PATH is /h/paule/svn/bin:/usr/bin:/bin which svn gives /h/paule/svn/bin/svn svn, version 1.1.3 (r12730) compiled Jan 29 2005, 17:52:45 Copyright (C) 2000-2004 CollabNet. Subversion is open source software, see http://subversion.tigris.org/ This product includes software developed by CollabNet (http://www.Collab.Net/). The following repository access (RA) modules are available: * ra_dav : Module for accessing a repository via WebDAV (DeltaV) protocol. - handles 'http' schema * ra_local : Module for accessing a repository on local disk. - handles 'file' schema * ra_svn : Module for accessing a repository using the svn network protocol. - handles 'svn' schema which swig gives /usr/bin/swig test for python /h/paule/python-2.5.1/bin/python test for swig /h/paule/swig/bin/swig here is the dir where we will do svn update /h/paule/Projects/coot doing svn update At revision 1467. doing svn status with conflict grep doing conflict check 1467 int svn_revision() { return 1467; } done svn update/status/conflicts -rw-r--r-- 1 paule people 18 Oct 6 13:52 svn-update-log Mon Oct 6 14:00:03 BST 2008 /h/paule/svn/bin/svn update lines: 1 svn diff lines: 12 diff 12 is greater than 1, so setting compile yes. compile is 1 making svn log... aclocal -I macros -I /h/paule/libtool/share/aclocal -I /h/paule/automake/share/aclocal-1.9 -I /h/paule/autobuild/Linux-bubbles/share/aclocal -I /h/paule/autobuild/Linux-bubbles-pre-release/share/aclocal -I /h/paule/autobuild/Linux-bubbles-pre-release-gtk2/share/aclocal -I /usr/share/aclocal -I /h/paule/build/share/aclocal /h/paule/autobuild/Linux-bubbles/share/aclocal/libart.m4:11: warning: underquoted definition of AM_PATH_LIBART run info '(automake)Extending aclocal' or see http://sources.redhat.com/automake/automake.html#Extending-aclocal /h/paule/autobuild/Linux-bubbles/share/aclocal/imlib.m4:9: warning: underquoted definition of AM_PATH_IMLIB /h/paule/autobuild/Linux-bubbles/share/aclocal/imlib.m4:167: warning: underquoted definition of AM_PATH_GDK_IMLIB /h/paule/autobuild/Linux-bubbles/share/aclocal/gtkgl.m4:4: warning: underquoted definition of AM_PATH_GTKGL /h/paule/autobuild/Linux-bubbles/share/aclocal/gtk.m4:7: warning: underquoted definition of AM_PATH_GTK /h/paule/autobuild/Linux-bubbles/share/aclocal/glib.m4:8: warning: underquoted definition of AM_PATH_GLIB /h/paule/autobuild/Linux-bubbles-pre-release/share/aclocal/libart.m4:11: warning: underquoted definition of AM_PATH_LIBART /h/paule/autobuild/Linux-bubbles-pre-release/share/aclocal/imlib.m4:9: warning: underquoted definition of AM_PATH_IMLIB /h/paule/autobuild/Linux-bubbles-pre-release/share/aclocal/imlib.m4:167: warning: underquoted definition of AM_PATH_GDK_IMLIB /h/paule/autobuild/Linux-bubbles-pre-release/share/aclocal/gtkgl.m4:4: warning: underquoted definition of AM_PATH_GTKGL /h/paule/autobuild/Linux-bubbles-pre-release/share/aclocal/gtk.m4:7: warning: underquoted definition of AM_PATH_GTK /h/paule/autobuild/Linux-bubbles-pre-release/share/aclocal/glib.m4:8: warning: underquoted definition of AM_PATH_GLIB /usr/share/aclocal/xml-i18n-tools.m4:24: warning: underquoted definition of XML_I18N_TOOLS_NEWER_THAN_0_9 /usr/share/aclocal/xml-i18n-tools.m4:28: warning: underquoted definition of AC_PROG_XML_I18N_TOOLS /usr/share/aclocal/xml-i18n-tools.m4:30: warning: underquoted definition of X18T_PFORG1 /usr/share/aclocal/xml-i18n-tools.m4:32: warning: underquoted definition of X18T_XML_KIND /usr/share/aclocal/xml-i18n-tools.m4:34: warning: underquoted definition of X18T_KEYS_KIND /usr/share/aclocal/xml-i18n-tools.m4:135: warning: underquoted definition of AM_PROG_XML_I18N_TOOLS /usr/share/aclocal/vorbis.m4:9: warning: underquoted definition of XIPH_PATH_VORBIS /usr/share/aclocal/sdl.m4:11: warning: underquoted definition of AM_PATH_SDL /usr/share/aclocal/pkg.m4:5: warning: underquoted definition of PKG_CHECK_MODULES /usr/share/aclocal/ogg.m4:8: warning: underquoted definition of XIPH_PATH_OGG /usr/share/aclocal/oaf.m4:4: warning: underquoted definition of AM_PATH_OAF /usr/share/aclocal/ltdl.m4:29: warning: underquoted definition of AC_LIB_LTDL /usr/share/aclocal/ltdl.m4:62: warning: underquoted definition of AC_LTDL_ENABLE_INSTALL /usr/share/aclocal/ltdl.m4:72: warning: underquoted definition of AC_LTDL_SYS_DLOPEN_DEPLIBS /usr/share/aclocal/ltdl.m4:101: warning: underquoted definition of AC_LTDL_SHLIBEXT /usr/share/aclocal/ltdl.m4:121: warning: underquoted definition of AC_LTDL_SHLIBPATH /usr/share/aclocal/ltdl.m4:133: warning: underquoted definition of AC_LTDL_SYSSEARCHPATH /usr/share/aclocal/ltdl.m4:157: warning: underquoted definition of AC_LTDL_OBJDIR /usr/share/aclocal/ltdl.m4:179: warning: underquoted definition of AC_LTDL_DLPREOPEN /usr/share/aclocal/ltdl.m4:197: warning: underquoted definition of AC_LTDL_DLLIB /usr/share/aclocal/ltdl.m4:228: warning: underquoted definition of AC_LTDL_SYMBOL_USCORE /usr/share/aclocal/ltdl.m4:267: warning: underquoted definition of AC_LTDL_DLSYM_USCORE /usr/share/aclocal/linc.m4:1: warning: underquoted definition of AM_PATH_LINC /usr/share/aclocal/libxml.m4:10: warning: underquoted definition of AM_PATH_XML /usr/share/aclocal/libxml.m4:205: warning: underquoted definition of AM_PATH_XML2 /usr/share/aclocal/librsvg.m4:11: warning: underquoted definition of AM_PATH_LIBRSVG /usr/share/aclocal/libole2.m4:18: warning: underquoted definition of AM_PATH_LIBOLE2 /usr/share/aclocal/libmikmod.m4:11: warning: underquoted definition of AM_PATH_LIBMIKMOD /usr/share/aclocal/libguppi.m4:11: warning: underquoted definition of AM_PATH_LIBGUPPI /usr/share/aclocal/libglade.m4:7: warning: underquoted definition of AM_PATH_LIBGLADE /usr/share/aclocal/libart.m4:11: warning: underquoted definition of AM_PATH_LIBART /usr/share/aclocal/libIDL.m4:6: warning: underquoted definition of AM_PATH_LIBIDL /usr/share/aclocal/intltool.m4:26: warning: underquoted definition of AC_PROG_INTLTOOL /usr/share/aclocal/imlib.m4:9: warning: underquoted definition of AM_PATH_IMLIB /usr/share/aclocal/imlib.m4:167: warning: underquoted definition of AM_PATH_GDK_IMLIB /usr/share/aclocal/gtk.m4:7: warning: underquoted definition of AM_PATH_GTK /usr/share/aclocal/gtk-2.0.m4:8: warning: underquoted definition of AM_PATH_GTK_2_0 /usr/share/aclocal/gsl.m4:5: warning: underquoted definition of AM_PATH_GSL /usr/share/aclocal/glib.m4:8: warning: underquoted definition of AM_PATH_GLIB /usr/share/aclocal/glib-gettext.m4:71: warning: underquoted definition of AM_GLIB_WITH_NLS /usr/share/aclocal/glib-gettext.m4:203: warning: underquoted definition of AM_GLIB_GNU_GETTEXT /usr/share/aclocal/glib-2.0.m4:8: warning: underquoted definition of AM_PATH_GLIB_2_0 /usr/share/aclocal/gdk-pixbuf.m4:12: warning: underquoted definition of AM_PATH_GDK_PIXBUF /usr/share/aclocal/gconf-2.m4:8: warning: underquoted definition of AM_GCONF_SOURCE_2 /usr/share/aclocal/gconf-1.m4:4: warning: underquoted definition of AM_PATH_GCONF /usr/share/aclocal/gconf-1.m4:71: warning: underquoted definition of AM_GCONF_SOURCE /usr/share/aclocal/esd.m4:10: warning: underquoted definition of AM_PATH_ESD /usr/share/aclocal/esd.m4:175: warning: underquoted definition of AM_ESD_SUPPORTS_MULTIPLE_RECORD /usr/share/aclocal/audiofile.m4:12: warning: underquoted definition of AM_PATH_AUDIOFILE /usr/share/aclocal/ORBit2.m4:4: warning: underquoted definition of AM_PATH_ORBIT2 /usr/share/aclocal/ORBit.m4:4: warning: underquoted definition of AM_PATH_ORBIT /h/paule/build/share/aclocal/libart.m4:11: warning: underquoted definition of AM_PATH_LIBART /h/paule/build/share/aclocal/gtkgl.m4:4: warning: underquoted definition of AM_PATH_GTKGL /h/paule/build/share/aclocal/cppunit.m4:4: warning: underquoted definition of AM_PATH_CPPUNIT autoconf automake --add-missing --copy PATH is /h/paule/autoconf/bin:/h/paule/autobuild/Linux-bubbles-pre-release/bin:/h/paule/python-2.5.1/bin:/h/paule/swig/bin:/h/paule/texinfo/bin:/h/paule/autoconf/bin:/h/paule/automake/bin:/h/paule/build/bin:/h/paule/mapview/bin:/h/paule/bin.Linux:/h/paule/svn/bin:/usr/bin:/bin ../coot/configure --prefix=/y/people/emsley/coot/Linux --with-imlib-prefix=/h/paule/autobuild/Linux-bubbles-pre-release --with-gtkcanvas-prefix=/h/paule/autobuild/Linux-bubbles-pre-release --with-mmdb-prefix=/h/paule/autobuild/Linux-bubbles-pre-release --with-ssmlib-prefix=/h/paule/autobuild/Linux-bubbles-pre-release --with-clipper-prefix=/h/paule/autobuild/Linux-bubbles-pre-release --with-gtkgl-prefix=/h/paule/autobuild/Linux-bubbles-pre-release --with-glut-prefix=/h/paule/autobuild/Linux-bubbles-pre-release --with-gsl-prefix=/h/paule/autobuild/Linux-bubbles-pre-release --with-guile --with-guile-gtk --with-guile-gtk-prefix=/h/paule/autobuild/Linux-bubbles-pre-release --with-python CXXFLAGS=-g -O --disable-shared checking for a BSD-compatible install... /h/paule/build/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking dependency style of gcc... gcc3 checking for library containing strerror... none required checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ANSI C... (cached) none needed checking dependency style of gcc... (cached) gcc3 checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ANSI C... (cached) none needed checking dependency style of gcc... (cached) gcc3 checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a sed that does not truncate output... /bin/sed checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking whether ln -s works... yes checking how to recognise dependent libraries... pass_all checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking how to run the C++ preprocessor... g++ -E checking for g77... g77 checking whether we are using the GNU Fortran 77 compiler... yes checking whether g77 accepts -g... yes checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from gcc object... ok checking for objdir... .libs checking for ar... ar checking for ranlib... ranlib checking for strip... strip checking if gcc static flag works... yes checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fPIC checking if gcc PIC flag -fPIC works... yes checking if gcc supports -c -o file.o... yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes configure: creating libtool appending configuration tag "CXX" to libtool checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC checking if g++ PIC flag -fPIC works... yes checking if g++ supports -c -o file.o... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes appending configuration tag "F77" to libtool checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for g77 option to produce PIC... -fPIC checking if g77 PIC flag -fPIC works... yes checking if g77 supports -c -o file.o... yes checking whether the g77 linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking for ranlib... (cached) ranlib checking sys/stdtypes.h usability... no checking sys/stdtypes.h presence... no checking for sys/stdtypes.h... no checking if this is MINGW on Windows... no checking for gsl-config... /h/paule/autobuild/Linux-bubbles-pre-release/bin/gsl-config checking for GSL - version >= 1.3... yes checking for glib-config... /h/paule/autobuild/Linux-bubbles-pre-release/bin/glib-config checking for GLIB - version >= 1.2.8... yes checking for gtk-config... /h/paule/autobuild/Linux-bubbles-pre-release/bin/gtk-config checking for GTK - version >= 0.99.7... yes checking for GL... yes checking for GtkGLArea... yes checking for imlib-config... /h/paule/autobuild/Linux-bubbles-pre-release/bin/imlib-config checking for IMLIB - version >= 1.8.2... yes checking for GtkCanvas... yes checking for GLUT... yes checking for MMDB... yes checking for SSMLib... /h/paule/autobuild/Linux-bubbles-pre-release checking for Clipper... done svn log yes Congratulations, you are using Guile checking for guile... /h/paule/autobuild/Linux-bubbles-pre-release/bin/guile checking for guile-config... /h/paule/autobuild/Linux-bubbles-pre-release/bin/guile-config checking for guile-tools... /h/paule/autobuild/Linux-bubbles-pre-release/bin/guile-tools checking libguile compile flags... -I/h/paule/autobuild/Linux-bubbles-pre-release/include checking libguile link flags... -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -lguile -lguile-ltdl -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -lcrypt -lm checking for Guile Goosh... yes checking for net-hhtp... Some deprecated features have been used. Set the environment variable GUILE_WARN_DEPRECATED to "detailed" and rerun the program to get more information. Set it to "no" to suppress this message. yes checking for Guile-Lib... yes checking for guile-gui... yes checking GUILE_VERSION: 1.6 checking for Python... checking Python.h usability... yes checking Python.h presence... yes checking for Python.h... yes Cool, using Python checking for guile-gtk... /h/paule/autobuild/Linux-bubbles-pre-release Not using database configure: creating ./config.status config.status: creating Makefile config.status: creating macros/Makefile config.status: creating scheme/Makefile config.status: creating python/Makefile config.status: creating compat/Makefile config.status: creating coot-utils/Makefile config.status: creating ccp4mg-utils/Makefile config.status: creating coords/Makefile config.status: creating db-main/Makefile config.status: creating density-contour/Makefile config.status: creating surface/Makefile config.status: creating coot-surface/Makefile config.status: creating angles/Makefile config.status: creating atom-utils/Makefile config.status: creating mini-mol/Makefile config.status: creating skeleton/Makefile config.status: creating ligand/Makefile config.status: creating geometry/Makefile config.status: creating ideal/Makefile config.status: creating build/Makefile config.status: creating analysis/Makefile config.status: creating high-res/Makefile config.status: creating sequence-view/Makefile config.status: creating tw/Makefile config.status: creating cootaneer/Makefile config.status: creating greg-tests/Makefile config.status: creating python-tests/Makefile config.status: creating doc/Makefile config.status: creating src/Makefile config.status: creating src/coot config.status: creating setup/coot.sh config.status: creating setup/coot.csh config.status: creating python/coot_load_modules.py config.status: creating rama-data/Makefile config.status: creating auxil/Makefile config.status: creating auxil/catcheck/Makefile config.status: creating auxil/rama/Makefile config.status: creating auxil/sec-str/Makefile config.status: creating auxil/strand-analysis/Makefile config.status: creating auxil/vectors/Makefile config.status: executing depfiles commands building.... Making all in auxil make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil' Making all in catcheck make[2]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil/catcheck' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil/catcheck' Making all in rama make[2]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil/rama' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil/rama' Making all in sec-str make[2]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil/sec-str' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil/sec-str' Making all in strand-analysis make[2]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil/strand-analysis' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil/strand-analysis' Making all in vectors make[2]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil/vectors' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil/vectors' make[2]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil' Making all in scheme make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/scheme' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/scheme' Making all in python make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/python' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/python' Making all in macros make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/macros' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/macros' Making all in compat make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/compat' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/compat' Making all in coot-utils make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/coot-utils' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/coot-utils' Making all in surface make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/surface' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/surface' Making all in coot-surface make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/coot-surface' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/coot-surface' Making all in skeleton make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/skeleton' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/skeleton' Making all in ccp4mg-utils make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/ccp4mg-utils' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/ccp4mg-utils' Making all in density-contour make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/density-contour' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/density-contour' Making all in coords make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/coords' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/coords' Making all in angles make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/angles' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/angles' Making all in mini-mol make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/mini-mol' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/mini-mol' Making all in db-main make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/db-main' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/db-main' Making all in geometry make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/geometry' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/geometry' Making all in ideal make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/ideal' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/ideal' Making all in ligand make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/ligand' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/ligand' Making all in high-res make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/high-res' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/high-res' Making all in build make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/build' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/build' Making all in greg-tests make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/greg-tests' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/greg-tests' Making all in python-tests make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/python-tests' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/python-tests' Making all in analysis make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/analysis' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/analysis' Making all in sequence-view make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/sequence-view' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/sequence-view' Making all in tw make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/tw' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/tw' Making all in atom-utils make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/atom-utils' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/atom-utils' Making all in cootaneer make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/cootaneer' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/cootaneer' Making all in src make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/src' if g++ -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"coot\" -DVERSION=\"0.5.1-pre-1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -I. -I../../coot/src -I../../coot/compat -I../../coot/coords -I../../coot/ccp4mg-utils -I../../coot/coot-utils -I../../coot/intl -I../../coot/skeleton -I../../coot/angles -I../../coot/atom-utils -I../../coot/db-main -I../../coot/mini-mol -I../../coot/ligand -I../../coot/sequence-view -I../../coot/geometry -I../../coot/ideal -I../../coot/coot-surface -I../../coot/surface -I../../coot/density-contour -I../../coot/build -I../../coot/high-res -I../../coot/analysis -I../../coot/cootaneer -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -I/h/paule/autobuild/Linux-bubbles-pre-release/include -I/h/paule/autobuild/Linux-bubbles-pre-release/include -DHAVE_GTK_CANVAS -I/h/paule/autobuild/Linux-bubbles-pre-release/include -I/h/paule/autobuild/Linux-bubbles-pre-release/include/gtk-canvas -I/h/paule/autobuild/Linux-bubbles-pre-release/include/gnome-1.0 -I/h/paule/autobuild/Linux-bubbles-pre-release/include -I/usr/X11R6/include -I/h/paule/autobuild/Linux-bubbles-pre-release/include -I/h/paule/autobuild/Linux-bubbles-pre-release/include/gtk-1.2 -I/h/paule/autobuild/Linux-bubbles-pre-release/include/glib-1.2 -I/h/paule/autobuild/Linux-bubbles-pre-release/lib/glib/include -I/usr/X11R6/include -I/h/paule/autobuild/Linux-bubbles-pre-release/include -DHAVE_SSMLIB -I/h/paule/autobuild/Linux-bubbles-pre-release/include -I/h/paule/autobuild/Linux-bubbles-pre-release/include/mmdb -DHAVE_MMDB_IGNORE_HASH -DHAVE_MMDB_WITH_CISPEP -I/h/paule/autobuild/Linux-bubbles-pre-release/include -I/h/paule/autobuild/Linux-bubbles-pre-release/include -DPKGDATADIR='"/y/people/emsley/coot/Linux/share/coot"' -DPACKAGE_LOCALE_DIR='"/y/people/emsley/coot/Linux/share/coot/locale"' -DDATADIR='"/y/people/emsley/coot/Linux/share"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -I/h/paule/autobuild/Linux-bubbles-pre-release/include -DUSE_PYTHON -I/h/paule/autobuild/Linux-bubbles-pre-release/include/python2.5 -DHAVE_GSL -static -MT svn-revision.o -MD -MP -MF ".deps/svn-revision.Tpo" -c -o svn-revision.o ../../coot/src/svn-revision.cc; \ then mv -f ".deps/svn-revision.Tpo" ".deps/svn-revision.Po"; else rm -f ".deps/svn-revision.Tpo"; exit 1; fi /bin/sh ../libtool --tag=CXX --mode=link g++ -DPKGDATADIR='"/y/people/emsley/coot/Linux/share/coot"' -DPACKAGE_LOCALE_DIR='"/y/people/emsley/coot/Linux/share/coot/locale"' -DDATADIR='"/y/people/emsley/coot/Linux/share"' -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -I/h/paule/autobuild/Linux-bubbles-pre-release/include -DUSE_PYTHON -I/h/paule/autobuild/Linux-bubbles-pre-release/include/python2.5 -DHAVE_GSL -static -o coot-real main.o svn-revision.o c-inner-main.o c-interface.o c-interface-gui.o c-interface-gtk2.o c-interface-ncs.o c-interface-scm.o c-interface-python.o c-interface-info.o c-interface-mmdb.o c-interface-build.o c-interface-waters.o c-interface-mutate.o c-interface-ligands.o c-interface-widgets.o c-interface-validate.o c-interface-database.o c-interface-superpose.o c-interface-preferences.o c-interface-nucleotides.o callbacks.o cmtz-interface.o command-line.o coot-align.o coot-nomenclature.o coot-glue.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot_pythonmodule.o geometry-graphs.o globjects.o graphics-info.o graphics-info-modelling.o graphics-info-graphs.o graphics-info-state.o graphics-info-defines.o graphics-info-lsq.o graphics-info-pick.o graphics-info-render.o graphics-info-mutate.o graphics-info-superpose.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o gl-matrix.o gtk-manual.o gtk2-interface.o interface.o molecule-class-info.o molecule-class-info-maps.o molecule-class-info-other.o molecule-class-info-mutate.o molecule-class-info-surface.o molecule-class-info-ncs.o molecule-class-info-widget-work.o trackball.o pick.o read-phs.o read-cif.o xmap-utils.o rama_mousey.o rama_plot.o restraints-editor.o support.o support-gtk2-extras.o testing.o ../ligand/libcoot-ligand.la ../density-contour/libcoot-isosurface.la ../build/libcoot-cabuild.la ../skeleton/libcoot-skeleton.la ../angles/libcoot-AngleInfo.la ../atom-utils/libcoot-atomutils.la ../db-main/libcoot-db-main.la ../sequence-view/libcoot-sequence-view.la ../high-res/libcoot-high-res.la ../ideal/libcoot-ideal.la ../geometry/libcoot-geometry.la ../coords/libcoot-coords.la ../coot-surface/libcoot-surface.la ../surface/libccp4mg-surface.la ../ccp4mg-utils/libccp4mg-utils.la ../mini-mol/libcoot-mini-mol.la ../coot-utils/libcoot-map-heavy.la ../coot-utils/libcoot-map-utils.la ../coot-utils/libcoot-coord-extras.la ../coot-utils/libcoot-coord-utils.la ../coot-utils/libcoot-shelx.la ../coot-utils/libcoot-utils.la ../analysis/libcoot-analysis.la ../cootaneer/libcootaneer.la ../compat/libcoot-compat.la libcoot-wrap-guile.la libcoot-wrap-python.la /h/paule/autobuild/Linux-bubbles-pre-release/lib/libguilegtk-1.2.la -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -lguile -lguile-ltdl -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -lcrypt -lm -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -lclipper-ccp4 -lclipper-cif -lclipper-phs -lclipper-contrib -lclipper-minimol -lclipper-cns -lclipper-mmdb -lclipper-core -lccp4c -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -L/h/paule/autobuild/Linux-bubbles-pre-release -lmmdb -lm -lrfftw -lfftw -lz -lm -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -lssm -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -L/h/paule/autobuild/Linux-bubbles-pre-release -lmmdb -lm -L/h/paule/autobuild/Linux-bubbles-pre-release/lib/python2.5/config -lpython2.5 -lutil -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -lgtkgl -lGL -lGLU -lGL -lGLU -lpthread -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -lglut -L/usr/X11R6/lib -lXmu -lGL -lGLU -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -lgtk-canvas -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -lImlib -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -ljpeg -ltiff -lungif -lpng -lz -lm -lXext -L/usr/X11R6/lib -lSM -lICE -lXext -lX11 -lart_lgpl -lm -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -lgsl -lgslcblas -lm -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -L/usr/X11R6/lib -lgtk -lgdk -rdynamic -lgmodule -lglib -ldl -lXext -lX11 -lm g++ -DPKGDATADIR=\"/y/people/emsley/coot/Linux/share/coot\" -DPACKAGE_LOCALE_DIR=\"/y/people/emsley/coot/Linux/share/coot/locale\" -DDATADIR=\"/y/people/emsley/coot/Linux/share\" -DHAVE_SYS_STDTYPES_H=0 -DUSE_GUILE -DUSE_GUILE_GTK -I/h/paule/autobuild/Linux-bubbles-pre-release/include -DUSE_PYTHON -I/h/paule/autobuild/Linux-bubbles-pre-release/include/python2.5 -DHAVE_GSL -o coot-real main.o svn-revision.o c-inner-main.o c-interface.o c-interface-gui.o c-interface-gtk2.o c-interface-ncs.o c-interface-scm.o c-interface-python.o c-interface-info.o c-interface-mmdb.o c-interface-build.o c-interface-waters.o c-interface-mutate.o c-interface-ligands.o c-interface-widgets.o c-interface-validate.o c-interface-database.o c-interface-superpose.o c-interface-preferences.o c-interface-nucleotides.o callbacks.o cmtz-interface.o command-line.o coot-align.o coot-nomenclature.o coot-glue.o coot-glue-gtk2.o coot-glue-gtk2-python.o coot_pythonmodule.o geometry-graphs.o globjects.o graphics-info.o graphics-info-modelling.o graphics-info-graphs.o graphics-info-state.o graphics-info-defines.o graphics-info-lsq.o graphics-info-pick.o graphics-info-render.o graphics-info-mutate.o graphics-info-superpose.o graphics-info-navigation.o graphics-info-navigation-gtk1.o graphics-info-navigation-gtk2.o graphics-info-preferences.o gl-matrix.o gtk-manual.o gtk2-interface.o interface.o molecule-class-info.o molecule-class-info-maps.o molecule-class-info-other.o molecule-class-info-mutate.o molecule-class-info-surface.o molecule-class-info-ncs.o molecule-class-info-widget-work.o trackball.o pick.o read-phs.o read-cif.o xmap-utils.o rama_mousey.o rama_plot.o restraints-editor.o support.o support-gtk2-extras.o testing.o -rdynamic ../ligand/.libs/libcoot-ligand.a ../density-contour/.libs/libcoot-isosurface.a ../build/.libs/libcoot-cabuild.a ../skeleton/.libs/libcoot-skeleton.a ../angles/.libs/libcoot-AngleInfo.a ../atom-utils/.libs/libcoot-atomutils.a ../db-main/.libs/libcoot-db-main.a ../sequence-view/.libs/libcoot-sequence-view.a ../high-res/.libs/libcoot-high-res.a ../ideal/.libs/libcoot-ideal.a ../geometry/.libs/libcoot-geometry.a ../coords/.libs/libcoot-coords.a ../coot-surface/.libs/libcoot-surface.a ../surface/.libs/libccp4mg-surface.a ../ccp4mg-utils/.libs/libccp4mg-utils.a -L/h/paule/build/lib ../mini-mol/.libs/libcoot-mini-mol.a ../coot-utils/.libs/libcoot-map-heavy.a ../coot-utils/.libs/libcoot-map-utils.a ../coot-utils/.libs/libcoot-coord-extras.a ../coot-utils/.libs/libcoot-coord-utils.a ../coot-utils/.libs/libcoot-shelx.a ../coot-utils/.libs/libcoot-utils.a ../analysis/.libs/libcoot-analysis.a ../cootaneer/.libs/libcootaneer.a ../compat/.libs/libcoot-compat.a ./.libs/libcoot-wrap-guile.a ./.libs/libcoot-wrap-python.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libguilegtk-1.2.a -L/h/paule/autobuild/Linux-bubbles-pre-release/lib -L/usr/X11R6/lib /h/paule/autobuild/Linux-bubbles-pre-release/lib/libgthread.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libguile.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libguile-ltdl.a -lcrypt /h/paule/autobuild/Linux-bubbles-pre-release/lib/libclipper-ccp4.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libclipper-cif.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libclipper-phs.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libclipper-contrib.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libclipper-minimol.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libclipper-cns.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libclipper-mmdb.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libclipper-core.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libccp4c.a -L/h/paule/autobuild/Linux-bubbles-pre-release /h/paule/autobuild/Linux-bubbles-pre-release/lib/librfftw.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libfftw.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libssm.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libmmdb.a -L/h/paule/autobuild/Linux-bubbles-pre-release/lib/python2.5/config -lpython2.5 -lutil /h/paule/autobuild/Linux-bubbles-pre-release/lib/libgtkgl.a -lpthread /h/paule/autobuild/Linux-bubbles-pre-release/lib/libglut.a -lXxf86vm -lXmu /usr/lib/libGL.so -lGLU /h/paule/autobuild/Linux-bubbles-pre-release/lib/libgtk-canvas.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libgdk_imlib.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libImlib.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libtiff.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libjpeg.a -lc /h/paule/autobuild/Linux-bubbles-pre-release/lib/libungif.a -lpng -lz -lSM -lICE /h/paule/autobuild/Linux-bubbles-pre-release/lib/libart_lgpl.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libgsl.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libgslcblas.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libgtk.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libgdk.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libgmodule.a /h/paule/autobuild/Linux-bubbles-pre-release/lib/libglib.a -ldl -lXext -lX11 -lm /h/paule/autobuild/Linux-bubbles-pre-release/lib/libguile.a(posix.o): In function `scm_tmpnam': posix.o(.text+0x1732): the use of `tmpnam' is dangerous, better use `mkstemp' /h/paule/autobuild/Linux-bubbles-pre-release/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function `posix_tmpnam': /y/work/emsley/autobuild/bubbles_2008-08-12__T06_08_46/Python-2.5.1/Modules/posixmodule.c:6850: the use of `tmpnam_r' is dangerous, better use `mkstemp' /h/paule/autobuild/Linux-bubbles-pre-release/lib/python2.5/config/libpython2.5.a(posixmodule.o): In function `posix_tempnam': /y/work/emsley/autobuild/bubbles_2008-08-12__T06_08_46/Python-2.5.1/Modules/posixmodule.c:6805: the use of `tempnam' is dangerous, better use `mkstemp' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/src' Making all in rama-data make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/rama-data' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/rama-data' Making all in doc make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/doc' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/doc' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too' make[1]: Nothing to be done for `all-am'. make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too' done make make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/scheme' make[1]: Nothing to be done for `install-exec-am'. test -z "/y/people/emsley/coot/Linux/share/coot/scheme" || mkdir -p -- "/y/people/emsley/coot/Linux/share/coot/scheme" /h/paule/build/bin/install -c -m 644 '../../coot/scheme/0-auto-rot.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/0-auto-rot.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/coot-utils.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/coot-utils.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/get-ebi.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/get-ebi.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/mutate.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/mutate.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/background-demo.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/background-demo.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/demo-script.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/demo-script.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/gtkin.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/gtkin.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/my-readline.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/my-readline.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/bit.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/bit.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/extra-top-level.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/extra-top-level.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/hello.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/hello.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/raster3d.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/raster3d.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/brute-lsqman.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/brute-lsqman.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/file-utils.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/file-utils.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/junk.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/junk.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/refmac.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/refmac.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/coot-gui.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/coot-gui.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/filter.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/filter.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/libcheck.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/libcheck.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/simple.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/simple.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/coot.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/coot.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/get-ebi.save.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/get-ebi.save.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/local-code.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/local-code.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/trivial.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/trivial.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/gap.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/gap.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/remote-control.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/remote-control.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/povray.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/povray.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/coot-lsq.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/coot-lsq.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/shelx.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/shelx.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/group-settings.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/group-settings.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/fitting.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/fitting.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/americanisms.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/americanisms.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/tips.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/tips.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/tips-gui.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/tips-gui.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/generic-objects.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/generic-objects.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/cns2coot.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/cns2coot.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/extensions.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/extensions.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/ncs.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/ncs.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/create-server.scsh' '/y/people/emsley/coot/Linux/share/coot/scheme/create-server.scsh' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/coot-crash-catcher.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/coot-crash-catcher.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/snarf-coot-docs.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/snarf-coot-docs.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/clear-backup.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/clear-backup.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/bones-reader.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/bones-reader.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/matrices.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/matrices.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/fascinating-things.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/fascinating-things.scm' /h/paule/build/bin/install -c -m 644 '../../coot/scheme/shelx-extensions.scm' '/y/people/emsley/coot/Linux/share/coot/scheme/shelx-extensions.scm' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/scheme' INFO:: ------ built latest coot making dist { test ! -d coot-0.5.1-pre-1 || { find coot-0.5.1-pre-1 -type d ! -perm -200 -exec chmod u+w {} ';' && rm -fr coot-0.5.1-pre-1; }; } mkdir coot-0.5.1-pre-1 mkdir -p -- coot-0.5.1-pre-1/macros coot-0.5.1-pre-1/python coot-0.5.1-pre-1/setup coot-0.5.1-pre-1/src list='auxil scheme python macros compat coot-utils surface coot-surface skeleton ccp4mg-utils density-contour coords angles mini-mol db-main geometry ideal ligand high-res build greg-tests python-tests analysis sequence-view tw atom-utils cootaneer src rama-data doc '; for subdir in $list; do \ if test "$subdir" = .; then :; else \ test -d "coot-0.5.1-pre-1/$subdir" \ || mkdir -p -- "coot-0.5.1-pre-1/$subdir" \ || exit 1; \ distdir=`CDPATH="${ZSH_VERSION+.}:" && cd coot-0.5.1-pre-1 && pwd`; \ top_distdir=`CDPATH="${ZSH_VERSION+.}:" && cd coot-0.5.1-pre-1 && pwd`; \ (cd $subdir && \ make \ top_distdir="$top_distdir" \ distdir="$distdir/$subdir" \ distdir) \ || exit 1; \ fi; \ done make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil' list='catcheck rama sec-str strand-analysis vectors '; for subdir in $list; do \ if test "$subdir" = .; then :; else \ test -d "/h/paule/Projects/build-coot-python-too/coot-0.5.1-pre-1/auxil/$subdir" \ || mkdir -p -- "/h/paule/Projects/build-coot-python-too/coot-0.5.1-pre-1/auxil/$subdir" \ || exit 1; \ distdir=`CDPATH="${ZSH_VERSION+.}:" && cd /h/paule/Projects/build-coot-python-too/coot-0.5.1-pre-1/auxil && pwd`; \ top_distdir=`CDPATH="${ZSH_VERSION+.}:" && cd /h/paule/Projects/build-coot-python-too/coot-0.5.1-pre-1 && pwd`; \ (cd $subdir && \ make \ top_distdir="$top_distdir" \ distdir="$distdir/$subdir" \ distdir) \ || exit 1; \ fi; \ done make[2]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil/catcheck' make[2]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil/catcheck' make[2]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil/rama' make[2]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil/rama' make[2]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil/sec-str' make[2]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil/sec-str' make[2]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil/strand-analysis' make[2]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil/strand-analysis' make[2]: Entering directory `/h/paule/Projects/build-coot-python-too/auxil/vectors' make[2]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil/vectors' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/auxil' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/scheme' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/scheme' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/python' mkdir -p -- /h/paule/Projects/build-coot-python-too/coot-0.5.1-pre-1/python/../src make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/python' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/macros' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/macros' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/compat' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/compat' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/coot-utils' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/coot-utils' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/surface' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/surface' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/coot-surface' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/coot-surface' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/skeleton' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/skeleton' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/ccp4mg-utils' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/ccp4mg-utils' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/density-contour' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/density-contour' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/coords' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/coords' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/angles' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/angles' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/mini-mol' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/mini-mol' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/db-main' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/db-main' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/geometry' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/geometry' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/ideal' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/ideal' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/ligand' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/ligand' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/high-res' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/high-res' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/build' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/build' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/greg-tests' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/greg-tests' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/python-tests' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/python-tests' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/analysis' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/analysis' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/sequence-view' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/sequence-view' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/tw' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/tw' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/atom-utils' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/atom-utils' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/cootaneer' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/cootaneer' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/src' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/src' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/rama-data' make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/rama-data' make[1]: Entering directory `/h/paule/Projects/build-coot-python-too/doc' echo passing on making function.tex passing on making function.tex make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too/doc' make \ top_distdir="coot-0.5.1-pre-1" distdir="coot-0.5.1-pre-1" \ dist-hook make[1]: Entering directory `/h/paule/Projects/build-coot-python-too' if test -d ../coot/pixmaps; then \ mkdir coot-0.5.1-pre-1/pixmaps; \ for pixmap in ../coot/pixmaps/*; do \ if test -f $pixmap; then \ cp -p $pixmap coot-0.5.1-pre-1/pixmaps; \ fi \ done \ fi make[1]: Leaving directory `/h/paule/Projects/build-coot-python-too' find coot-0.5.1-pre-1 -type d ! -perm -777 -exec chmod a+rwx {} \; -o \ ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \ ! -type d ! -perm -400 -exec chmod a+r {} \; -o \ ! -type d ! -perm -444 -exec /bin/sh /h/paule/Projects/coot/install-sh -c -m a+r {} {} \; \ || chmod -R a+r coot-0.5.1-pre-1 tardir=coot-0.5.1-pre-1 && /bin/sh /h/paule/Projects/coot/missing --run tar chof - "$tardir" | GZIP=--best gzip -c >coot-0.5.1-pre-1.tar.gz { test ! -d coot-0.5.1-pre-1 || { find coot-0.5.1-pre-1 -type d ! -perm -200 -exec chmod u+w {} ';' && rm -fr coot-0.5.1-pre-1; }; } DEBUG:: tar_file is coot-0.5.1-pre-1.tar.gz debug:: svn_revision is 1467 debug::new_file_name is coot-0.5.1-pre-1-revision-1467.tar.gz Note: /y/people/emsley/public_html/software/pre-release/coot-0.5.1-pre-1-revision-1467.tar.gz already exists, not overwriting so that Bill/Fink is not put out. DEBUG:: making docs from directory /h/paule/Projects/build-coot-python-too/doc make: `booklet.ps' is up to date. make: `coot-manual.ps' is up to date. make: `tutorial.ps' is up to date. make: `coot-keys-and-buttons.pdf' is up to date. make: `user-manual.html' is up to date. echo passing on making functions.texi passing on making functions.texi Warning: ignoring unsupported tag `CREATE_SUBDIRS =' at line 42, file coot-dox.cfg Warning: ignoring unsupported tag `USE_WINDOWS_ENCODING =' at line 64, file coot-dox.cfg Warning: ignoring unsupported tag `ABBREVIATE_BRIEF =' at line 90, file coot-dox.cfg Warning: ignoring unsupported tag `STRIP_FROM_INC_PATH =' at line 127, file coot-dox.cfg Warning: ignoring unsupported tag `MULTILINE_CPP_IS_BRIEF =' at line 149, file coot-dox.cfg Warning: ignoring unsupported tag `DETAILS_AT_TOP =' at line 156, file coot-dox.cfg Warning: ignoring unsupported tag `SEPARATE_MEMBER_PAGES =' at line 175, file coot-dox.cfg Warning: ignoring unsupported tag `OPTIMIZE_OUTPUT_JAVA =' at line 203, file coot-dox.cfg Warning: ignoring unsupported tag `SUBGROUPING =' at line 211, file coot-dox.cfg Warning: ignoring unsupported tag `EXTRACT_LOCAL_METHODS =' at line 245, file coot-dox.cfg Warning: ignoring unsupported tag `HIDE_FRIEND_COMPOUNDS =' at line 267, file coot-dox.cfg Warning: ignoring unsupported tag `HIDE_IN_BODY_DOCS =' at line 274, file coot-dox.cfg Warning: ignoring unsupported tag `SORT_BRIEF_DOCS =' at line 320, file coot-dox.cfg Warning: ignoring unsupported tag `SORT_BY_SCOPE_NAME =' at line 330, file coot-dox.cfg Warning: ignoring unsupported tag `GENERATE_DEPRECATEDLIST=' at line 354, file coot-dox.cfg Warning: ignoring unsupported tag `SHOW_DIRECTORIES =' at line 381, file coot-dox.cfg Warning: ignoring unsupported tag `FILE_VERSION_FILTER =' at line 391, file coot-dox.cfg Warning: ignoring unsupported tag `WARN_IF_DOC_ERROR =' at line 419, file coot-dox.cfg Warning: ignoring unsupported tag `WARN_NO_PARAMDOC =' at line 427, file coot-dox.cfg Warning: ignoring unsupported tag `FILTER_PATTERNS =' at line 531, file coot-dox.cfg Warning: ignoring unsupported tag `CHM_FILE =' at line 662, file coot-dox.cfg Warning: ignoring unsupported tag `HHC_LOCATION =' at line 669, file coot-dox.cfg Warning: ignoring unsupported tag `LATEX_CMD_NAME =' at line 732, file coot-dox.cfg Warning: ignoring unsupported tag `MAKEINDEX_CMD_NAME =' at line 738, file coot-dox.cfg Warning: ignoring unsupported tag `LATEX_HIDE_INDICES =' at line 788, file coot-dox.cfg Warning: ignoring unsupported tag `XML_OUTPUT =' at line 874, file coot-dox.cfg Warning: ignoring unsupported tag `XML_SCHEMA =' at line 880, file coot-dox.cfg Warning: ignoring unsupported tag `XML_DTD =' at line 886, file coot-dox.cfg Warning: ignoring unsupported tag `XML_PROGRAMLISTING =' at line 893, file coot-dox.cfg Warning: ignoring unsupported tag `GENERATE_PERLMOD =' at line 917, file coot-dox.cfg Warning: ignoring unsupported tag `PERLMOD_LATEX =' at line 923, file coot-dox.cfg Warning: ignoring unsupported tag `PERLMOD_PRETTY =' at line 931, file coot-dox.cfg Warning: ignoring unsupported tag `PERLMOD_MAKEVAR_PREFIX =' at line 938, file coot-dox.cfg Warning: ignoring unsupported tag `GROUP_GRAPHS =' at line 1092, file coot-dox.cfg Warning: ignoring unsupported tag `UML_LOOK =' at line 1098, file coot-dox.cfg Warning: ignoring unsupported tag `CALL_GRAPH =' at line 1125, file coot-dox.cfg Warning: ignoring unsupported tag `DIRECTORY_GRAPH =' at line 1137, file coot-dox.cfg Warning: ignoring unsupported tag `MAX_DOT_GRAPH_DEPTH =' at line 1182, file coot-dox.cfg Warning: ignoring unsupported tag `DOT_TRANSPARENT =' at line 1190, file coot-dox.cfg Warning: ignoring unsupported tag `DOT_MULTI_TARGETS =' at line 1197, file coot-dox.cfg Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for files to exclude Reading input files... Preprocessing /h/paule/Projects/coot/src/c-interface.h... Read 178903 bytes Reading tag files Parsing input... Parsing file /h/paule/Projects/coot/src/c-interface.h... Freeing input... Building group list... Building namespace list... Building file list... Building class list... Building example list... Searching for documented variables... Building member list... Searching for friends... Searching for documented defines... Computing template instances... Creating members for template instances... Computing class relations... Searching for enumerations... Searching for member function documentation... Building page list... Building package list... Search for main page... Sorting lists... Freeing entry tree Determining which enums are documented Computing member relations... Adding classes to their packages... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Adding source references... Adding todo/test/bug list items... Counting data structures... Generating disk names... Resolving user defined references... Generating index page... Generating file index... Generating example documentation... Generating file sources... Generating code for file c-interface.h... Generating file documentation... Generating docs for file c-interface.h... Generating class documentation... Generating annotated compound index... Generating hierarchical class index... Generating member index... Generating page documentation... Generating group documentation... Generating namespace index... Generating group index... Generating package index... Generating example index... Generating file member index... Generating namespace member index... Generating page index... Generating graph info page... Generating search index... Generating style sheet... cp -r doxygen /y/people/emsley/public_html/coot/doc snafing coot docs... snafing coot docs done. texi2html coot-scheme.texi ================== svn revision 1467 ================== done.