[med-svn] r1023 - in trunk/packages/pdb2pqr/trunk: . debian pdb2pka pdb2pka/substruct propka
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Wed Dec 26 01:26:46 UTC 2007
Author: smoe-guest
Date: 2007-12-26 01:26:46 +0000 (Wed, 26 Dec 2007)
New Revision: 1023
Added:
trunk/packages/pdb2pqr/trunk/Makefile
trunk/packages/pdb2pqr/trunk/config.log
trunk/packages/pdb2pqr/trunk/debian/
trunk/packages/pdb2pqr/trunk/debian/README.Debian.binary
trunk/packages/pdb2pqr/trunk/debian/README.Debian.source
trunk/packages/pdb2pqr/trunk/debian/changelog
trunk/packages/pdb2pqr/trunk/debian/compat
trunk/packages/pdb2pqr/trunk/debian/control
trunk/packages/pdb2pqr/trunk/debian/copyright
trunk/packages/pdb2pqr/trunk/debian/dirs
trunk/packages/pdb2pqr/trunk/debian/docs
trunk/packages/pdb2pqr/trunk/debian/examples
trunk/packages/pdb2pqr/trunk/debian/pycompat
trunk/packages/pdb2pqr/trunk/debian/rules
trunk/packages/pdb2pqr/trunk/debian/watch
trunk/packages/pdb2pqr/trunk/debian/wrapper.sh
trunk/packages/pdb2pqr/trunk/pdb2pka/
trunk/packages/pdb2pqr/trunk/pdb2pka/Makefile
trunk/packages/pdb2pqr/trunk/pdb2pka/substruct/
trunk/packages/pdb2pqr/trunk/pdb2pka/substruct/Makefile
trunk/packages/pdb2pqr/trunk/propka/
trunk/packages/pdb2pqr/trunk/propka/Makefile
trunk/packages/pdb2pqr/trunk/propka/config.log
trunk/packages/pdb2pqr/trunk/propka/config.status
Log:
[svn-inject] Applying Debian modifications to trunk
Added: trunk/packages/pdb2pqr/trunk/Makefile
===================================================================
--- trunk/packages/pdb2pqr/trunk/Makefile (rev 0)
+++ trunk/packages/pdb2pqr/trunk/Makefile 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,585 @@
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+ -rm -f Makefile
+distclean-am: clean-am distclean-generic distclean-local \
+ distclean-tags
+
+dvi: dvi-recursive
+
+dvi-am:
+
+html: html-recursive
+
+info: info-recursive
+
+info-am:
+
+install-data-am:
+
+install-exec-am:
+
+install-info: install-info-recursive
+
+install-man:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-recursive
+ -rm -f $(am__CONFIG_DISTCLEAN_FILES)
+ -rm -rf $(top_srcdir)/autom4te.cache
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-recursive
+
+mostlyclean-am: mostlyclean-generic
+
+pdf: pdf-recursive
+
+pdf-am:
+
+ps: ps-recursive
+
+ps-am:
+
+uninstall-am: uninstall-info-am
+
+uninstall-info: uninstall-info-recursive
+
+.PHONY: $(RECURSIVE_TARGETS) CTAGS GTAGS all all-am am--refresh check \
+ check-am clean clean-generic clean-local clean-recursive ctags \
+ ctags-recursive dist dist-all dist-bzip2 dist-gzip dist-shar \
+ dist-tarZ dist-zip distcheck distclean distclean-generic \
+ distclean-local distclean-recursive distclean-tags \
+ distcleancheck distdir distuninstallcheck dvi dvi-am html \
+ html-am info info-am install install-am install-data \
+ install-data-am install-exec install-exec-am install-info \
+ install-info-am install-man install-strip installcheck \
+ installcheck-am installdirs installdirs-am maintainer-clean \
+ maintainer-clean-generic maintainer-clean-recursive \
+ mostlyclean mostlyclean-generic mostlyclean-recursive pdf \
+ pdf-am ps ps-am tags tags-recursive uninstall uninstall-am \
+ uninstall-info-am
+
+distclean-local: clean-local
+clean-local: clean-ac
+clean-ac:
+ -rm -rf autom4te.cache
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
Added: trunk/packages/pdb2pqr/trunk/config.log
===================================================================
--- trunk/packages/pdb2pqr/trunk/config.log (rev 0)
+++ trunk/packages/pdb2pqr/trunk/config.log 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,419 @@
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by PDB2PQR configure 1.2.0, which was
+generated by GNU Autoconf 2.59. Invocation command line was
+
+ $ ./configure --enable-pdb2pka
+
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = notebook
+uname -m = x86_64
+uname -r = 2.6.23-1-amd64
+uname -s = Linux
+uname -v = #1 SMP Fri Nov 30 12:19:15 UTC 2007
+
+/usr/bin/uname -p = unknown
+/bin/uname -X = unknown
+
+/bin/arch = unknown
+/usr/bin/arch -k = unknown
+/usr/convex/getsysinfo = unknown
+hostinfo = unknown
+/bin/machine = unknown
+/usr/bin/oslevel = unknown
+/bin/universe = unknown
+
+PATH: /home/moeller/bin
+PATH: /usr/local/bin
+PATH: /usr/bin
+PATH: /bin
+PATH: /usr/games
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+configure:1311: checking build system type
+configure:1329: result: x86_64-unknown-linux
+configure:1337: checking host system type
+configure:1351: result: x86_64-unknown-linux
+configure:1359: checking target system type
+configure:1373: result: x86_64-unknown-linux
+configure:1402: checking for a BSD-compatible install
+configure:1457: result: /usr/bin/install -c
+configure:1468: checking whether build environment is sane
+configure:1511: result: yes
+configure:1576: checking for gawk
+configure:1592: found /usr/bin/gawk
+configure:1602: result: gawk
+configure:1612: checking whether make sets $(MAKE)
+configure:1632: result: yes
+configure:1862: checking for g++
+configure:1878: found /usr/bin/g++
+configure:1888: result: g++
+configure:1904: checking for C++ compiler version
+configure:1907: g++ --version </dev/null >&5
+g++ (GCC) 4.2.3 20071123 (prerelease) (Debian 4.2.2-4)
+Copyright (C) 2007 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+configure:1910: $? = 0
+configure:1912: g++ -v </dev/null >&5
+Using built-in specs.
+Target: x86_64-linux-gnu
+Configured with: ../src/configure -v --enable-languages=c,c++,fortran,objc,obj-c++,treelang --prefix=/usr --enable-shared --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --enable-nls --with-gxx-include-dir=/usr/include/c++/4.2 --program-suffix=-4.2 --enable-clocale=gnu --enable-libstdcxx-debug --enable-mpfr --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
+Thread model: posix
+gcc version 4.2.3 20071123 (prerelease) (Debian 4.2.2-4)
+configure:1915: $? = 0
+configure:1917: g++ -V </dev/null >&5
+g++: '-V' option must have argument
+configure:1920: $? = 1
+configure:1943: checking for C++ compiler default output file name
+configure:1946: g++ conftest.cc >&5
+configure:1949: $? = 0
+configure:1995: result: a.out
+configure:2000: checking whether the C++ compiler works
+configure:2006: ./a.out
+configure:2009: $? = 0
+configure:2026: result: yes
+configure:2033: checking whether we are cross compiling
+configure:2035: result: no
+configure:2038: checking for suffix of executables
+configure:2040: g++ -o conftest conftest.cc >&5
+configure:2043: $? = 0
+configure:2068: result:
+configure:2074: checking for suffix of object files
+configure:2095: g++ -c conftest.cc >&5
+configure:2098: $? = 0
+configure:2120: result: o
+configure:2124: checking whether we are using the GNU C++ compiler
+configure:2148: g++ -c conftest.cc >&5
+configure:2154: $? = 0
+configure:2158: test -z
+ || test ! -s conftest.err
+configure:2161: $? = 0
+configure:2164: test -s conftest.o
+configure:2167: $? = 0
+configure:2180: result: yes
+configure:2186: checking whether g++ accepts -g
+configure:2207: g++ -c -g conftest.cc >&5
+configure:2213: $? = 0
+configure:2217: test -z
+ || test ! -s conftest.err
+configure:2220: $? = 0
+configure:2223: test -s conftest.o
+configure:2226: $? = 0
+configure:2237: result: yes
+configure:2279: g++ -c -g -O2 conftest.cc >&5
+configure:2285: $? = 0
+configure:2289: test -z
+ || test ! -s conftest.err
+configure:2292: $? = 0
+configure:2295: test -s conftest.o
+configure:2298: $? = 0
+configure:2324: g++ -c -g -O2 conftest.cc >&5
+conftest.cc: In function 'int main()':
+conftest.cc:15: error: 'exit' was not declared in this scope
+configure:2330: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+|
+| #define PACKAGE_NAME "PDB2PQR"
+| #define PACKAGE_TARNAME "pdb2pqr"
+| #define PACKAGE_VERSION "1.2.0"
+| #define PACKAGE_STRING "PDB2PQR 1.2.0"
+| #define PACKAGE_BUGREPORT "todd at ccb.wustl.edu"
+| #define PACKAGE "PDB2PQR"
+| #define VERSION "1.2.0"
+| /* end confdefs.h. */
+|
+| int
+| main ()
+| {
+| exit (42);
+| ;
+| return 0;
+| }
+configure:2279: g++ -c -g -O2 conftest.cc >&5
+conftest.cc:11: error: 'void std::exit(int)' should have been declared inside 'std'
+configure:2285: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+|
+| #define PACKAGE_NAME "PDB2PQR"
+| #define PACKAGE_TARNAME "pdb2pqr"
+| #define PACKAGE_VERSION "1.2.0"
+| #define PACKAGE_STRING "PDB2PQR 1.2.0"
+| #define PACKAGE_BUGREPORT "todd at ccb.wustl.edu"
+| #define PACKAGE "PDB2PQR"
+| #define VERSION "1.2.0"
+| /* end confdefs.h. */
+| extern "C" void std::exit (int) throw (); using std::exit;
+| #include <stdlib.h>
+| int
+| main ()
+| {
+| exit (42);
+| ;
+| return 0;
+| }
+configure:2279: g++ -c -g -O2 conftest.cc >&5
+conftest.cc:11: error: 'void std::exit(int)' should have been declared inside 'std'
+In file included from conftest.cc:12:
+/usr/include/stdlib.h:531: error: declaration of 'void std::exit(int) throw ()' throws different exceptions
+conftest.cc:11: error: from previous declaration 'void std::exit(int)'
+configure:2285: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+|
+| #define PACKAGE_NAME "PDB2PQR"
+| #define PACKAGE_TARNAME "pdb2pqr"
+| #define PACKAGE_VERSION "1.2.0"
+| #define PACKAGE_STRING "PDB2PQR 1.2.0"
+| #define PACKAGE_BUGREPORT "todd at ccb.wustl.edu"
+| #define PACKAGE "PDB2PQR"
+| #define VERSION "1.2.0"
+| /* end confdefs.h. */
+| extern "C" void std::exit (int); using std::exit;
+| #include <stdlib.h>
+| int
+| main ()
+| {
+| exit (42);
+| ;
+| return 0;
+| }
+configure:2279: g++ -c -g -O2 conftest.cc >&5
+configure:2285: $? = 0
+configure:2289: test -z
+ || test ! -s conftest.err
+configure:2292: $? = 0
+configure:2295: test -s conftest.o
+configure:2298: $? = 0
+configure:2324: g++ -c -g -O2 conftest.cc >&5
+configure:2330: $? = 0
+configure:2334: test -z
+ || test ! -s conftest.err
+configure:2337: $? = 0
+configure:2340: test -s conftest.o
+configure:2343: $? = 0
+configure:2377: checking for style of include used by make
+configure:2405: result: GNU
+configure:2433: checking dependency style of g++
+configure:2523: result: none
+configure:2544: checking for python
+configure:2562: found /usr/bin/python
+configure:2574: result: /usr/bin/python
+configure:2587: checking for python include directory
+configure:2593: result: -I/usr/include/python2.4
+configure:2637: checking for --disable-propka
+configure:2649: result: no
+configure:2651: result:
+configure:2653: result: ------------- Begin Processing PropKa Configure Options -----------
+configure:2658: result: ------------- End Processing PropKa Configure Options -----------
+configure:2660: result:
+configure:2670: checking for --enable-pdb2pka
+configure:2683: result: yes
+configure:2686: result:
+configure:2688: result: ------------- Begin Processing pdb2pka Configure Options -----------
+configure:2693: checking for Numeric include files
+configure:2697: result: -I/usr/include/python2.4/Numeric
+configure:2762: result: ------------- End Processing pdb2ka Configure Options -----------
+configure:2764: result:
+configure:2780: result: ------------- End Processing PDB2PQR Configure Options -----------
+configure:2782: result:
+configure:2926: creating ./config.status
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by PDB2PQR config.status 1.2.0, which was
+generated by GNU Autoconf 2.59. Invocation command line was
+
+ CONFIG_FILES =
+ CONFIG_HEADERS =
+ CONFIG_LINKS =
+ CONFIG_COMMANDS =
+ $ ./config.status
+
+on notebook
+
+config.status:701: creating Makefile
+config.status:701: creating pdb2pka/Makefile
+config.status:701: creating pdb2pka/substruct/Makefile
+config.status:884: executing depfiles commands
+configure:3979: result: Please type "make" to complete the installation.
+
+## ---------------- ##
+## Cache variables. ##
+## ---------------- ##
+
+ac_cv_build=x86_64-unknown-linux
+ac_cv_build_alias=x86_64-unknown-linux
+ac_cv_cxx_compiler_gnu=yes
+ac_cv_env_CPPFLAGS_set=
+ac_cv_env_CPPFLAGS_value=
+ac_cv_env_CXXFLAGS_set=
+ac_cv_env_CXXFLAGS_value=
+ac_cv_env_CXX_set=
+ac_cv_env_CXX_value=
+ac_cv_env_LDFLAGS_set=
+ac_cv_env_LDFLAGS_value=
+ac_cv_env_build_alias_set=
+ac_cv_env_build_alias_value=
+ac_cv_env_host_alias_set=
+ac_cv_env_host_alias_value=
+ac_cv_env_target_alias_set=
+ac_cv_env_target_alias_value=
+ac_cv_exeext=
+ac_cv_host=x86_64-unknown-linux
+ac_cv_host_alias=x86_64-unknown-linux
+ac_cv_objext=o
+ac_cv_path_install='/usr/bin/install -c'
+ac_cv_path_py_path=/usr/bin/python
+ac_cv_prog_AWK=gawk
+ac_cv_prog_ac_ct_CXX=g++
+ac_cv_prog_cxx_g=yes
+ac_cv_prog_make_make_set=yes
+ac_cv_target=x86_64-unknown-linux
+ac_cv_target_alias=x86_64-unknown-linux
+am_cv_CXX_dependencies_compiler_type=none
+
+## ----------------- ##
+## Output variables. ##
+## ----------------- ##
+
+ACLOCAL=':'
+AMDEPBACKSLASH='\'
+AMDEP_FALSE='#'
+AMDEP_TRUE=''
+AMTAR='${SHELL} /home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/config/missing --run tar'
+AUTOCONF=':'
+AUTOHEADER=':'
+AUTOMAKE=':'
+AWK='gawk'
+CPPFLAGS=''
+CXX='g++'
+CXXDEPMODE='depmode=none'
+CXXFLAGS='-g -O2'
+CYGPATH_W='echo'
+DEFS='-DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.2.0\" -DPACKAGE_STRING=\"PDB2PQR\ 1.2.0\" -DPACKAGE_BUGREPORT=\"todd at ccb.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.2.0\" '
+DEPDIR='.deps'
+ECHO_C=''
+ECHO_N='-n'
+ECHO_T=''
+EXEEXT=''
+INSTALL_DATA='${INSTALL} -m 644'
+INSTALL_PROGRAM='${INSTALL}'
+INSTALL_SCRIPT='${INSTALL}'
+INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
+LDFLAGS=''
+LIBOBJS=''
+LIBS=''
+LTLIBOBJS=''
+MAKEINFO='${SHELL} /home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/config/missing --run makeinfo'
+OBJEXT='o'
+PACKAGE='PDB2PQR'
+PACKAGE_BUGREPORT='todd at ccb.wustl.edu'
+PACKAGE_NAME='PDB2PQR'
+PACKAGE_STRING='PDB2PQR 1.2.0'
+PACKAGE_TARNAME='pdb2pqr'
+PACKAGE_VERSION='1.2.0'
+PATH_SEPARATOR=':'
+PDB2PQR_SUBDIRS='propka pdb2pka'
+PDB2PQR_VERSION='1:2:0'
+PY_CFLAGS='-I/usr/include/python2.4 -I/usr/include/python2.4/Numeric'
+PY_FLAGS='-fPIC'
+PY_HEADER='-I/usr/include/python2.4'
+PY_LDFLAGS=''
+PY_SHARED='-shared'
+SET_MAKE=''
+SHELL='/bin/sh'
+STRIP=''
+VERSION='1.2.0'
+ac_ct_CXX='g++'
+ac_ct_STRIP=''
+am__fastdepCXX_FALSE=''
+am__fastdepCXX_TRUE='#'
+am__include='include'
+am__leading_dot='.'
+am__quote=''
+am__tar='${AMTAR} chof - "$$tardir"'
+am__untar='${AMTAR} xf -'
+bindir='${exec_prefix}/bin'
+build='x86_64-unknown-linux'
+build_alias=''
+build_cpu='x86_64'
+build_os='linux'
+build_vendor='unknown'
+datadir='${prefix}/share'
+exec_prefix='${prefix}'
+host='x86_64-unknown-linux'
+host_alias=''
+host_cpu='x86_64'
+host_os='linux'
+host_vendor='unknown'
+includedir='${prefix}/include'
+infodir='${prefix}/info'
+install_sh='/home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/config/install-sh'
+libdir='${exec_prefix}/lib'
+libexecdir='${exec_prefix}/libexec'
+localstatedir='${prefix}/var'
+mandir='${prefix}/man'
+mkdir_p='mkdir -p --'
+oldincludedir='/usr/include'
+prefix='/home/moeller'
+program_transform_name='s,x,x,'
+py_path='/usr/bin/python'
+sbindir='${exec_prefix}/sbin'
+sharedstatedir='${prefix}/com'
+sysconfdir='${prefix}/etc'
+target='x86_64-unknown-linux'
+target_alias=''
+target_cpu='x86_64'
+target_os='linux'
+target_vendor='unknown'
+
+## ----------- ##
+## confdefs.h. ##
+## ----------- ##
+
+#define PACKAGE "PDB2PQR"
+#define PACKAGE_BUGREPORT "todd at ccb.wustl.edu"
+#define PACKAGE_NAME "PDB2PQR"
+#define PACKAGE_STRING "PDB2PQR 1.2.0"
+#define PACKAGE_TARNAME "pdb2pqr"
+#define PACKAGE_VERSION "1.2.0"
+#define VERSION "1.2.0"
+#endif
+#ifdef __cplusplus
+extern "C" void exit (int) throw ();
+
+configure: exit 0
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by PDB2PQR config.status 1.2.0, which was
+generated by GNU Autoconf 2.59. Invocation command line was
+
+ CONFIG_FILES =
+ CONFIG_HEADERS =
+ CONFIG_LINKS =
+ CONFIG_COMMANDS =
+ $ ./config.status
+
+on notebook
+
+config.status:701: creating Makefile
+config.status:701: creating pdb2pka/Makefile
+config.status:701: creating pdb2pka/substruct/Makefile
+config.status:884: executing depfiles commands
Property changes on: trunk/packages/pdb2pqr/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/pdb2pqr/trunk/debian/README.Debian.binary
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/README.Debian.binary (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/README.Debian.binary 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,23 @@
+The packaging of PDB2PQR was stimulated by the AutoDockTools
+and their dependency on it to visualise properties of the
+protein. And yes, if you have interest in this package, please
+help with completing the packaging.
+
+At the time this is written it remains unclear if this package
+can be distributed in Debian at all due to the more restrictive
+license of the PROPKA package that is shipped with it. However,
+the python code itself can also be used independent of PROPKA,
+which motivates to ship a stripped-down DFSG-variant. At this
+time, the main interest was in functionality. The whole part seems
+to work just fine.
+
+Upstream does not seem to have prepared the installation of
+their work into distinct directories. No time was yet allocated to
+address this.
+
+The code to offer pdb2pqr as a web service was omitted. The extensions
+directory was added as a documentation.
+
+Steffen Moeller
+
+Wed 26. Dez 01:19:54 CET 2007
Added: trunk/packages/pdb2pqr/trunk/debian/README.Debian.source
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/README.Debian.source (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/README.Debian.source 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1 @@
+The source was stripped from .svn directories.
Added: trunk/packages/pdb2pqr/trunk/debian/changelog
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/changelog (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/changelog 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,6 @@
+pdb2pqr (1.2.1-1) unstable; urgency=low
+
+ * Initial release.
+
+ -- Steffen Moeller <moeller at debian.org> Thu, 20 Dec 2007 16:27:31 +0100
+
Added: trunk/packages/pdb2pqr/trunk/debian/compat
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/compat (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/compat 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1 @@
+5
Added: trunk/packages/pdb2pqr/trunk/debian/control
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/control (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/control 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,23 @@
+Source: pdb2pqr
+Section: non-free/science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Build-Depends: debhelper (>= 5.0.38), python-central (>= 0.5.6), cdbs (>= 0.4.49), python-all-dev (>= 2.3.5-11), swig
+Standards-Version: 3.7.2
+XS-Python-Version: current
+Homepage: http://pdb2pqr.sourceforge.net
+
+Package: pdb2pqr
+XB-Python-Version: ${python:Versions}
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
+Description: Preparation of protein structures for electrostatics calculations
+ PDB2PQR is a Python software package that automates many of the common
+ tasks of preparing structures for continuum electrostatics calculations,
+ providing a platform-independent utility for converting protein files
+ in PDB format to PQR format. These tasks include:
+ * Adding a limited number of missing heavy atoms to biomolecular structures
+ * Determining side-chain pKas
+ * Placing missing hydrogens
+ * Optimizing the protein for favorable hydrogen bonding
+ * Assigning charge and radius parameters from a variety of force fields
Added: trunk/packages/pdb2pqr/trunk/debian/copyright
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/copyright (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/copyright 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,103 @@
+This package was debianized by Steffen Moeller <moeller at debian.org> on
+Thu, 20 Dec 2007 16:27:31 +0100.
+
+It was downloaded from http://mdltools.scripps.edu
+
+Upstream Authors:
+
+ Dr Chandrajit Bajaj,
+
+Copyright:
+
+
+ The University of Texas
+
+License:
+
+
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+ 1. This software is the copyright of THE UNIVERSITY OF TEXAS AT AUSTIN, 2005.
+
+ 2. The software is available under multiple licenses.
+
+ 3. For non commercial educational and non commercial academic use, the software including source code, interface definitions and compile scripts are freely available. Any distribution of code, library or executables which contains any modules from this software should contain, conspicously and appropriately, on each copy, this copyright and license notice and should be freely distributed.
+
+ 4. If you wish to incorporate parts of the Library into other free programs whose distribution conditions are incompatible with these, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation.
+
+ 5. For any other purpose, including commercial purposes, please contact The University of Texas at Austin for a different license.
+
+ 6. Credits:
+
+ This software has been developed at the Computational and Visualization center under
+
+ Dr Chandrajit Bajaj,
+ Computational Applied Mathematics Chair in Visualization,
+ Professor of Computer Sciences,
+ Director of Center for Computational Visualization,
+ Department of Computer Sciences & The Institute of Computational Engineering and Sciences , Center for Computational Visualization,
+ 201 East 24th Street, ACES 2.324A,
+ 1 University Station, C0200,
+ Austin, TX 78712-0027.
+
+We request that you agree to acknowledge the use of the software that results in any published work, including scientific papers, films and videotapes by citing the references listed below
+
+For UTblur:
+
+C. Bajaj, V. Siddavanahalli
+Fast Feature Adaptive Surfaces and Derivatives Computation for Volumetric Particle Data
+ICES and CS technical reports, The University of Texas at Austin, 2005.
+
+
+For UTisocontour:
+
+C. Bajaj, V. Pascucci, D. Schikore
+Accelerated IsoContouring of Scalar Fields
+Data Visualization Techniques, edited by C. Bajaj, John Wiley and Sons (1998).
+
+C. Bajaj, V. Pascucci, D. Schikore
+Fast Isocontouring for Improved Interactivity
+Proceedings: ACM Siggraph/IEEE Symposium on Volume Visualization, ACM Press, (1996), San Francisco, CA. Pages: 39-46 99
+
+
+For UTmesh:
+
+Y. Zhang, C. Bajaj
+Adaptive and Quality Quadrilateral/Hexahedral Meshing from Volumetric Data
+Computer Methods in Applied Mechanics and Engineering (CMAME), in press, 2005.
+
+Y. Zhang, C. Bajaj, B-S. Sohn
+3D Finite Element Meshing from Imaging Data
+The special issue of Computer Methods in Applied Mechanics and Engineering (CMAME) on Unstructured Mesh Generation, 194(48-49):5083-5106, 2005.
+
+
+For UTsdf:
+
+C. Bajaj, V. Siddavanahalli
+An Adaptive Grid Based Method for Computing Molecular Surfaces and Properties
+ICES and CS Technical Reports, The University of Texas at Austin, 2005.
+
+
+For UTvolrend:
+
+C. Bajaj, Z. Yu, M. Auer
+Volumetric Feature Extraction and Visualization of Tomographic Molecular Imaging.
+Journal of Structural Biology, Volume 144, Issues 1-2, October 2003, Pages 132-143
+
+
+For UTmolderivatives:
+
+C. Bajaj, V. Siddavanahalli
+Fast Feature Adaptive Surfaces and Derivatives Computation for Volumetric Particle Data
+ICES and CS Technical Reports, The University of Texas at Austin, 2005.
+
+7. No warranty
+
+7a. Because the library is licensed free of charge, there is no warranty for the library, to the extent permitted by applicable law. except when otherwise stated in writing the copyright holders and/or other parties provide the library "as is" without warranty of any kind, either expressed or implied, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. the entire risk as to the quality and performance of the library is with you. should the library prove defective, you assume the cost of all necessary servicing, repair or correction.
+
+7b. In no event unless required by applicable law or agreed to in writing will any copyright holder, or any other party who may modify and/or redistribute the library as permitted above, be liable to you for damages, including any general, special, incidental or consequential damages arising out of the use or inability to use the library (including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties or a failure of the library to operate with any other software), even if such holder or other party has been advised of the possibility of such damages.
+
+END OF TERMS AND CONDITIONS
+
+The Debian packaging is (C) 2007, Steffen Moeller <moeller at debian.org> and
+is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
Added: trunk/packages/pdb2pqr/trunk/debian/dirs
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/dirs (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/dirs 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,3 @@
+/usr/bin
+/usr/share/pdb2pqr
+/usr/share/doc/pdb2pqr
Added: trunk/packages/pdb2pqr/trunk/debian/docs
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/docs (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/docs 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,8 @@
+README
+AUTHORS
+doc/userguide.html
+doc/programmerguide.html
+NEWS
+ChangeLog
+doc/images
+doc/pydoc
Added: trunk/packages/pdb2pqr/trunk/debian/examples
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/examples (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/examples 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1 @@
+examples/*
Added: trunk/packages/pdb2pqr/trunk/debian/pycompat
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pycompat (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/pycompat 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1 @@
+2
Added: trunk/packages/pdb2pqr/trunk/debian/rules
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/rules (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/rules 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,51 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+
+configure: config.status
+
+config.status:
+ ./configure --enable-pdb2pka
+ touch $@
+
+
+build: build-stamp
+
+build-stamp: configure
+ make
+ touch $@
+
+install: build
+ if [ ! -d $(CURDIR)/debian/pdb2pqr/usr/share/pdb2pqr ]; then \
+ echo directory $(CURDIR)/debian/pdb2pqr/usr/share/pdb2pqr/ should have been created via debian/dirs ; \
+ mkdir -p $(CURDIR)/debian/pdb2pqr/usr/share/pdb2pqr ; \
+ fi
+ cp dat/* $(CURDIR)/debian/pdb2pqr/usr/share/pdb2pqr/
+ cp -r pdb2pqr.py src extensions $(CURDIR)/debian/pdb2pqr/usr/share/pdb2pqr/
+ if [ ! -d $(CURDIR)/debian/pdb2pqr/usr/bin ]; then \
+ echo directory $(CURDIR)/debian/pdb2pqr/usr/bin should have been created via debian/dirs ; \
+ mkdir -p $(CURDIR)/debian/pdb2pqr/usr/bin ; \
+ fi
+ cp debian/wrapper.sh $(CURDIR)/debian/pdb2pqr/usr/bin/pdb2pqr
+ chmod 755 $(CURDIR)/debian/pdb2pqr/usr/bin/pdb2pqr
+ cp propka/propka $(CURDIR)/debian/pdb2pqr/usr/bin/
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+
+common-binary-predeb-arch::install
+
+clean::
+ rm -rf build-stamp config.status propka/propka
+ find . -name *.o -o -name *.so | xargs -r rm
+ find . -name "*.pdb" -exec chmod 644 {} \;
+
+.PHONY: install
Property changes on: trunk/packages/pdb2pqr/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/pdb2pqr/trunk/debian/watch
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/watch (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/watch 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,4 @@
+version=3
+http://sf.net/pdb2pqr/pdb2pqr-(.*)\.tar\.gz
+
+
Added: trunk/packages/pdb2pqr/trunk/debian/wrapper.sh
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/wrapper.sh (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/wrapper.sh 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,8 @@
+#!/bin/sh
+app=/usr/share/pdb2pqr/pdb2pqr.py
+if [ -x $app ]; then
+ $app $*
+else
+ echo "No executable at '$app'."
+ exit -1
+fi
Added: trunk/packages/pdb2pqr/trunk/pdb2pka/Makefile
===================================================================
--- trunk/packages/pdb2pqr/trunk/pdb2pka/Makefile (rev 0)
+++ trunk/packages/pdb2pqr/trunk/pdb2pka/Makefile 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,506 @@
+# Makefile.in generated by automake 1.9.6 from Makefile.am.
+# pdb2pka/Makefile. Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+
+
+srcdir = .
+top_srcdir = ..
+
+pkgdatadir = $(datadir)/PDB2PQR
+pkglibdir = $(libdir)/PDB2PQR
+pkgincludedir = $(includedir)/PDB2PQR
+top_builddir = ..
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+INSTALL = /usr/bin/install -c
+install_sh_DATA = $(install_sh) -c -m 644
+install_sh_PROGRAM = $(install_sh) -c
+install_sh_SCRIPT = $(install_sh) -c
+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = x86_64-unknown-linux
+host_triplet = x86_64-unknown-linux
+target_triplet = x86_64-unknown-linux
+noinst_PROGRAMS = _pMC_mult.so$(EXEEXT)
+subdir = pdb2pka
+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
+ $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
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+CONFIG_CLEAN_FILES =
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+am__pMC_mult_so_OBJECTS = pMC_mult.$(OBJEXT) pMC_mult_wrap.$(OBJEXT)
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+_pMC_mult_so_DEPENDENCIES = $(am__DEPENDENCIES_1)
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+ install-exec-recursive install-info-recursive \
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+ACLOCAL = :
+AMDEP_FALSE = #
+AMDEP_TRUE =
+AMTAR = ${SHELL} /home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/config/missing --run tar
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+AUTOHEADER = :
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+CXXDEPMODE = depmode=none
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+DEPDIR = .deps
+ECHO_C =
+ECHO_N = -n
+ECHO_T =
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+LDFLAGS =
+LIBOBJS =
+LIBS =
+LTLIBOBJS =
+MAKEINFO = ${SHELL} /home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/config/missing --run makeinfo
+OBJEXT = o
+PACKAGE = PDB2PQR
+PACKAGE_BUGREPORT = todd at ccb.wustl.edu
+PACKAGE_NAME = PDB2PQR
+PACKAGE_STRING = PDB2PQR 1.2.0
+PACKAGE_TARNAME = pdb2pqr
+PACKAGE_VERSION = 1.2.0
+PATH_SEPARATOR = :
+PDB2PQR_SUBDIRS = propka pdb2pka
+PDB2PQR_VERSION = 1:2:0
+PY_CFLAGS = -I/usr/include/python2.4 -I/usr/include/python2.4/Numeric
+PY_FLAGS = -fPIC
+PY_HEADER = -I/usr/include/python2.4
+PY_LDFLAGS =
+PY_SHARED = -shared
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+build_vendor = unknown
+datadir = ${prefix}/share
+exec_prefix = ${prefix}
+host = x86_64-unknown-linux
+host_alias =
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+host_os = linux
+host_vendor = unknown
+includedir = ${prefix}/include
+infodir = ${prefix}/info
+install_sh = /home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/config/install-sh
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Added: trunk/packages/pdb2pqr/trunk/pdb2pka/substruct/Makefile
===================================================================
--- trunk/packages/pdb2pqr/trunk/pdb2pka/substruct/Makefile (rev 0)
+++ trunk/packages/pdb2pqr/trunk/pdb2pka/substruct/Makefile 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,389 @@
+# Makefile.in generated by automake 1.9.6 from Makefile.am.
+# pdb2pka/substruct/Makefile. Generated from Makefile.in by configure.
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
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+
+
+
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Added: trunk/packages/pdb2pqr/trunk/propka/Makefile
===================================================================
--- trunk/packages/pdb2pqr/trunk/propka/Makefile (rev 0)
+++ trunk/packages/pdb2pqr/trunk/propka/Makefile 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,483 @@
+# Makefile.in generated by automake 1.7 from Makefile.am.
+# Makefile. Generated from Makefile.in by configure.
+
+# Copyright 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002
+# Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
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+
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Added: trunk/packages/pdb2pqr/trunk/propka/config.log
===================================================================
--- trunk/packages/pdb2pqr/trunk/propka/config.log (rev 0)
+++ trunk/packages/pdb2pqr/trunk/propka/config.log 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,386 @@
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by PropKa configure 1.0.0, which was
+generated by GNU Autoconf 2.59. Invocation command line was
+
+ $ ./configure
+
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = notebook
+uname -m = x86_64
+uname -r = 2.6.23-1-amd64
+uname -s = Linux
+uname -v = #1 SMP Fri Nov 30 12:19:15 UTC 2007
+
+/usr/bin/uname -p = unknown
+/bin/uname -X = unknown
+
+/bin/arch = unknown
+/usr/bin/arch -k = unknown
+/usr/convex/getsysinfo = unknown
+hostinfo = unknown
+/bin/machine = unknown
+/usr/bin/oslevel = unknown
+/bin/universe = unknown
+
+PATH: /home/moeller/bin
+PATH: /usr/local/bin
+PATH: /usr/bin
+PATH: /bin
+PATH: /usr/games
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+configure:1324: checking build system type
+configure:1342: result: x86_64-unknown-linux
+configure:1350: checking host system type
+configure:1364: result: x86_64-unknown-linux
+configure:1372: checking target system type
+configure:1386: result: x86_64-unknown-linux
+configure:1415: checking for a BSD-compatible install
+configure:1470: result: /usr/bin/install -c
+configure:1481: checking whether build environment is sane
+configure:1524: result: yes
+configure:1557: checking for gawk
+configure:1573: found /usr/bin/gawk
+configure:1583: result: gawk
+configure:1593: checking whether make sets $(MAKE)
+configure:1613: result: yes
+configure:1780: checking for python
+configure:1798: found /usr/bin/python
+configure:1810: result: /usr/bin/python
+configure:1874: checking for gcc
+configure:1890: found /usr/bin/gcc
+configure:1900: result: gcc
+configure:2144: checking for C compiler version
+configure:2147: gcc --version </dev/null >&5
+gcc (GCC) 4.2.3 20071123 (prerelease) (Debian 4.2.2-4)
+Copyright (C) 2007 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+configure:2150: $? = 0
+configure:2152: gcc -v </dev/null >&5
+Using built-in specs.
+Target: x86_64-linux-gnu
+Configured with: ../src/configure -v --enable-languages=c,c++,fortran,objc,obj-c++,treelang --prefix=/usr --enable-shared --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --enable-nls --with-gxx-include-dir=/usr/include/c++/4.2 --program-suffix=-4.2 --enable-clocale=gnu --enable-libstdcxx-debug --enable-mpfr --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
+Thread model: posix
+gcc version 4.2.3 20071123 (prerelease) (Debian 4.2.2-4)
+configure:2155: $? = 0
+configure:2157: gcc -V </dev/null >&5
+gcc: '-V' option must have argument
+configure:2160: $? = 1
+configure:2183: checking for C compiler default output file name
+configure:2186: gcc conftest.c >&5
+configure:2189: $? = 0
+configure:2235: result: a.out
+configure:2240: checking whether the C compiler works
+configure:2246: ./a.out
+configure:2249: $? = 0
+configure:2266: result: yes
+configure:2273: checking whether we are cross compiling
+configure:2275: result: no
+configure:2278: checking for suffix of executables
+configure:2280: gcc -o conftest conftest.c >&5
+configure:2283: $? = 0
+configure:2308: result:
+configure:2314: checking for suffix of object files
+configure:2335: gcc -c conftest.c >&5
+configure:2338: $? = 0
+configure:2360: result: o
+configure:2364: checking whether we are using the GNU C compiler
+configure:2388: gcc -c conftest.c >&5
+configure:2394: $? = 0
+configure:2398: test -z
+ || test ! -s conftest.err
+configure:2401: $? = 0
+configure:2404: test -s conftest.o
+configure:2407: $? = 0
+configure:2420: result: yes
+configure:2426: checking whether gcc accepts -g
+configure:2447: gcc -c -g conftest.c >&5
+configure:2453: $? = 0
+configure:2457: test -z
+ || test ! -s conftest.err
+configure:2460: $? = 0
+configure:2463: test -s conftest.o
+configure:2466: $? = 0
+configure:2477: result: yes
+configure:2494: checking for gcc option to accept ANSI C
+configure:2564: gcc -c -g -O2 conftest.c >&5
+configure:2570: $? = 0
+configure:2574: test -z
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+configure:2583: $? = 0
+configure:2601: result: none needed
+configure:2619: gcc -c -g -O2 conftest.c >&5
+conftest.c:2: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'me'
+configure:2625: $? = 1
+configure: failed program was:
+| #ifndef __cplusplus
+| choke me
+| #endif
+configure:2777: checking for style of include used by make
+configure:2805: result: GNU
+configure:2833: checking dependency style of gcc
+configure:2895: result: none
+configure:2963: checking for g77
+configure:2979: found /usr/bin/g77
+configure:2989: result: g77
+configure:3004: checking for Fortran 77 compiler version
+configure:3007: g77 --version </dev/null >&5
+GNU Fortran (GCC) 3.4.6 (Debian 3.4.6-6)
+Copyright (C) 2006 Free Software Foundation, Inc.
+
+GNU Fortran comes with NO WARRANTY, to the extent permitted by law.
+You may redistribute copies of GNU Fortran
+under the terms of the GNU General Public License.
+For more information about these matters, see the file named COPYING
+or type the command `info -f g77 Copying'.
+configure:3010: $? = 0
+configure:3012: g77 -v </dev/null >&5
+Reading specs from /usr/lib/gcc/x86_64-linux-gnu/3.4.6/specs
+Configured with: ../src/configure -v --enable-languages=c,c++,f77,pascal --prefix=/usr --libexecdir=/usr/lib --with-gxx-include-dir=/usr/include/c++/3.4 --enable-shared --with-system-zlib --enable-nls --without-included-gettext --program-suffix=-3.4 --enable-__cxa_atexit --enable-clocale=gnu --enable-libstdcxx-debug x86_64-linux-gnu
+Thread model: posix
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+configure:3015: $? = 0
+configure:3017: g77 -V </dev/null >&5
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+configure:3028: checking whether we are using the GNU Fortran 77 compiler
+configure:3042: g77 -c conftest.F >&5
+configure:3048: $? = 0
+configure:3052: test -z
+ || test ! -s conftest.err
+configure:3055: $? = 0
+configure:3058: test -s conftest.o
+configure:3061: $? = 0
+configure:3074: result: yes
+configure:3080: checking whether g77 accepts -g
+configure:3092: g77 -c -g conftest.f >&5
+configure:3098: $? = 0
+configure:3102: test -z
+ || test ! -s conftest.err
+configure:3105: $? = 0
+configure:3108: test -s conftest.o
+configure:3111: $? = 0
+configure:3123: result: yes
+configure:3195: checking how to run the C preprocessor
+configure:3230: gcc -E conftest.c
+configure:3236: $? = 0
+configure:3268: gcc -E conftest.c
+conftest.c:11:28: error: ac_nonexistent.h: No such file or directory
+configure:3274: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+|
+| #define PACKAGE_NAME "PropKa"
+| #define PACKAGE_TARNAME "propka"
+| #define PACKAGE_VERSION "1.0.0"
+| #define PACKAGE_STRING "PropKa 1.0.0"
+| #define PACKAGE_BUGREPORT "Jan-Jensen at uiowa.edu"
+| #define PACKAGE "PropKa"
+| #define VERSION "1.0.0"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:3313: result: gcc -E
+configure:3337: gcc -E conftest.c
+configure:3343: $? = 0
+configure:3375: gcc -E conftest.c
+conftest.c:11:28: error: ac_nonexistent.h: No such file or directory
+configure:3381: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+|
+| #define PACKAGE_NAME "PropKa"
+| #define PACKAGE_TARNAME "propka"
+| #define PACKAGE_VERSION "1.0.0"
+| #define PACKAGE_STRING "PropKa 1.0.0"
+| #define PACKAGE_BUGREPORT "Jan-Jensen at uiowa.edu"
+| #define PACKAGE "PropKa"
+| #define VERSION "1.0.0"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:3425: checking for python include directory
+configure:3431: result: -I/usr/include/python2.4
+configure:3612: creating ./config.status
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by PropKa config.status 1.0.0, which was
+generated by GNU Autoconf 2.59. Invocation command line was
+
+ CONFIG_FILES =
+ CONFIG_HEADERS =
+ CONFIG_LINKS =
+ CONFIG_COMMANDS =
+ $ ./config.status
+
+on notebook
+
+config.status:697: creating Makefile
+config.status:880: executing depfiles commands
+
+## ---------------- ##
+## Cache variables. ##
+## ---------------- ##
+
+ac_cv_build=x86_64-unknown-linux
+ac_cv_build_alias=x86_64-unknown-linux
+ac_cv_c_compiler_gnu=yes
+ac_cv_env_CC_set=
+ac_cv_env_CC_value=
+ac_cv_env_CFLAGS_set=
+ac_cv_env_CFLAGS_value=
+ac_cv_env_CPPFLAGS_set=
+ac_cv_env_CPPFLAGS_value=
+ac_cv_env_CPP_set=
+ac_cv_env_CPP_value=
+ac_cv_env_F77_set=
+ac_cv_env_F77_value=
+ac_cv_env_FFLAGS_set=
+ac_cv_env_FFLAGS_value=
+ac_cv_env_LDFLAGS_set=
+ac_cv_env_LDFLAGS_value=
+ac_cv_env_build_alias_set=
+ac_cv_env_build_alias_value=
+ac_cv_env_host_alias_set=
+ac_cv_env_host_alias_value=
+ac_cv_env_target_alias_set=
+ac_cv_env_target_alias_value=
+ac_cv_exeext=
+ac_cv_f77_compiler_gnu=yes
+ac_cv_host=x86_64-unknown-linux
+ac_cv_host_alias=x86_64-unknown-linux
+ac_cv_objext=o
+ac_cv_path_install='/usr/bin/install -c'
+ac_cv_path_py_path=/usr/bin/python
+ac_cv_prog_AWK=gawk
+ac_cv_prog_CPP='gcc -E'
+ac_cv_prog_ac_ct_CC=gcc
+ac_cv_prog_ac_ct_F77=g77
+ac_cv_prog_cc_g=yes
+ac_cv_prog_cc_stdc=
+ac_cv_prog_f77_g=yes
+ac_cv_prog_make_make_set=yes
+ac_cv_target=x86_64-unknown-linux
+ac_cv_target_alias=x86_64-unknown-linux
+am_cv_CC_dependencies_compiler_type=none
+
+## ----------------- ##
+## Output variables. ##
+## ----------------- ##
+
+ACLOCAL=':'
+AMDEPBACKSLASH='\'
+AMDEP_FALSE='#'
+AMDEP_TRUE=''
+AMTAR='${SHELL} /home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/propka/config/missing --run tar'
+AUTOCONF=':'
+AUTOHEADER=':'
+AUTOMAKE=':'
+AWK='gawk'
+CC='gcc'
+CCDEPMODE='depmode=none'
+CFLAGS='-g -O2'
+CPP='gcc -E'
+CPPFLAGS=''
+CYGPATH_W='echo'
+DEFS='-DPACKAGE_NAME=\"PropKa\" -DPACKAGE_TARNAME=\"propka\" -DPACKAGE_VERSION=\"1.0.0\" -DPACKAGE_STRING=\"PropKa\ 1.0.0\" -DPACKAGE_BUGREPORT=\"Jan-Jensen at uiowa.edu\" -DPACKAGE=\"PropKa\" -DVERSION=\"1.0.0\" '
+DEPDIR='.deps'
+ECHO_C=''
+ECHO_N='-n'
+ECHO_T=''
+EXEEXT=''
+F77='g77'
+FFLAGS=' -g -O2'
+INSTALL_DATA='${INSTALL} -m 644'
+INSTALL_PROGRAM='${INSTALL}'
+INSTALL_SCRIPT='${INSTALL}'
+INSTALL_STRIP_PROGRAM='${SHELL} $(install_sh) -c -s'
+LDFLAGS=''
+LIBOBJS=''
+LIBS=''
+LTLIBOBJS=''
+MAKEINFO='${SHELL} /home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/propka/config/missing --run makeinfo'
+OBJEXT='o'
+PACKAGE='PropKa'
+PACKAGE_BUGREPORT='Jan-Jensen at uiowa.edu'
+PACKAGE_NAME='PropKa'
+PACKAGE_STRING='PropKa 1.0.0'
+PACKAGE_TARNAME='propka'
+PACKAGE_VERSION='1.0.0'
+PATH_SEPARATOR=':'
+PROPKA_VERSION='1:0:0'
+PY_CFLAGS='-I/usr/include/python2.4'
+PY_FLAGS='-fPIC'
+PY_LDFLAGS=''
+PY_SHARED='-shared'
+SET_MAKE=''
+SHELL='/bin/sh'
+STRIP=''
+VERSION='1.0.0'
+ac_ct_CC='gcc'
+ac_ct_F77='g77'
+ac_ct_STRIP=''
+am__fastdepCC_FALSE=''
+am__fastdepCC_TRUE='#'
+am__include='include'
+am__quote=''
+bindir='${exec_prefix}/bin'
+build='x86_64-unknown-linux'
+build_alias=''
+build_cpu='x86_64'
+build_os='linux'
+build_vendor='unknown'
+datadir='${prefix}/share'
+exec_prefix='${prefix}'
+host='x86_64-unknown-linux'
+host_alias=''
+host_cpu='x86_64'
+host_os='linux'
+host_vendor='unknown'
+includedir='${prefix}/include'
+infodir='${prefix}/info'
+install_sh='/home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/propka/config/install-sh'
+libdir='${exec_prefix}/lib'
+libexecdir='${exec_prefix}/libexec'
+localstatedir='${prefix}/var'
+mandir='${prefix}/man'
+oldincludedir='/usr/include'
+prefix='/home/moeller'
+program_transform_name='s,x,x,'
+py_path='/usr/bin/python'
+sbindir='${exec_prefix}/sbin'
+sharedstatedir='${prefix}/com'
+sysconfdir='${prefix}/etc'
+target='x86_64-unknown-linux'
+target_alias=''
+target_cpu='x86_64'
+target_os='linux'
+target_vendor='unknown'
+
+## ----------- ##
+## confdefs.h. ##
+## ----------- ##
+
+#define PACKAGE "PropKa"
+#define PACKAGE_BUGREPORT "Jan-Jensen at uiowa.edu"
+#define PACKAGE_NAME "PropKa"
+#define PACKAGE_STRING "PropKa 1.0.0"
+#define PACKAGE_TARNAME "propka"
+#define PACKAGE_VERSION "1.0.0"
+#define VERSION "1.0.0"
+
+configure: exit 0
Added: trunk/packages/pdb2pqr/trunk/propka/config.status
===================================================================
--- trunk/packages/pdb2pqr/trunk/propka/config.status (rev 0)
+++ trunk/packages/pdb2pqr/trunk/propka/config.status 2007-12-26 01:26:46 UTC (rev 1023)
@@ -0,0 +1,977 @@
+#! /bin/sh
+# Generated by configure.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+SHELL=${CONFIG_SHELL-/bin/sh}
+## --------------------- ##
+## M4sh Initialization. ##
+## --------------------- ##
+
+# Be Bourne compatible
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+elif test -n "${BASH_VERSION+set}" && (set -o posix) >/dev/null 2>&1; then
+ set -o posix
+fi
+DUALCASE=1; export DUALCASE # for MKS sh
+
+# Support unset when possible.
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ as_unset=unset
+else
+ as_unset=false
+fi
+
+
+# Work around bugs in pre-3.0 UWIN ksh.
+$as_unset ENV MAIL MAILPATH
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+for as_var in \
+ LANG LANGUAGE LC_ADDRESS LC_ALL LC_COLLATE LC_CTYPE LC_IDENTIFICATION \
+ LC_MEASUREMENT LC_MESSAGES LC_MONETARY LC_NAME LC_NUMERIC LC_PAPER \
+ LC_TELEPHONE LC_TIME
+do
+ if (set +x; test -z "`(eval $as_var=C; export $as_var) 2>&1`"); then
+ eval $as_var=C; export $as_var
+ else
+ $as_unset $as_var
+ fi
+done
+
+# Required to use basename.
+if expr a : '\(a\)' >/dev/null 2>&1; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename /) >/dev/null 2>&1 && test "X`basename / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+
+# Name of the executable.
+as_me=`$as_basename "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)$' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{ s//\1/; q; }
+ /^X\/\(\/\/\)$/{ s//\1/; q; }
+ /^X\/\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+
+
+# PATH needs CR, and LINENO needs CR and PATH.
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ echo "#! /bin/sh" >conf$$.sh
+ echo "exit 0" >>conf$$.sh
+ chmod +x conf$$.sh
+ if (PATH="/nonexistent;."; conf$$.sh) >/dev/null 2>&1; then
+ PATH_SEPARATOR=';'
+ else
+ PATH_SEPARATOR=:
+ fi
+ rm -f conf$$.sh
+fi
+
+
+ as_lineno_1=$LINENO
+ as_lineno_2=$LINENO
+ as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null`
+ test "x$as_lineno_1" != "x$as_lineno_2" &&
+ test "x$as_lineno_3" = "x$as_lineno_2" || {
+ # Find who we are. Look in the path if we contain no path at all
+ # relative or not.
+ case $0 in
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+done
+
+ ;;
+ esac
+ # We did not find ourselves, most probably we were run as `sh COMMAND'
+ # in which case we are not to be found in the path.
+ if test "x$as_myself" = x; then
+ as_myself=$0
+ fi
+ if test ! -f "$as_myself"; then
+ { { echo "$as_me:$LINENO: error: cannot find myself; rerun with an absolute path" >&5
+echo "$as_me: error: cannot find myself; rerun with an absolute path" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ case $CONFIG_SHELL in
+ '')
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for as_base in sh bash ksh sh5; do
+ case $as_dir in
+ /*)
+ if ("$as_dir/$as_base" -c '
+ as_lineno_1=$LINENO
+ as_lineno_2=$LINENO
+ as_lineno_3=`(expr $as_lineno_1 + 1) 2>/dev/null`
+ test "x$as_lineno_1" != "x$as_lineno_2" &&
+ test "x$as_lineno_3" = "x$as_lineno_2" ') 2>/dev/null; then
+ $as_unset BASH_ENV || test "${BASH_ENV+set}" != set || { BASH_ENV=; export BASH_ENV; }
+ $as_unset ENV || test "${ENV+set}" != set || { ENV=; export ENV; }
+ CONFIG_SHELL=$as_dir/$as_base
+ export CONFIG_SHELL
+ exec "$CONFIG_SHELL" "$0" ${1+"$@"}
+ fi;;
+ esac
+ done
+done
+;;
+ esac
+
+ # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
+ # uniformly replaced by the line number. The first 'sed' inserts a
+ # line-number line before each line; the second 'sed' does the real
+ # work. The second script uses 'N' to pair each line-number line
+ # with the numbered line, and appends trailing '-' during
+ # substitution so that $LINENO is not a special case at line end.
+ # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
+ # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-)
+ sed '=' <$as_myself |
+ sed '
+ N
+ s,$,-,
+ : loop
+ s,^\(['$as_cr_digits']*\)\(.*\)[$]LINENO\([^'$as_cr_alnum'_]\),\1\2\1\3,
+ t loop
+ s,-$,,
+ s,^['$as_cr_digits']*\n,,
+ ' >$as_me.lineno &&
+ chmod +x $as_me.lineno ||
+ { { echo "$as_me:$LINENO: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&5
+echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2;}
+ { (exit 1); exit 1; }; }
+
+ # Don't try to exec as it changes $[0], causing all sort of problems
+ # (the dirname of $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensible to this).
+ . ./$as_me.lineno
+ # Exit status is that of the last command.
+ exit
+}
+
+
+case `echo "testing\c"; echo 1,2,3`,`echo -n testing; echo 1,2,3` in
+ *c*,-n*) ECHO_N= ECHO_C='
+' ECHO_T=' ' ;;
+ *c*,* ) ECHO_N=-n ECHO_C= ECHO_T= ;;
+ *) ECHO_N= ECHO_C='\c' ECHO_T= ;;
+esac
+
+if expr a : '\(a\)' >/dev/null 2>&1; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+rm -f conf$$ conf$$.exe conf$$.file
+echo >conf$$.file
+if ln -s conf$$.file conf$$ 2>/dev/null; then
+ # We could just check for DJGPP; but this test a) works b) is more generic
+ # and c) will remain valid once DJGPP supports symlinks (DJGPP 2.04).
+ if test -f conf$$.exe; then
+ # Don't use ln at all; we don't have any links
+ as_ln_s='cp -p'
+ else
+ as_ln_s='ln -s'
+ fi
+elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.file
+
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p=:
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+as_executable_p="test -f"
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+# IFS
+# We need space, tab and new line, in precisely that order.
+as_nl='
+'
+IFS=" $as_nl"
+
+# CDPATH.
+$as_unset CDPATH
+
+exec 6>&1
+
+# Open the log real soon, to keep \$[0] and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling. Logging --version etc. is OK.
+exec 5>>config.log
+{
+ echo
+ sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
+## Running $as_me. ##
+_ASBOX
+} >&5
+cat >&5 <<_CSEOF
+
+This file was extended by PropKa $as_me 1.0.0, which was
+generated by GNU Autoconf 2.59. Invocation command line was
+
+ CONFIG_FILES = $CONFIG_FILES
+ CONFIG_HEADERS = $CONFIG_HEADERS
+ CONFIG_LINKS = $CONFIG_LINKS
+ CONFIG_COMMANDS = $CONFIG_COMMANDS
+ $ $0 $@
+
+_CSEOF
+echo "on `(hostname || uname -n) 2>/dev/null | sed 1q`" >&5
+echo >&5
+config_files=" Makefile"
+config_commands=" depfiles"
+
+ac_cs_usage="\
+\`$as_me' instantiates files from templates according to the
+current configuration.
+
+Usage: $0 [OPTIONS] [FILE]...
+
+ -h, --help print this help, then exit
+ -V, --version print version number, then exit
+ -q, --quiet do not print progress messages
+ -d, --debug don't remove temporary files
+ --recheck update $as_me by reconfiguring in the same conditions
+ --file=FILE[:TEMPLATE]
+ instantiate the configuration file FILE
+
+Configuration files:
+$config_files
+
+Configuration commands:
+$config_commands
+
+Report bugs to <bug-autoconf at gnu.org>."
+ac_cs_version="\
+PropKa config.status 1.0.0
+configured by ./configure, generated by GNU Autoconf 2.59,
+ with options \"\"
+
+Copyright (C) 2003 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+srcdir=.
+INSTALL="/usr/bin/install -c"
+# If no file are specified by the user, then we need to provide default
+# value. By we need to know if files were specified by the user.
+ac_need_defaults=:
+while test $# != 0
+do
+ case $1 in
+ --*=*)
+ ac_option=`expr "x$1" : 'x\([^=]*\)='`
+ ac_optarg=`expr "x$1" : 'x[^=]*=\(.*\)'`
+ ac_shift=:
+ ;;
+ -*)
+ ac_option=$1
+ ac_optarg=$2
+ ac_shift=shift
+ ;;
+ *) # This is not an option, so the user has probably given explicit
+ # arguments.
+ ac_option=$1
+ ac_need_defaults=false;;
+ esac
+
+ case $ac_option in
+ # Handling of the options.
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ ac_cs_recheck=: ;;
+ --version | --vers* | -V )
+ echo "$ac_cs_version"; exit 0 ;;
+ --he | --h)
+ # Conflict between --help and --header
+ { { echo "$as_me:$LINENO: error: ambiguous option: $1
+Try \`$0 --help' for more information." >&5
+echo "$as_me: error: ambiguous option: $1
+Try \`$0 --help' for more information." >&2;}
+ { (exit 1); exit 1; }; };;
+ --help | --hel | -h )
+ echo "$ac_cs_usage"; exit 0 ;;
+ --debug | --d* | -d )
+ debug=: ;;
+ --file | --fil | --fi | --f )
+ $ac_shift
+ CONFIG_FILES="$CONFIG_FILES $ac_optarg"
+ ac_need_defaults=false;;
+ --header | --heade | --head | --hea )
+ $ac_shift
+ CONFIG_HEADERS="$CONFIG_HEADERS $ac_optarg"
+ ac_need_defaults=false;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil | --si | --s)
+ ac_cs_silent=: ;;
+
+ # This is an error.
+ -*) { { echo "$as_me:$LINENO: error: unrecognized option: $1
+Try \`$0 --help' for more information." >&5
+echo "$as_me: error: unrecognized option: $1
+Try \`$0 --help' for more information." >&2;}
+ { (exit 1); exit 1; }; } ;;
+
+ *) ac_config_targets="$ac_config_targets $1" ;;
+
+ esac
+ shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+ exec 6>/dev/null
+ ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+if $ac_cs_recheck; then
+ echo "running /bin/sh ./configure " $ac_configure_extra_args " --no-create --no-recursion" >&6
+ exec /bin/sh ./configure $ac_configure_extra_args --no-create --no-recursion
+fi
+
+#
+# INIT-COMMANDS section.
+#
+
+AMDEP_TRUE="" ac_aux_dir="config"
+
+for ac_config_target in $ac_config_targets
+do
+ case "$ac_config_target" in
+ # Handling of arguments.
+ "Makefile" ) CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+ "depfiles" ) CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ *) { { echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
+echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
+ { (exit 1); exit 1; }; };;
+ esac
+done
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used. Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+ test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+ test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
+fi
+
+# Have a temporary directory for convenience. Make it in the build tree
+# simply because there is no reason to put it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Create a temporary directory, and hook for its removal unless debugging.
+$debug ||
+{
+ trap 'exit_status=$?; rm -rf $tmp && exit $exit_status' 0
+ trap '{ (exit 1); exit 1; }' 1 2 13 15
+}
+
+# Create a (secure) tmp directory for tmp files.
+
+{
+ tmp=`(umask 077 && mktemp -d -q "./confstatXXXXXX") 2>/dev/null` &&
+ test -n "$tmp" && test -d "$tmp"
+} ||
+{
+ tmp=./confstat$$-$RANDOM
+ (umask 077 && mkdir $tmp)
+} ||
+{
+ echo "$me: cannot create a temporary directory in ." >&2
+ { (exit 1); exit 1; }
+}
+
+
+#
+# CONFIG_FILES section.
+#
+
+# No need to generate the scripts if there are no CONFIG_FILES.
+# This happens for instance when ./config.status config.h
+if test -n "$CONFIG_FILES"; then
+ # Protect against being on the right side of a sed subst in config.status.
+ sed 's/,@/@@/; s/@,/@@/; s/,;t t$/@;t t/; /@;t t$/s/[\\&,]/\\&/g;
+ s/@@/,@/; s/@@/@,/; s/@;t t$/,;t t/' >$tmp/subs.sed <<\CEOF
+s, at SHELL@,/bin/sh,;t t
+s, at PATH_SEPARATOR@,:,;t t
+s, at PACKAGE_NAME@,PropKa,;t t
+s, at PACKAGE_TARNAME@,propka,;t t
+s, at PACKAGE_VERSION@,1.0.0,;t t
+s, at PACKAGE_STRING@,PropKa 1.0.0,;t t
+s, at PACKAGE_BUGREPORT@,Jan-Jensen at uiowa.edu,;t t
+s, at exec_prefix@,${prefix},;t t
+s, at prefix@,/home/moeller,;t t
+s, at program_transform_name@,s,x,x,,;t t
+s, at bindir@,${exec_prefix}/bin,;t t
+s, at sbindir@,${exec_prefix}/sbin,;t t
+s, at libexecdir@,${exec_prefix}/libexec,;t t
+s, at datadir@,${prefix}/share,;t t
+s, at sysconfdir@,${prefix}/etc,;t t
+s, at sharedstatedir@,${prefix}/com,;t t
+s, at localstatedir@,${prefix}/var,;t t
+s, at libdir@,${exec_prefix}/lib,;t t
+s, at includedir@,${prefix}/include,;t t
+s, at oldincludedir@,/usr/include,;t t
+s, at infodir@,${prefix}/info,;t t
+s, at mandir@,${prefix}/man,;t t
+s, at build_alias@,,;t t
+s, at host_alias@,,;t t
+s, at target_alias@,,;t t
+s, at DEFS@,-DPACKAGE_NAME=\"PropKa\" -DPACKAGE_TARNAME=\"propka\" -DPACKAGE_VERSION=\"1.0.0\" -DPACKAGE_STRING=\"PropKa\ 1.0.0\" -DPACKAGE_BUGREPORT=\"Jan-Jensen at uiowa.edu\" -DPACKAGE=\"PropKa\" -DVERSION=\"1.0.0\" ,;t t
+s, at ECHO_C@,,;t t
+s, at ECHO_N@,-n,;t t
+s, at ECHO_T@,,;t t
+s, at LIBS@,,;t t
+s, at build@,x86_64-unknown-linux,;t t
+s, at build_cpu@,x86_64,;t t
+s, at build_vendor@,unknown,;t t
+s, at build_os@,linux,;t t
+s, at host@,x86_64-unknown-linux,;t t
+s, at host_cpu@,x86_64,;t t
+s, at host_vendor@,unknown,;t t
+s, at host_os@,linux,;t t
+s, at target@,x86_64-unknown-linux,;t t
+s, at target_cpu@,x86_64,;t t
+s, at target_vendor@,unknown,;t t
+s, at target_os@,linux,;t t
+s, at INSTALL_PROGRAM@,${INSTALL},;t t
+s, at INSTALL_SCRIPT@,${INSTALL},;t t
+s, at INSTALL_DATA@,${INSTALL} -m 644,;t t
+s, at CYGPATH_W@,echo,;t t
+s, at PACKAGE@,PropKa,;t t
+s, at VERSION@,1.0.0,;t t
+s, at ACLOCAL@,:,;t t
+s, at AUTOCONF@,:,;t t
+s, at AUTOMAKE@,:,;t t
+s, at AUTOHEADER@,:,;t t
+s, at MAKEINFO@,${SHELL} /home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/propka/config/missing --run makeinfo,;t t
+s, at AMTAR@,${SHELL} /home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/propka/config/missing --run tar,;t t
+s, at install_sh@,/home/moeller/svn/debian-med/trunk/packages/tmp/pdb2pqr/pdb2pqr-1.2.1/propka/config/install-sh,;t t
+s, at STRIP@,,;t t
+s, at ac_ct_STRIP@,,;t t
+s, at INSTALL_STRIP_PROGRAM@,${SHELL} $(install_sh) -c -s,;t t
+s, at AWK@,gawk,;t t
+s, at SET_MAKE@,,;t t
+s, at PROPKA_VERSION@,1:0:0,;t t
+s, at py_path@,/usr/bin/python,;t t
+s, at CC@,gcc,;t t
+s, at CFLAGS@,-g -O2,;t t
+s, at LDFLAGS@,,;t t
+s, at CPPFLAGS@,,;t t
+s, at ac_ct_CC@,gcc,;t t
+s, at EXEEXT@,,;t t
+s, at OBJEXT@,o,;t t
+s, at DEPDIR@,.deps,;t t
+s, at am__include@,include,;t t
+s, at am__quote@,,;t t
+s, at AMDEP_TRUE@,,;t t
+s, at AMDEP_FALSE@,#,;t t
+s, at AMDEPBACKSLASH@,\,;t t
+s, at CCDEPMODE@,depmode=none,;t t
+s, at am__fastdepCC_TRUE@,#,;t t
+s, at am__fastdepCC_FALSE@,,;t t
+s, at F77@,g77,;t t
+s, at FFLAGS@, -g -O2,;t t
+s, at ac_ct_F77@,g77,;t t
+s, at CPP@,gcc -E,;t t
+s, at PY_SHARED@,-shared,;t t
+s, at PY_LDFLAGS@,,;t t
+s, at PY_CFLAGS@,-I/usr/include/python2.4,;t t
+s, at PY_FLAGS@,-fPIC,;t t
+s, at LIBOBJS@,,;t t
+s, at LTLIBOBJS@,,;t t
+CEOF
+
+ # Split the substitutions into bite-sized pieces for seds with
+ # small command number limits, like on Digital OSF/1 and HP-UX.
+ ac_max_sed_lines=48
+ ac_sed_frag=1 # Number of current file.
+ ac_beg=1 # First line for current file.
+ ac_end=$ac_max_sed_lines # Line after last line for current file.
+ ac_more_lines=:
+ ac_sed_cmds=
+ while $ac_more_lines; do
+ if test $ac_beg -gt 1; then
+ sed "1,${ac_beg}d; ${ac_end}q" $tmp/subs.sed >$tmp/subs.frag
+ else
+ sed "${ac_end}q" $tmp/subs.sed >$tmp/subs.frag
+ fi
+ if test ! -s $tmp/subs.frag; then
+ ac_more_lines=false
+ else
+ # The purpose of the label and of the branching condition is to
+ # speed up the sed processing (if there are no `@' at all, there
+ # is no need to browse any of the substitutions).
+ # These are the two extra sed commands mentioned above.
+ (echo ':t
+ /@[a-zA-Z_][a-zA-Z_0-9]*@/!b' && cat $tmp/subs.frag) >$tmp/subs-$ac_sed_frag.sed
+ if test -z "$ac_sed_cmds"; then
+ ac_sed_cmds="sed -f $tmp/subs-$ac_sed_frag.sed"
+ else
+ ac_sed_cmds="$ac_sed_cmds | sed -f $tmp/subs-$ac_sed_frag.sed"
+ fi
+ ac_sed_frag=`expr $ac_sed_frag + 1`
+ ac_beg=$ac_end
+ ac_end=`expr $ac_end + $ac_max_sed_lines`
+ fi
+ done
+ if test -z "$ac_sed_cmds"; then
+ ac_sed_cmds=cat
+ fi
+fi # test -n "$CONFIG_FILES"
+
+for ac_file in : $CONFIG_FILES; do test "x$ac_file" = x: && continue
+ # Support "outfile[:infile[:infile...]]", defaulting infile="outfile.in".
+ case $ac_file in
+ - | *:- | *:-:* ) # input from stdin
+ cat >$tmp/stdin
+ ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'`
+ ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;;
+ *:* ) ac_file_in=`echo "$ac_file" | sed 's,[^:]*:,,'`
+ ac_file=`echo "$ac_file" | sed 's,:.*,,'` ;;
+ * ) ac_file_in=$ac_file.in ;;
+ esac
+
+ # Compute @srcdir@, @top_srcdir@, and @INSTALL@ for subdirectories.
+ ac_dir=`(dirname "$ac_file") 2>/dev/null ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ { if $as_mkdir_p; then
+ mkdir -p "$ac_dir"
+ else
+ as_dir="$ac_dir"
+ as_dirs=
+ while test ! -d "$as_dir"; do
+ as_dirs="$as_dir $as_dirs"
+ as_dir=`(dirname "$as_dir") 2>/dev/null ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ done
+ test ! -n "$as_dirs" || mkdir $as_dirs
+ fi || { { echo "$as_me:$LINENO: error: cannot create directory \"$ac_dir\"" >&5
+echo "$as_me: error: cannot create directory \"$ac_dir\"" >&2;}
+ { (exit 1); exit 1; }; }; }
+
+ ac_builddir=.
+
+if test "$ac_dir" != .; then
+ ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'`
+ # A "../" for each directory in $ac_dir_suffix.
+ ac_top_builddir=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,../,g'`
+else
+ ac_dir_suffix= ac_top_builddir=
+fi
+
+case $srcdir in
+ .) # No --srcdir option. We are building in place.
+ ac_srcdir=.
+ if test -z "$ac_top_builddir"; then
+ ac_top_srcdir=.
+ else
+ ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'`
+ fi ;;
+ [\\/]* | ?:[\\/]* ) # Absolute path.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir ;;
+ *) # Relative path.
+ ac_srcdir=$ac_top_builddir$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_builddir$srcdir ;;
+esac
+
+# Do not use `cd foo && pwd` to compute absolute paths, because
+# the directories may not exist.
+case `pwd` in
+.) ac_abs_builddir="$ac_dir";;
+*)
+ case "$ac_dir" in
+ .) ac_abs_builddir=`pwd`;;
+ [\\/]* | ?:[\\/]* ) ac_abs_builddir="$ac_dir";;
+ *) ac_abs_builddir=`pwd`/"$ac_dir";;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_top_builddir=${ac_top_builddir}.;;
+*)
+ case ${ac_top_builddir}. in
+ .) ac_abs_top_builddir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_top_builddir=${ac_top_builddir}.;;
+ *) ac_abs_top_builddir=$ac_abs_builddir/${ac_top_builddir}.;;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_srcdir=$ac_srcdir;;
+*)
+ case $ac_srcdir in
+ .) ac_abs_srcdir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_srcdir=$ac_srcdir;;
+ *) ac_abs_srcdir=$ac_abs_builddir/$ac_srcdir;;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_top_srcdir=$ac_top_srcdir;;
+*)
+ case $ac_top_srcdir in
+ .) ac_abs_top_srcdir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_top_srcdir=$ac_top_srcdir;;
+ *) ac_abs_top_srcdir=$ac_abs_builddir/$ac_top_srcdir;;
+ esac;;
+esac
+
+
+ case $INSTALL in
+ [\\/$]* | ?:[\\/]* ) ac_INSTALL=$INSTALL ;;
+ *) ac_INSTALL=$ac_top_builddir$INSTALL ;;
+ esac
+
+ if test x"$ac_file" != x-; then
+ { echo "$as_me:$LINENO: creating $ac_file" >&5
+echo "$as_me: creating $ac_file" >&6;}
+ rm -f "$ac_file"
+ fi
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ if test x"$ac_file" = x-; then
+ configure_input=
+ else
+ configure_input="$ac_file. "
+ fi
+ configure_input=$configure_input"Generated from `echo $ac_file_in |
+ sed 's,.*/,,'` by configure."
+
+ # First look for the input files in the build tree, otherwise in the
+ # src tree.
+ ac_file_inputs=`IFS=:
+ for f in $ac_file_in; do
+ case $f in
+ -) echo $tmp/stdin ;;
+ [\\/$]*)
+ # Absolute (can't be DOS-style, as IFS=:)
+ test -f "$f" || { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5
+echo "$as_me: error: cannot find input file: $f" >&2;}
+ { (exit 1); exit 1; }; }
+ echo "$f";;
+ *) # Relative
+ if test -f "$f"; then
+ # Build tree
+ echo "$f"
+ elif test -f "$srcdir/$f"; then
+ # Source tree
+ echo "$srcdir/$f"
+ else
+ # /dev/null tree
+ { { echo "$as_me:$LINENO: error: cannot find input file: $f" >&5
+echo "$as_me: error: cannot find input file: $f" >&2;}
+ { (exit 1); exit 1; }; }
+ fi;;
+ esac
+ done` || { (exit 1); exit 1; }
+ sed "/^[ ]*VPATH[ ]*=/{
+s/:*\$(srcdir):*/:/;
+s/:*\${srcdir}:*/:/;
+s/:*@srcdir@:*/:/;
+s/^\([^=]*=[ ]*\):*/\1/;
+s/:*$//;
+s/^[^=]*=[ ]*$//;
+}
+
+:t
+/@[a-zA-Z_][a-zA-Z_0-9]*@/!b
+s, at configure_input@,$configure_input,;t t
+s, at srcdir@,$ac_srcdir,;t t
+s, at abs_srcdir@,$ac_abs_srcdir,;t t
+s, at top_srcdir@,$ac_top_srcdir,;t t
+s, at abs_top_srcdir@,$ac_abs_top_srcdir,;t t
+s, at builddir@,$ac_builddir,;t t
+s, at abs_builddir@,$ac_abs_builddir,;t t
+s, at top_builddir@,$ac_top_builddir,;t t
+s, at abs_top_builddir@,$ac_abs_top_builddir,;t t
+s, at INSTALL@,$ac_INSTALL,;t t
+" $ac_file_inputs | (eval "$ac_sed_cmds") >$tmp/out
+ rm -f $tmp/stdin
+ if test x"$ac_file" != x-; then
+ mv $tmp/out $ac_file
+ else
+ cat $tmp/out
+ rm -f $tmp/out
+ fi
+
+done
+
+#
+# CONFIG_COMMANDS section.
+#
+for ac_file in : $CONFIG_COMMANDS; do test "x$ac_file" = x: && continue
+ ac_dest=`echo "$ac_file" | sed 's,:.*,,'`
+ ac_source=`echo "$ac_file" | sed 's,[^:]*:,,'`
+ ac_dir=`(dirname "$ac_dest") 2>/dev/null ||
+$as_expr X"$ac_dest" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_dest" : 'X\(//\)[^/]' \| \
+ X"$ac_dest" : 'X\(//\)$' \| \
+ X"$ac_dest" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$ac_dest" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ { if $as_mkdir_p; then
+ mkdir -p "$ac_dir"
+ else
+ as_dir="$ac_dir"
+ as_dirs=
+ while test ! -d "$as_dir"; do
+ as_dirs="$as_dir $as_dirs"
+ as_dir=`(dirname "$as_dir") 2>/dev/null ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ done
+ test ! -n "$as_dirs" || mkdir $as_dirs
+ fi || { { echo "$as_me:$LINENO: error: cannot create directory \"$ac_dir\"" >&5
+echo "$as_me: error: cannot create directory \"$ac_dir\"" >&2;}
+ { (exit 1); exit 1; }; }; }
+
+ ac_builddir=.
+
+if test "$ac_dir" != .; then
+ ac_dir_suffix=/`echo "$ac_dir" | sed 's,^\.[\\/],,'`
+ # A "../" for each directory in $ac_dir_suffix.
+ ac_top_builddir=`echo "$ac_dir_suffix" | sed 's,/[^\\/]*,../,g'`
+else
+ ac_dir_suffix= ac_top_builddir=
+fi
+
+case $srcdir in
+ .) # No --srcdir option. We are building in place.
+ ac_srcdir=.
+ if test -z "$ac_top_builddir"; then
+ ac_top_srcdir=.
+ else
+ ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'`
+ fi ;;
+ [\\/]* | ?:[\\/]* ) # Absolute path.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir ;;
+ *) # Relative path.
+ ac_srcdir=$ac_top_builddir$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_builddir$srcdir ;;
+esac
+
+# Do not use `cd foo && pwd` to compute absolute paths, because
+# the directories may not exist.
+case `pwd` in
+.) ac_abs_builddir="$ac_dir";;
+*)
+ case "$ac_dir" in
+ .) ac_abs_builddir=`pwd`;;
+ [\\/]* | ?:[\\/]* ) ac_abs_builddir="$ac_dir";;
+ *) ac_abs_builddir=`pwd`/"$ac_dir";;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_top_builddir=${ac_top_builddir}.;;
+*)
+ case ${ac_top_builddir}. in
+ .) ac_abs_top_builddir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_top_builddir=${ac_top_builddir}.;;
+ *) ac_abs_top_builddir=$ac_abs_builddir/${ac_top_builddir}.;;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_srcdir=$ac_srcdir;;
+*)
+ case $ac_srcdir in
+ .) ac_abs_srcdir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_srcdir=$ac_srcdir;;
+ *) ac_abs_srcdir=$ac_abs_builddir/$ac_srcdir;;
+ esac;;
+esac
+case $ac_abs_builddir in
+.) ac_abs_top_srcdir=$ac_top_srcdir;;
+*)
+ case $ac_top_srcdir in
+ .) ac_abs_top_srcdir=$ac_abs_builddir;;
+ [\\/]* | ?:[\\/]* ) ac_abs_top_srcdir=$ac_top_srcdir;;
+ *) ac_abs_top_srcdir=$ac_abs_builddir/$ac_top_srcdir;;
+ esac;;
+esac
+
+
+ { echo "$as_me:$LINENO: executing $ac_dest commands" >&5
+echo "$as_me: executing $ac_dest commands" >&6;}
+ case $ac_dest in
+ depfiles ) test x"$AMDEP_TRUE" != x"" || for mf in $CONFIG_FILES; do
+ # Strip MF so we end up with the name of the file.
+ mf=`echo "$mf" | sed -e 's/:.*$//'`
+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # So let's grep whole file.
+ if grep '^#.*generated by automake' $mf > /dev/null 2>&1; then
+ dirpart=`(dirname "$mf") 2>/dev/null ||
+$as_expr X"$mf" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$mf" : 'X\(//\)[^/]' \| \
+ X"$mf" : 'X\(//\)$' \| \
+ X"$mf" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$mf" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ else
+ continue
+ fi
+ grep '^DEP_FILES *= *[^ #]' < "$mf" > /dev/null || continue
+ # Extract the definition of DEP_FILES from the Makefile without
+ # running `make'.
+ DEPDIR=`sed -n -e '/^DEPDIR = / s///p' < "$mf"`
+ test -z "$DEPDIR" && continue
+ # When using ansi2knr, U may be empty or an underscore; expand it
+ U=`sed -n -e '/^U = / s///p' < "$mf"`
+ test -d "$dirpart/$DEPDIR" || mkdir "$dirpart/$DEPDIR"
+ # We invoke sed twice because it is the simplest approach to
+ # changing $(DEPDIR) to its actual value in the expansion.
+ for file in `sed -n -e '
+ /^DEP_FILES = .*\\\\$/ {
+ s/^DEP_FILES = //
+ :loop
+ s/\\\\$//
+ p
+ n
+ /\\\\$/ b loop
+ p
+ }
+ /^DEP_FILES = / s/^DEP_FILES = //p' < "$mf" | \
+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
+ # Make sure the directory exists.
+ test -f "$dirpart/$file" && continue
+ fdir=`(dirname "$file") 2>/dev/null ||
+$as_expr X"$file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$file" : 'X\(//\)[^/]' \| \
+ X"$file" : 'X\(//\)$' \| \
+ X"$file" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ { if $as_mkdir_p; then
+ mkdir -p $dirpart/$fdir
+ else
+ as_dir=$dirpart/$fdir
+ as_dirs=
+ while test ! -d "$as_dir"; do
+ as_dirs="$as_dir $as_dirs"
+ as_dir=`(dirname "$as_dir") 2>/dev/null ||
+$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$as_dir" : 'X\(//\)[^/]' \| \
+ X"$as_dir" : 'X\(//\)$' \| \
+ X"$as_dir" : 'X\(/\)' \| \
+ . : '\(.\)' 2>/dev/null ||
+echo X"$as_dir" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ s//\1/; q; }
+ /^X\(\/\/\)[^/].*/{ s//\1/; q; }
+ /^X\(\/\/\)$/{ s//\1/; q; }
+ /^X\(\/\).*/{ s//\1/; q; }
+ s/.*/./; q'`
+ done
+ test ! -n "$as_dirs" || mkdir $as_dirs
+ fi || { { echo "$as_me:$LINENO: error: cannot create directory $dirpart/$fdir" >&5
+echo "$as_me: error: cannot create directory $dirpart/$fdir" >&2;}
+ { (exit 1); exit 1; }; }; }
+
+ # echo "creating $dirpart/$file"
+ echo '# dummy' > "$dirpart/$file"
+ done
+done
+ ;;
+ esac
+done
+
+{ (exit 0); exit 0; }
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