.lo -MD -MP -MF .deps/daca.Tpo -c -o daca.lo daca.cc
  734. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT bfkurt.lo -MD -MP -MF .deps/bfkurt.Tpo -c bfkurt.cc -o bfkurt.o
  735. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT stats.lo -MD -MP -MF .deps/stats.Tpo -c stats.cc -o stats.o
  736. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT cablam.lo -MD -MP -MF .deps/cablam.Tpo -c cablam.cc -o cablam.o
  737. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT kolmogorov.lo -MD -MP -MF .deps/kolmogorov.Tpo -c kolmogorov.cc -o kolmogorov.o
  738. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT typed-distances.lo -MD -MP -MF .deps/typed-distances.Tpo -c typed-distances.cc -o typed-distances.o
  739. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT b-factor-histogram.lo -MD -MP -MF .deps/b-factor-histogram.Tpo -c b-factor-histogram.cc -o b-factor-histogram.o
  740. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT daca.lo -MD -MP -MF .deps/daca.Tpo -c daca.cc -o daca.o
  741. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT mogul.lo -MD -MP -MF .deps/mogul.Tpo -c mogul.cc -o mogul.o
  742. mv -f .deps/stats.Tpo .deps/stats.Plo
  743. g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT bfactan.o -MD -MP -MF .deps/bfactan.Tpo -c -o bfactan.o bfactan.cc
  744. mv -f .deps/kolmogorov.Tpo .deps/kolmogorov.Plo
  745. mv -f .deps/b-factor-histogram.Tpo .deps/b-factor-histogram.Plo
  746. mv -f .deps/cablam.Tpo .deps/cablam.Plo
  747. mv -f .deps/bfactan.Tpo .deps/bfactan.Po
  748. mv -f .deps/typed-distances.Tpo .deps/typed-distances.Plo
  749. mv -f .deps/bfkurt.Tpo .deps/bfkurt.Plo
  750. In file included from mogul.cc:31:0:
  751. mogul-interface.hh: In member function 'coot::mogul_item coot::mogul::parse_angle_line(const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&) const':
  752. mogul-interface.hh:32:10: warning: '<anonymous>.coot::mogul_item::idx_4' may be used uninitialized in this function [-Wmaybe-uninitialized]
  753.    class mogul_item {
  754.          ^~~~~~~~~~
  755. mogul-interface.hh:32:10: warning: '<anonymous>.coot::mogul_item::dmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
  756. mogul-interface.hh: In member function 'coot::mogul_item coot::mogul::parse_item_line(const std::vector<std::__cxx11::basic_string<char> >&, int) const':
  757. mogul-interface.hh:32:10: warning: '<anonymous>.coot::mogul_item::idx_3' may be used uninitialized in this function [-Wmaybe-uninitialized]
  758.    class mogul_item {
  759.          ^~~~~~~~~~
  760. mogul-interface.hh:32:10: warning: '<anonymous>.coot::mogul_item::idx_4' may be used uninitialized in this function [-Wmaybe-uninitialized]
  761. mogul-interface.hh:32:10: warning: '<anonymous>.coot::mogul_item::dmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
  762. mogul-interface.hh:32:10: warning: '<anonymous>.coot::mogul_item::idx_4' may be used uninitialized in this function [-Wmaybe-uninitialized]
  763.    class mogul_item {
  764.          ^~~~~~~~~~
  765. mogul-interface.hh:32:10: warning: '<anonymous>.coot::mogul_item::dmin' may be used uninitialized in this function [-Wmaybe-uninitialized]
  766. mogul-interface.hh:32:10: warning: '<anonymous>.coot::mogul_item::mean' may be used uninitialized in this function [-Wmaybe-uninitialized]
  767.    class mogul_item {
  768.          ^~~~~~~~~~
  769. mogul-interface.hh:32:10: warning: '<anonymous>.coot::mogul_item::median' may be used uninitialized in this function [-Wmaybe-uninitialized]
  770. mogul-interface.hh:32:10: warning: '<anonymous>.coot::mogul_item::std_dev' may be used uninitialized in this function [-Wmaybe-uninitialized]
  771. mogul-interface.hh:32:10: warning: '<anonymous>.coot::mogul_item::z' may be used uninitialized in this function [-Wmaybe-uninitialized]
  772. mv -f .deps/mogul.Tpo .deps/mogul.Plo
  773. mv -f .deps/daca.Tpo .deps/daca.Plo
  774. /bin/bash ../libtool  --tag=CXX   --mode=link g++  -g -O -Wall -Wno-unused    -o libcoot-analysis.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib bfkurt.lo mogul.lo kolmogorov.lo stats.lo cablam.lo typed-distances.lo b-factor-histogram.lo daca.lo ../coot-utils/libcoot-coord-utils.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lmmdb2 -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lgsl -lgslcblas -lm  
  775. libtool: link: ar cru .libs/libcoot-analysis.a  bfkurt.o mogul.o kolmogorov.o stats.o cablam.o typed-distances.o b-factor-histogram.o daca.o
  776. ar: `u' modifier ignored since `D' is the default (see `U')
  777. libtool: link: ranlib .libs/libcoot-analysis.a
  778. libtool: link: ( cd ".libs" && rm -f "libcoot-analysis.la" && ln -s "../libcoot-analysis.la" "libcoot-analysis.la" )
  779. /bin/bash ../libtool  --tag=CXX   --mode=link g++  -g -O -Wall -Wno-unused    -o coot-bfactan bfactan.o libcoot-analysis.la ../coot-utils/libcoot-coord-utils.la ../lidia-core/libcoot-lidia-core.la ../geometry/libcoot-geometry.la ../mini-mol/libcoot-mini-mol.la ../utils/libcoot-utils.la  -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2 -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lmmdb2
  780. libtool: link: g++ -g -O -Wall -Wno-unused -o coot-bfactan bfactan.o  ./.libs/libcoot-analysis.a -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -L=/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib:-L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib: /home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/coot-utils/.libs/libcoot-coord-utils.a ../coot-utils/.libs/libcoot-coord-utils.a /home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/lidia-core/.libs/libcoot-lidia-core.a /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libgsl.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libgslcblas.so -lpython2.7 -ldl -lutil ../lidia-core/.libs/libcoot-lidia-core.a /home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/geometry/.libs/libcoot-geometry.a ../geometry/.libs/libcoot-geometry.a /home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/mini-mol/.libs/libcoot-mini-mol.a ../mini-mol/.libs/libcoot-mini-mol.a /home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/utils/.libs/libcoot-utils.a ../utils/.libs/libcoot-utils.a /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-ccp4.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-cif.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-minimol.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-mmdb.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-cns.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-phs.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-contrib.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libclipper-core.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/librfftw.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libfftw.so -lm -lpthread /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libccp4c.so /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib/libmmdb2.so -Wl,-rpath -Wl,/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -Wl,-rpath -Wl,/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib
  781. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/analysis'
  782. Making all in cootaneer
  783. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/cootaneer'
  784. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT buccaneer-lib.lo -MD -MP -MF .deps/buccaneer-lib.Tpo -c -o buccaneer-lib.lo buccaneer-lib.cpp
  785. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT buccaneer-prot.lo -MD -MP -MF .deps/buccaneer-prot.Tpo -c -o buccaneer-prot.lo buccaneer-prot.cpp
  786. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT buccaneer-sequence.lo -MD -MP -MF .deps/buccaneer-sequence.Tpo -c -o buccaneer-sequence.lo buccaneer-sequence.cpp
  787. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include   -g -O -Wall -Wno-unused  -MT cootaneer-sequence.lo -MD -MP -MF .deps/cootaneer-sequence.Tpo -c -o cootaneer-sequence.lo cootaneer-sequence.cpp
  788. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT buccaneer-lib.lo -MD -MP -MF .deps/buccaneer-lib.Tpo -c buccaneer-lib.cpp -o buccaneer-lib.o
  789. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT buccaneer-prot.lo -MD -MP -MF .deps/buccaneer-prot.Tpo -c buccaneer-prot.cpp -o buccaneer-prot.o
  790. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT cootaneer-sequence.lo -MD -MP -MF .deps/cootaneer-sequence.Tpo -c cootaneer-sequence.cpp -o cootaneer-sequence.o
  791. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -g -O -Wall -Wno-unused -MT buccaneer-sequence.lo -MD -MP -MF .deps/buccaneer-sequence.Tpo -c buccaneer-sequence.cpp -o buccaneer-sequence.o
  792. mv -f .deps/buccaneer-lib.Tpo .deps/buccaneer-lib.Plo
  793. mv -f .deps/cootaneer-sequence.Tpo .deps/cootaneer-sequence.Plo
  794. mv -f .deps/buccaneer-prot.Tpo .deps/buccaneer-prot.Plo
  795. mv -f .deps/buccaneer-sequence.Tpo .deps/buccaneer-sequence.Plo
  796. /bin/bash ../libtool  --tag=CXX   --mode=link g++  -g -O -Wall -Wno-unused    -o libcootaneer.la -rpath /home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib buccaneer-lib.lo buccaneer-prot.lo buccaneer-sequence.lo cootaneer-sequence.lo -L/home/erwinp/autobuild/Linux-cn1200-gtk2-python/lib -lclipper-ccp4 -lclipper-cif -lclipper-minimol -lclipper-mmdb -lclipper-cns -lclipper-phs -lclipper-contrib -lclipper-core -lccp4c -lmmdb2
  797. libtool: link: ar cru .libs/libcootaneer.a  buccaneer-lib.o buccaneer-prot.o buccaneer-sequence.o cootaneer-sequence.o
  798. ar: `u' modifier ignored since `D' is the default (see `U')
  799. libtool: link: ranlib .libs/libcootaneer.a
  800. libtool: link: ( cd ".libs" && rm -f "libcootaneer.la" && ln -s "../libcootaneer.la" "libcootaneer.la" )
  801. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/cootaneer'
  802. Making all in ideal
  803. make[1]: Entering directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/ideal'
  804. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL  -g -O -Wall -Wno-unused  -MT simple-restraint.lo -MD -MP -MF .deps/simple-restraint.Tpo -c -o simple-restraint.lo simple-restraint.cc
  805. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL  -g -O -Wall -Wno-unused  -MT ng.lo -MD -MP -MF .deps/ng.Tpo -c -o ng.lo ng.cc
  806. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL  -g -O -Wall -Wno-unused  -MT mods.lo -MD -MP -MF .deps/mods.Tpo -c -o mods.lo mods.cc
  807. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL  -g -O -Wall -Wno-unused  -MT distortion.lo -MD -MP -MF .deps/distortion.Tpo -c -o distortion.lo distortion.cc
  808. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL  -g -O -Wall -Wno-unused  -MT chirals.lo -MD -MP -MF .deps/chirals.Tpo -c -o chirals.lo chirals.cc
  809. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL  -g -O -Wall -Wno-unused  -MT flanking.lo -MD -MP -MF .deps/flanking.Tpo -c -o flanking.lo flanking.cc
  810. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL  -g -O -Wall -Wno-unused  -MT gradients.lo -MD -MP -MF .deps/gradients.Tpo -c -o gradients.lo gradients.cc
  811. /bin/bash ../libtool  --tag=CXX   --mode=compile g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" -DPACKAGE_STRING=\"coot\ 0.9\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 -DHAVE_BOOST=/\*\*/ -DHAVE_PYTHON=\"2.7\" -DHAVE_BOOST_PYTHON=/\*\*/ -I.  -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include  -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL  -g -O -Wall -Wno-unused  -MT extra-restraints.lo -MD -MP -MF .deps/extra-restraints.Tpo -c -o extra-restraints.lo extra-restraints.cc
  812. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL -g -O -Wall -Wno-unused -MT mods.lo -MD -MP -MF .deps/mods.Tpo -c mods.cc -o mods.o
  813. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL -g -O -Wall -Wno-unused -MT simple-restraint.lo -MD -MP -MF .deps/simple-restraint.Tpo -c simple-restraint.cc -o simple-restraint.o
  814. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL -g -O -Wall -Wno-unused -MT flanking.lo -MD -MP -MF .deps/flanking.Tpo -c flanking.cc -o flanking.o
  815. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL -g -O -Wall -Wno-unused -MT ng.lo -MD -MP -MF .deps/ng.Tpo -c ng.cc -o ng.o
  816. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL -g -O -Wall -Wno-unused -MT distortion.lo -MD -MP -MF .deps/distortion.Tpo -c distortion.cc -o distortion.o
  817. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL -g -O -Wall -Wno-unused -MT gradients.lo -MD -MP -MF .deps/gradients.Tpo -c gradients.cc -o gradients.o
  818. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL -g -O -Wall -Wno-unused -MT chirals.lo -MD -MP -MF .deps/chirals.Tpo -c chirals.cc -o chirals.o
  819. libtool: compile:  g++ -DPACKAGE_NAME=\"coot\" -DPACKAGE_TARNAME=\"coot\" -DPACKAGE_VERSION=\"0.9\" "-DPACKAGE_STRING=\"coot 0.9\"" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.9\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_OPENMP=1 "-DHAVE_BOOST=/**/" -DHAVE_PYTHON=\"2.7\" "-DHAVE_BOOST_PYTHON=/**/" -I. -I.. -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DHAVE_GSL -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DCLIPPER_HAS_TOP8000 -I/home/erwinp/autobuild/Linux-cn1200-gtk2-python/include -DMMDB_HAS_LINK_DISTANCE -DHAVE_GSL -g -O -Wall -Wno-unused -MT extra-restraints.lo -MD -MP -MF .deps/extra-restraints.Tpo -c extra-restraints.cc -o extra-restraints.o
  820. In file included from extra-restraints.cc:30:0:
  821. simple-restraint.hh:2306:25: error: field 'restraints_lock' has incomplete type 'std::atomic<bool>'
  822.       std::atomic<bool> restraints_lock;
  823.                         ^~~~~~~~~~~~~~~
  824. In file included from /usr/include/c++/7/bits/shared_ptr_atomic.h:33:0,
  825.                 from /usr/include/c++/7/memory:82,
  826.                 from simple-restraint.hh:32,
  827.                 from extra-restraints.cc:30:
  828. /usr/include/c++/7/bits/atomic_base.h:126:12: note: declaration of 'struct std::atomic<bool>'
  829.     struct atomic;
  830.            ^~~~~~
  831. In file included from flanking.cc:35:0:
  832. simple-restraint.hh:2306:25: error: field 'restraints_lock' has incomplete type 'std::atomic<bool>'
  833.       std::atomic<bool> restraints_lock;
  834.                         ^~~~~~~~~~~~~~~
  835. In file included from /usr/include/c++/7/bits/shared_ptr_atomic.h:33:0,
  836.                 from /usr/include/c++/7/memory:82,
  837.                 from simple-restraint.hh:32,
  838.                 from flanking.cc:35:
  839. /usr/include/c++/7/bits/atomic_base.h:126:12: note: declaration of 'struct std::atomic<bool>'
  840.     struct atomic;
  841.            ^~~~~~
  842. In file included from extra-restraints.cc:30:0:
  843. simple-restraint.hh: In member function 'void coot::restraints_container_t::init()':
  844. simple-restraint.hh:1146:3: error: 'thread_pool_p' was not declared in this scope
  845.   thread_pool_p = 0; // null pointer
  846.   ^~~~~~~~~~~~~
  847. In file included from mods.cc:35:0:
  848. simple-restraint.hh:2306:25: error: field 'restraints_lock' has incomplete type 'std::atomic<bool>'
  849.       std::atomic<bool> restraints_lock;
  850.                         ^~~~~~~~~~~~~~~
  851. In file included from /usr/include/c++/7/bits/shared_ptr_atomic.h:33:0,
  852.                 from /usr/include/c++/7/memory:82,
  853.                 from simple-restraint.hh:32,
  854.                 from mods.cc:35:
  855. /usr/include/c++/7/bits/atomic_base.h:126:12: note: declaration of 'struct std::atomic<bool>'
  856.     struct atomic;
  857.            ^~~~~~
  858. In file included from flanking.cc:35:0:
  859. simple-restraint.hh: In member function 'void coot::restraints_container_t::init()':
  860. simple-restraint.hh:1146:3: error: 'thread_pool_p' was not declared in this scope
  861.   thread_pool_p = 0; // null pointer
  862.   ^~~~~~~~~~~~~
  863. simple-restraint.hh:1146:3: note: suggested alternative: 'pthread_cond_t'
  864.   thread_pool_p = 0; // null pointer
  865.   ^~~~~~~~~~~~~
  866.   pthread_cond_t
  867. simple-restraint.hh:1146:3: note: suggested alternative: 'pthread_cond_t'
  868.   thread_pool_p = 0; // null pointer
  869.   ^~~~~~~~~~~~~
  870.   pthread_cond_t
  871. In file included from mods.cc:35:0:
  872. simple-restraint.hh: In member function 'void coot::restraints_container_t::init()':
  873. simple-restraint.hh:1146:3: error: 'thread_pool_p' was not declared in this scope
  874.   thread_pool_p = 0; // null pointer
  875.   ^~~~~~~~~~~~~
  876. In file included from ng.cc:3:0:
  877. simple-restraint.hh:2306:25: error: field 'restraints_lock' has incomplete type 'std::atomic<bool>'
  878.       std::atomic<bool> restraints_lock;
  879.                         ^~~~~~~~~~~~~~~
  880. In file included from /usr/include/c++/7/bits/shared_ptr_atomic.h:33:0,
  881.                 from /usr/include/c++/7/memory:82,
  882.                 from simple-restraint.hh:32,
  883.                 from ng.cc:3:
  884. /usr/include/c++/7/bits/atomic_base.h:126:12: note: declaration of 'struct std::atomic<bool>'
  885.     struct atomic;
  886.            ^~~~~~
  887. simple-restraint.hh:1146:3: note: suggested alternative: 'pthread_cond_t'
  888.   thread_pool_p = 0; // null pointer
  889.   ^~~~~~~~~~~~~
  890.   pthread_cond_t
  891. In file included from ng.cc:3:0:
  892. simple-restraint.hh: In member function 'void coot::restraints_container_t::init()':
  893. simple-restraint.hh:1146:3: error: 'thread_pool_p' was not declared in this scope
  894.   thread_pool_p = 0; // null pointer
  895.   ^~~~~~~~~~~~~
  896. simple-restraint.hh:1146:3: note: suggested alternative: 'pthread_cond_t'
  897.   thread_pool_p = 0; // null pointer
  898.   ^~~~~~~~~~~~~
  899.   pthread_cond_t
  900. In file included from gradients.cc:42:0:
  901. simple-restraint.hh:2306:25: error: field 'restraints_lock' has incomplete type 'std::atomic<bool>'
  902.       std::atomic<bool> restraints_lock;
  903.                         ^~~~~~~~~~~~~~~
  904. In file included from /usr/include/c++/7/bits/shared_ptr_atomic.h:33:0,
  905.                 from /usr/include/c++/7/memory:82,
  906.                 from simple-restraint.hh:32,
  907.                 from gradients.cc:42:
  908. /usr/include/c++/7/bits/atomic_base.h:126:12: note: declaration of 'struct std::atomic<bool>'
  909.     struct atomic;
  910.            ^~~~~~
  911. In file included from gradients.cc:42:0:
  912. simple-restraint.hh: In member function 'void coot::restraints_container_t::init()':
  913. simple-restraint.hh:1146:3: error: 'thread_pool_p' was not declared in this scope
  914.   thread_pool_p = 0; // null pointer
  915.   ^~~~~~~~~~~~~
  916. In file included from simple-restraint.cc:49:0:
  917. simple-restraint.hh:2306:25: error: field 'restraints_lock' has incomplete type 'std::atomic<bool>'
  918.       std::atomic<bool> restraints_lock;
  919.                         ^~~~~~~~~~~~~~~
  920. In file included from /usr/include/c++/7/bits/shared_ptr_atomic.h:33:0,
  921.                 from /usr/include/c++/7/memory:82,
  922.                 from simple-restraint.hh:32,
  923.                 from simple-restraint.cc:49:
  924. /usr/include/c++/7/bits/atomic_base.h:126:12: note: declaration of 'struct std::atomic<bool>'
  925.     struct atomic;
  926.            ^~~~~~
  927. ng.cc: In member function 'int coot::restraints_container_t::make_restraints_ng(int, const coot::protein_geometry&, coot::restraint_usage_Flags, bool, bool, float, bool, bool, bool, bool, coot::pseudo_restraint_bond_type, bool, bool)':
  928. ng.cc:26:10: error: 'thread_pool_p' was not declared in this scope
  929.    if (! thread_pool_p) {
  930.          ^~~~~~~~~~~~~
  931. simple-restraint.hh:1146:3: note: suggested alternative: 'pthread_cond_t'
  932.   thread_pool_p = 0; // null pointer
  933.   ^~~~~~~~~~~~~
  934.   pthread_cond_t
  935. ng.cc:26:10: note: suggested alternative: 'pthread_cond_t'
  936.    if (! thread_pool_p) {
  937.          ^~~~~~~~~~~~~
  938.          pthread_cond_t
  939. ng.cc:33:21: error: 'std::chrono' has not been declared
  940.    auto tp_0 = std::chrono::high_resolution_clock::now();
  941.                     ^~~~~~
  942. ng.cc:39:24: error: 'std::chrono' has not been declared
  943.       auto tp_1 = std::chrono::high_resolution_clock::now();
  944.                        ^~~~~~
  945. In file included from distortion.cc:45:0:
  946. simple-restraint.hh:2306:25: error: field 'restraints_lock' has incomplete type 'std::atomic<bool>'
  947.       std::atomic<bool> restraints_lock;
  948.                         ^~~~~~~~~~~~~~~
  949. In file included from simple-restraint.cc:49:0:
  950. simple-restraint.hh: In member function 'void coot::restraints_container_t::init()':
  951. simple-restraint.hh:1146:3: error: 'thread_pool_p' was not declared in this scope
  952.   thread_pool_p = 0; // null pointer
  953.   ^~~~~~~~~~~~~
  954. In file included from /usr/include/c++/7/bits/shared_ptr_atomic.h:33:0,
  955.                 from /usr/include/c++/7/memory:82,
  956.                 from simple-restraint.hh:32,
  957.                 from distortion.cc:45:
  958. /usr/include/c++/7/bits/atomic_base.h:126:12: note: declaration of 'struct std::atomic<bool>'
  959.     struct atomic;
  960.            ^~~~~~
  961. simple-restraint.hh:1146:3: note: suggested alternative: 'pthread_cond_t'
  962.   thread_pool_p = 0; // null pointer
  963.   ^~~~~~~~~~~~~
  964.   pthread_cond_t
  965. In file included from distortion.cc:45:0:
  966. simple-restraint.hh: In member function 'void coot::restraints_container_t::init()':
  967. simple-restraint.hh:1146:3: error: 'thread_pool_p' was not declared in this scope
  968.   thread_pool_p = 0; // null pointer
  969.   ^~~~~~~~~~~~~
  970. ng.cc:86:24: error: 'std::chrono' has not been declared
  971.       auto tp_2 = std::chrono::high_resolution_clock::now();
  972.                        ^~~~~~
  973. ng.cc:88:24: error: 'std::chrono' has not been declared
  974.       auto tp_3 = std::chrono::high_resolution_clock::now();
  975.                        ^~~~~~
  976. ng.cc:91:24: error: 'std::chrono' has not been declared
  977.       auto tp_4 = std::chrono::high_resolution_clock::now();
  978.                        ^~~~~~
  979. ng.cc:103:13: error: 'thread_pool_p' was not declared in this scope
  980.       if (! thread_pool_p) {
  981.             ^~~~~~~~~~~~~
  982. simple-restraint.hh:1146:3: note: suggested alternative: 'pthread_cond_t'
  983.   thread_pool_p = 0; // null pointer
  984.   ^~~~~~~~~~~~~
  985.   pthread_cond_t
  986. ng.cc:103:13: note: suggested alternative: 'pthread_cond_t'
  987.       if (! thread_pool_p) {
  988.             ^~~~~~~~~~~~~
  989.             pthread_cond_t
  990. ng.cc:111:24: error: 'std::chrono' has not been declared
  991.       auto tp_5 = std::chrono::high_resolution_clock::now();
  992.                        ^~~~~~
  993. ng.cc:117:26: error: 'std::chrono' has not been declared
  994.          auto d10 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_1 - tp_0).count();
  995.                          ^~~~~~
  996. ng.cc:117:53: error: 'std::chrono' has not been declared
  997.          auto d10 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_1 - tp_0).count();
  998.                                                     ^~~~~~
  999. ng.cc:118:26: error: 'std::chrono' has not been declared
  1000.          auto d21 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2 - tp_1).count();
  1001.                          ^~~~~~
  1002. ng.cc:118:53: error: 'std::chrono' has not been declared
  1003.          auto d21 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2 - tp_1).count();
  1004.                                                     ^~~~~~
  1005. ng.cc:119:26: error: 'std::chrono' has not been declared
  1006.          auto d32 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_3 - tp_2).count();
  1007.                          ^~~~~~
  1008. ng.cc:119:53: error: 'std::chrono' has not been declared
  1009.          auto d32 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_3 - tp_2).count();
  1010.                                                     ^~~~~~
  1011. ng.cc:120:26: error: 'std::chrono' has not been declared
  1012.          auto d43 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_4 - tp_3).count();
  1013.                          ^~~~~~
  1014. ng.cc:120:53: error: 'std::chrono' has not been declared
  1015.          auto d43 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_4 - tp_3).count();
  1016.                                                     ^~~~~~
  1017. ng.cc:121:26: error: 'std::chrono' has not been declared
  1018.          auto d54 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_5 - tp_4).count();
  1019.                          ^~~~~~
  1020. ng.cc:121:53: error: 'std::chrono' has not been declared
  1021.          auto d54 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_5 - tp_4).count();
  1022.                                                     ^~~~~~
  1023. ng.cc:144:7: error: 'make_df_restraints_indices' was not declared in this scope
  1024.       make_df_restraints_indices();
  1025.       ^~~~~~~~~~~~~~~~~~~~~~~~~~
  1026. In file included from chirals.cc:38:0:
  1027. simple-restraint.hh:2306:25: error: field 'restraints_lock' has incomplete type 'std::atomic<bool>'
  1028.       std::atomic<bool> restraints_lock;
  1029.                         ^~~~~~~~~~~~~~~
  1030. In file included from /usr/include/c++/7/bits/shared_ptr_atomic.h:33:0,
  1031.                 from /usr/include/c++/7/memory:82,
  1032.                 from ../coot-utils/tree.hh:32,
  1033.                 from ../coot-utils/coot-coord-extras.hh:29,
  1034.                 from chirals.cc:36:
  1035. /usr/include/c++/7/bits/atomic_base.h:126:12: note: declaration of 'struct std::atomic<bool>'
  1036.     struct atomic;
  1037.            ^~~~~~
  1038. In file included from chirals.cc:38:0:
  1039. simple-restraint.hh: In member function 'void coot::restraints_container_t::init()':
  1040. simple-restraint.hh:1146:3: error: 'thread_pool_p' was not declared in this scope
  1041.   thread_pool_p = 0; // null pointer
  1042.   ^~~~~~~~~~~~~
  1043. gradients.cc: In function 'void coot::my_df(const gsl_vector*, void*, gsl_vector*)':
  1044. gradients.cc:206:7: error: 'split_the_gradients_with_threads' was not declared in this scope
  1045.       split_the_gradients_with_threads(v, restraints_p, df);
  1046.       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  1047. ng.cc:144:7: note: suggested alternative: 'make_restraints_ng'
  1048.       make_df_restraints_indices();
  1049.       ^~~~~~~~~~~~~~~~~~~~~~~~~~
  1050.       make_restraints_ng
  1051. ng.cc:145:7: error: 'make_distortion_electron_density_ranges' was not declared in this scope
  1052.       make_distortion_electron_density_ranges();
  1053.       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  1054. simple-restraint.hh:1146:3: note: suggested alternative: 'pthread_cond_t'
  1055.   thread_pool_p = 0; // null pointer
  1056.   ^~~~~~~~~~~~~
  1057.   pthread_cond_t
  1058. gradients.cc:206:7: note: suggested alternative: 'split_the_gradients_with_threads_flag'
  1059.       split_the_gradients_with_threads(v, restraints_p, df);
  1060.       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  1061.       split_the_gradients_with_threads_flag
  1062. ng.cc: In member function 'void coot::restraints_container_t::make_base_pairing_and_stacking_restraints_ng(int, const coot::protein_geometry&)':
  1063. ng.cc:164:21: error: 'std::chrono' has not been declared
  1064.    auto tp_6 = std::chrono::high_resolution_clock::now();
  1065.                     ^~~~~~
  1066. ng.cc:179:21: error: 'std::chrono' has not been declared
  1067.    auto tp_7 = std::chrono::high_resolution_clock::now();
  1068.                     ^~~~~~
  1069. ng.cc:186:21: error: 'std::chrono' has not been declared
  1070.    auto tp_8 = std::chrono::high_resolution_clock::now();
  1071.                     ^~~~~~
  1072. ng.cc:211:21: error: 'std::chrono' has not been declared
  1073.    auto tp_9 = std::chrono::high_resolution_clock::now();
  1074.                     ^~~~~~
  1075. ng.cc:216:22: error: 'std::chrono' has not been declared
  1076.    auto tp_10 = std::chrono::high_resolution_clock::now();
  1077.                      ^~~~~~
  1078. ng.cc:217:21: error: 'std::chrono' has not been declared
  1079.    auto d76  = std::chrono::duration_cast<std::chrono::milliseconds>(tp_7  - tp_6).count();
  1080.                     ^~~~~~
  1081. ng.cc:217:48: error: 'std::chrono' has not been declared
  1082.    auto d76  = std::chrono::duration_cast<std::chrono::milliseconds>(tp_7  - tp_6).count();
  1083.                                                ^~~~~~
  1084. ng.cc:218:21: error: 'std::chrono' has not been declared
  1085.    auto d87  = std::chrono::duration_cast<std::chrono::milliseconds>(tp_8  - tp_7).count();
  1086.                     ^~~~~~
  1087. ng.cc:218:48: error: 'std::chrono' has not been declared
  1088.    auto d87  = std::chrono::duration_cast<std::chrono::milliseconds>(tp_8  - tp_7).count();
  1089.                                                ^~~~~~
  1090. ng.cc:219:21: error: 'std::chrono' has not been declared
  1091.    auto d98  = std::chrono::duration_cast<std::chrono::milliseconds>(tp_9  - tp_8).count();
  1092.                     ^~~~~~
  1093. ng.cc:219:48: error: 'std::chrono' has not been declared
  1094.    auto d98  = std::chrono::duration_cast<std::chrono::milliseconds>(tp_9  - tp_8).count();
  1095.                                                ^~~~~~
  1096. ng.cc:220:21: error: 'std::chrono' has not been declared
  1097.    auto d109 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_10 - tp_9).count();
  1098.                     ^~~~~~
  1099. ng.cc:220:48: error: 'std::chrono' has not been declared
  1100.    auto d109 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_10 - tp_9).count();
  1101.                                                ^~~~~~
  1102. simple-restraint.cc: In member function 'void coot::restraints_container_t::clear()':
  1103. simple-restraint.cc:67:12: error: 'std::this_thread' has not been declared
  1104.       std::this_thread::sleep_for(std::chrono::microseconds(10));
  1105.            ^~~~~~~~~~~
  1106. simple-restraint.cc:67:40: error: 'std::chrono' has not been declared
  1107.       std::this_thread::sleep_for(std::chrono::microseconds(10));
  1108.                                        ^~~~~~
  1109. ng.cc: In static member function 'static void coot::restraints_container_t::make_non_bonded_contact_restraints_workpackage_ng(int, int, const coot::protein_geometry&, const std::vector<std::set<int> >&, const coot::restraints_container_t::reduced_angle_info_container_t&, const std::vector<std::set<unsigned int> >&, std::pair<unsigned int, unsigned int>, const std::set<int>&, const std::vector<std::__cxx11::basic_string<char> >&, bool, mmdb::PPAtom, const std::vector<bool>&, const std::vector<bool>&, const std::vector<bool>&, const std::vector<bool>&, std::vector<std::set<int> >*, std::vector<coot::simple_restraint>*, std::atomic<unsigned int>&)':
  1110. ng.cc:801:15: error: no match for 'operator+=' (operand types are 'std::atomic<unsigned int>' and 'int')
  1111.    done_count += 1; // atomic
  1112.    ~~~~~~~~~~~^~~~
  1113. ng.cc: In member function 'void coot::restraints_container_t::make_non_bonded_contact_restraints_using_threads_ng(int, const coot::protein_geometry&)':
  1114. ng.cc:808:21: error: 'std::chrono' has not been declared
  1115.    auto tp_0 = std::chrono::high_resolution_clock::now();
  1116.                     ^~~~~~
  1117. ng.cc:836:21: error: 'std::chrono' has not been declared
  1118.    auto tp_1 = std::chrono::high_resolution_clock::now();
  1119.                     ^~~~~~
  1120. ng.cc:837:20: error: 'std::chrono' has not been declared
  1121.    auto d10 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_1 - tp_0).count();
  1122.                    ^~~~~~
  1123. ng.cc:837:47: error: 'std::chrono' has not been declared
  1124.    auto d10 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_1 - tp_0).count();
  1125.                                               ^~~~~~
  1126. ng.cc:848:21: error: 'std::chrono' has not been declared
  1127.    auto tp_2 = std::chrono::high_resolution_clock::now();
  1128.                     ^~~~~~
  1129. ng.cc:856:22: error: 'std::chrono' has not been declared
  1130.    auto tp_2a = std::chrono::high_resolution_clock::now();
  1131.                      ^~~~~~
  1132. ng.cc:870:22: error: 'std::chrono' has not been declared
  1133.    auto tp_2b = std::chrono::high_resolution_clock::now();
  1134.                      ^~~~~~
  1135. ng.cc:891:22: error: 'std::chrono' has not been declared
  1136.    auto tp_2c = std::chrono::high_resolution_clock::now();
  1137.                      ^~~~~~
  1138. ng.cc:898:20: error: 'std::chrono' has not been declared
  1139.    auto d2a = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2a - tp_2 ).count();
  1140.                    ^~~~~~
  1141. ng.cc:898:47: error: 'std::chrono' has not been declared
  1142.    auto d2a = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2a - tp_2 ).count();
  1143.                                               ^~~~~~
  1144. ng.cc:899:20: error: 'std::chrono' has not been declared
  1145.    auto d2b = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2b - tp_2a).count();
  1146.                    ^~~~~~
  1147. ng.cc:899:47: error: 'std::chrono' has not been declared
  1148.    auto d2b = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2b - tp_2a).count();
  1149.                                               ^~~~~~
  1150. ng.cc:900:20: error: 'std::chrono' has not been declared
  1151.    auto d2c = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2c - tp_2b).count();
  1152.                    ^~~~~~
  1153. ng.cc:900:47: error: 'std::chrono' has not been declared
  1154.    auto d2c = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2c - tp_2b).count();
  1155.                                               ^~~~~~
  1156. ng.cc:904:40: error: variable 'std::atomic<unsigned int> done_count' has initializer but incomplete type
  1157.    std::atomic<unsigned int> done_count(0);
  1158.                                        ^
  1159. ng.cc:907:21: error: 'std::chrono' has not been declared
  1160.    auto tp_3 = std::chrono::high_resolution_clock::now();
  1161.                     ^~~~~~
  1162. ng.cc:909:7: error: 'thread_pool_p' was not declared in this scope
  1163.       thread_pool_p->push(make_non_bonded_contact_restraints_workpackage_ng,
  1164.       ^~~~~~~~~~~~~
  1165. ng.cc:909:7: note: suggested alternative: 'pthread_cond_t'
  1166.       thread_pool_p->push(make_non_bonded_contact_restraints_workpackage_ng,
  1167.       ^~~~~~~~~~~~~
  1168.       pthread_cond_t
  1169. ng.cc:929:21: error: 'std::chrono' has not been declared
  1170.    auto tp_4 = std::chrono::high_resolution_clock::now();
  1171.                     ^~~~~~
  1172. ng.cc:933:12: error: 'std::this_thread' has not been declared
  1173.       std::this_thread::sleep_for(std::chrono::microseconds(10000));
  1174.            ^~~~~~~~~~~
  1175. ng.cc:933:40: error: 'std::chrono' has not been declared
  1176.       std::this_thread::sleep_for(std::chrono::microseconds(10000));
  1177.                                        ^~~~~~
  1178. ng.cc:935:21: error: 'std::chrono' has not been declared
  1179.    auto tp_5 = std::chrono::high_resolution_clock::now();
  1180.                     ^~~~~~
  1181. ng.cc:949:21: error: 'std::chrono' has not been declared
  1182.    auto tp_6 = std::chrono::high_resolution_clock::now();
  1183.                     ^~~~~~
  1184. ng.cc:950:20: error: 'std::chrono' has not been declared
  1185.    auto d32 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_3 - tp_2).count();
  1186.                    ^~~~~~
  1187. ng.cc:950:47: error: 'std::chrono' has not been declared
  1188.    auto d32 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_3 - tp_2).count();
  1189.                                               ^~~~~~
  1190. ng.cc:951:20: error: 'std::chrono' has not been declared
  1191.    auto d43 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_4 - tp_3).count();
  1192.                    ^~~~~~
  1193. ng.cc:951:47: error: 'std::chrono' has not been declared
  1194.    auto d43 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_4 - tp_3).count();
  1195.                                               ^~~~~~
  1196. ng.cc:952:20: error: 'std::chrono' has not been declared
  1197.    auto d54 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_5 - tp_4).count();
  1198.                    ^~~~~~
  1199. ng.cc:952:47: error: 'std::chrono' has not been declared
  1200.    auto d54 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_5 - tp_4).count();
  1201.                                               ^~~~~~
  1202. ng.cc:953:20: error: 'std::chrono' has not been declared
  1203.    auto d65 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_6 - tp_5).count();
  1204.                    ^~~~~~
  1205. ng.cc:953:47: error: 'std::chrono' has not been declared
  1206.    auto d65 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_6 - tp_5).count();
  1207.                                               ^~~~~~
  1208. ng.cc: In member function 'unsigned int coot::restraints_container_t::make_non_bonded_contact_restraints_ng(int, const coot::protein_geometry&)':
  1209. ng.cc:988:21: error: 'std::chrono' has not been declared
  1210.    auto tp_0 = std::chrono::high_resolution_clock::now();
  1211.                     ^~~~~~
  1212. ng.cc:1003:21: error: 'std::chrono' has not been declared
  1213.    auto tp_1 = std::chrono::high_resolution_clock::now();
  1214.                     ^~~~~~
  1215. ng.cc:1004:20: error: 'std::chrono' has not been declared
  1216.    auto d10 = std::chrono::duration_cast<std::chrono::microseconds>(tp_1 - tp_0).count();
  1217.                    ^~~~~~
  1218. ng.cc:1004:47: error: 'std::chrono' has not been declared
  1219.    auto d10 = std::chrono::duration_cast<std::chrono::microseconds>(tp_1 - tp_0).count();
  1220.                                               ^~~~~~
  1221. ng.cc:1285:4: error: 'make_df_restraints_indices' was not declared in this scope
  1222.    make_df_restraints_indices();
  1223.    ^~~~~~~~~~~~~~~~~~~~~~~~~~
  1224. ng.cc:1285:4: note: suggested alternative: 'make_restraints_ng'
  1225.    make_df_restraints_indices();
  1226.    ^~~~~~~~~~~~~~~~~~~~~~~~~~
  1227.    make_restraints_ng
  1228. ng.cc:1287:4: error: 'make_distortion_electron_density_ranges' was not declared in this scope
  1229.    make_distortion_electron_density_ranges();
  1230.    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  1231. simple-restraint.cc: In member function 'coot::refinement_results_t coot::restraints_container_t::minimize(int, coot::restraint_usage_Flags, int, short int, const coot::protein_geometry&)':
  1232. simple-restraint.cc:1303:24: error: 'std::chrono' has not been declared
  1233.       auto tp_0 = std::chrono::high_resolution_clock::now();
  1234.                        ^~~~~~
  1235. simple-restraint.cc:1305:24: error: 'std::chrono' has not been declared
  1236.       auto tp_1 = std::chrono::high_resolution_clock::now();
  1237.                        ^~~~~~
  1238. simple-restraint.cc:1308:27: error: 'std::chrono' has not been declared
  1239.          auto tp_2 = std::chrono::high_resolution_clock::now();
  1240.                           ^~~~~~
  1241. simple-restraint.cc:1309:26: error: 'std::chrono' has not been declared
  1242.          auto d10 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_1 - tp_0).count();
  1243.                          ^~~~~~
  1244. simple-restraint.cc:1309:53: error: 'std::chrono' has not been declared
  1245.          auto d10 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_1 - tp_0).count();
  1246.                                                     ^~~~~~
  1247. simple-restraint.cc:1310:26: error: 'std::chrono' has not been declared
  1248.          auto d21 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2 - tp_1).count();
  1249.                          ^~~~~~
  1250. simple-restraint.cc:1310:53: error: 'std::chrono' has not been declared
  1251.          auto d21 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2 - tp_1).count();
  1252.                                                     ^~~~~~
  1253. simple-restraint.cc: In member function 'coot::refinement_results_t coot::restraints_container_t::minimize_inner(coot::restraint_usage_Flags, int, short int)':
  1254. simple-restraint.cc:1389:11: error: 'std::this_thread' has not been declared
  1255.      std::this_thread::sleep_for(std::chrono::microseconds(10));
  1256.           ^~~~~~~~~~~
  1257. simple-restraint.cc:1389:39: error: 'std::chrono' has not been declared
  1258.      std::this_thread::sleep_for(std::chrono::microseconds(10));
  1259.                                       ^~~~~~
  1260. simple-restraint.cc:1505:8: error: 'std::this_thread' has not been declared
  1261.   std::this_thread::sleep_for(std::chrono::microseconds(10));
  1262.        ^~~~~~~~~~~
  1263. simple-restraint.cc:1505:36: error: 'std::chrono' has not been declared
  1264.   std::this_thread::sleep_for(std::chrono::microseconds(10));
  1265.                                    ^~~~~~
  1266. simple-restraint.cc: In member function 'void coot::restraints_container_t::make_helix_pseudo_bond_restraints_from_res_vec_auto()':
  1267. simple-restraint.cc:3204:21: error: 'std::chrono' has not been declared
  1268.    auto tp_0 = std::chrono::high_resolution_clock::now();
  1269.                     ^~~~~~
  1270. simple-restraint.cc:3366:21: error: 'std::chrono' has not been declared
  1271.    auto tp_1 = std::chrono::high_resolution_clock::now();
  1272.                     ^~~~~~
  1273. simple-restraint.cc:3367:20: error: 'std::chrono' has not been declared
  1274.    auto d10 = std::chrono::duration_cast<std::chrono::microseconds>(tp_1 - tp_0).count();
  1275.                    ^~~~~~
  1276. simple-restraint.cc:3367:47: error: 'std::chrono' has not been declared
  1277.    auto d10 = std::chrono::duration_cast<std::chrono::microseconds>(tp_1 - tp_0).count();
  1278.                                               ^~~~~~
  1279. simple-restraint.cc: In member function 'void coot::restraints_container_t::make_h_bond_restraints_from_res_vec_auto(const coot::protein_geometry&)':
  1280. simple-restraint.cc:3630:21: error: 'std::chrono' has not been declared
  1281.    auto tp_0 = std::chrono::high_resolution_clock::now();
  1282.                     ^~~~~~
  1283. simple-restraint.cc:3634:21: error: 'std::chrono' has not been declared
  1284.    auto tp_1 = std::chrono::high_resolution_clock::now();
  1285.                     ^~~~~~
  1286. simple-restraint.cc:3639:21: error: 'std::chrono' has not been declared
  1287.    auto tp_2 = std::chrono::high_resolution_clock::now();
  1288.                     ^~~~~~
  1289. simple-restraint.cc:3641:21: error: 'std::chrono' has not been declared
  1290.    auto tp_3 = std::chrono::high_resolution_clock::now();
  1291.                     ^~~~~~
  1292. simple-restraint.cc:3674:20: error: 'std::chrono' has not been declared
  1293.    auto d10 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_1 - tp_0).count();
  1294.                    ^~~~~~
  1295. simple-restraint.cc:3674:47: error: 'std::chrono' has not been declared
  1296.    auto d10 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_1 - tp_0).count();
  1297.                                               ^~~~~~
  1298. simple-restraint.cc:3675:20: error: 'std::chrono' has not been declared
  1299.    auto d21 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2 - tp_1).count();
  1300.                    ^~~~~~
  1301. simple-restraint.cc:3675:47: error: 'std::chrono' has not been declared
  1302.    auto d21 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2 - tp_1).count();
  1303.                                               ^~~~~~
  1304. simple-restraint.cc:3676:20: error: 'std::chrono' has not been declared
  1305.    auto d32 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_3 - tp_2).count();
  1306.                    ^~~~~~
  1307. simple-restraint.cc:3676:47: error: 'std::chrono' has not been declared
  1308.    auto d32 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_3 - tp_2).count();
  1309.                                               ^~~~~~
  1310. ng.cc: In member function 'void coot::restraints_container_t::make_link_restraints_ng(const coot::protein_geometry&, bool, bool, std::map<mmdb::Residue*, std::vector<mmdb::Residue*> >*, std::set<std::pair<mmdb::Residue*, mmdb::Residue*> >*)':
  1311. ng.cc:1989:21: error: 'std::chrono' has not been declared
  1312.    auto tp_0 = std::chrono::high_resolution_clock::now();
  1313.                     ^~~~~~
  1314. ng.cc:1994:21: error: 'std::chrono' has not been declared
  1315.    auto tp_1 = std::chrono::high_resolution_clock::now();
  1316.                     ^~~~~~
  1317. ng.cc:2007:24: error: 'std::chrono' has not been declared
  1318.       auto tp_2 = std::chrono::high_resolution_clock::now();
  1319.                        ^~~~~~
  1320. ng.cc:2012:24: error: 'std::chrono' has not been declared
  1321.       auto tp_3 = std::chrono::high_resolution_clock::now();
  1322.                        ^~~~~~
  1323. ng.cc:2013:23: error: 'std::chrono' has not been declared
  1324.       auto d10 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_1 - tp_0).count();
  1325.                       ^~~~~~
  1326. ng.cc:2013:50: error: 'std::chrono' has not been declared
  1327.       auto d10 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_1 - tp_0).count();
  1328.                                                  ^~~~~~
  1329. ng.cc:2014:23: error: 'std::chrono' has not been declared
  1330.       auto d21 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2 - tp_1).count();
  1331.                       ^~~~~~
  1332. ng.cc:2014:50: error: 'std::chrono' has not been declared
  1333.       auto d21 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_2 - tp_1).count();
  1334.                                                  ^~~~~~
  1335. ng.cc:2015:23: error: 'std::chrono' has not been declared
  1336.       auto d32 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_3 - tp_2).count();
  1337.                       ^~~~~~
  1338. ng.cc:2015:50: error: 'std::chrono' has not been declared
  1339.       auto d32 = std::chrono::duration_cast<std::chrono::milliseconds>(tp_3 - tp_2).count();
  1340.                                                  ^~~~~~
  1341. Makefile:980: recipe for target 'gradients.lo' failed
  1342. make[1]: *** [gradients.lo] Error 1
  1343. make[1]: *** Waiting for unfinished jobs....
  1344. Makefile:980: recipe for target 'mods.lo' failed
  1345. make[1]: *** [mods.lo] Error 1
  1346. Makefile:980: recipe for target 'flanking.lo' failed
  1347. make[1]: *** [flanking.lo] Error 1
  1348. Makefile:980: recipe for target 'distortion.lo' failed
  1349. make[1]: *** [distortion.lo] Error 1
  1350. Makefile:980: recipe for target 'extra-restraints.lo' failed
  1351. make[1]: *** [extra-restraints.lo] Error 1
  1352. Makefile:980: recipe for target 'chirals.lo' failed
  1353. make[1]: *** [chirals.lo] Error 1
  1354. Makefile:980: recipe for target 'ng.lo' failed
  1355. make[1]: *** [ng.lo] Error 1
  1356. Makefile:980: recipe for target 'simple-restraint.lo' failed
  1357. make[1]: *** [simple-restraint.lo] Error 1
  1358. make[1]: Leaving directory '/home/erwinp/autobuild/building/cn1200_2020-05-18__T19_52_18/coot-0.9/ideal'
  1359. Makefile:700: recipe for target 'all-recursive' failed
  1360. make: *** [all-recursive] Error 1
  1361. make failed.
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