Version Bump, removed old

(Portage version: 2.2_rc67/git/Linux x86_64)
 (Signed Manifest commit)

3 files changed, 138 insertions, 761 deletions

diff --git a/sci-chemistry/simpson/files/2.0.0-gentoo.patch b/sci-chemistry/simpson/files/2.0.0-gentoo.patch
deleted file mode 100644
index c61fe4342..000000000
--- a/sci-chemistry/simpson/files/2.0.0-gentoo.patch
+++ /dev/null
@@ -1,761 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index b4cee2c..ee97cc6 100755
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -1,6 +1,6 @@
- EXTRA_DIST = autogen.sh div.m4
- 
--SUBDIRS = f2c $(SUBDIR_ADD) simpson cryst
-+SUBDIRS = $(SUBDIR_ADD) simpson cryst
- 
- bindist: bindistdir
- 	-chmod -R a+r $(BINDISTDIR)
-diff --git a/config.h.in b/config.h.in
-index b1e9a27..d078f0b 100644
---- a/config.h.in
-+++ b/config.h.in
-@@ -24,6 +24,12 @@
- /* Disable networking */
- #undef DISABLE_NETWORK
- 
-+/* #undef ENABLE_MINUIT */
-+#undef ENABLE_MINUIT
-+
-+/* #undef ENABLE_SIMMOL */
-+#undef ENABLE_SIMMOL
-+
- /* Compile with Tk support */
- #undef ENABLE_TK
- 
-@@ -33,6 +39,12 @@
- /* Define to 1 if you don't have `vprintf' but do have `_doprnt.' */
- #undef HAVE_DOPRNT
- 
-+/* #undef HAVE_F_EXIT */
-+#undef HAVE_F_EXIT
-+
-+/* #undef HAVE_GETLINE */
-+#undef HAVE_GETLINE
-+
- /* Define to 1 if you have the <inttypes.h> header file. */
- #undef HAVE_INTTYPES_H
- 
-@@ -66,6 +78,9 @@
- /* Define to 1 if you have the <memory.h> header file. */
- #undef HAVE_MEMORY_H
- 
-+/* #undef HAVE_POW_DI */
-+#undef HAVE_POW_DI
-+
- /* Define to 1 if you have the <stdint.h> header file. */
- #undef HAVE_STDINT_H
- 
-@@ -105,9 +120,15 @@
- /* Define to the address where bug reports for this package should be sent. */
- #undef PACKAGE_BUGREPORT
- 
-+/* #undef PACKAGE_DATA_DIR */
-+#undef PACKAGE_DATA_DIR
-+
- /* Define to the full name of this package. */
- #undef PACKAGE_NAME
- 
-+/* #undef PACKAGE_SOURCE_DIR */
-+#undef PACKAGE_SOURCE_DIR
-+
- /* Define to the full name and version of this package. */
- #undef PACKAGE_STRING
- 
-@@ -120,15 +141,27 @@
- /* Make the code multithreaded */
- #undef PARALLEL
- 
-+/* #undef PIVOT_PHASE */
-+#undef PIVOT_PHASE
-+
- /* Define as the return type of signal handlers (`int' or `void'). */
- #undef RETSIGTYPE
- 
--/* Enable serverlogging */
-+/* #undef REVERSEBYTES */
-+#undef REVERSEBYTES
-+
-+/* #undef SECURE_SERVER */
-+#undef SECURE_SERVER
-+
-+/* #undef SERVER_LOGGING */
- #undef SERVER_LOGGING
- 
- /* Define to 1 if you have the ANSI C header files. */
- #undef STDC_HEADERS
- 
-+/* #undef USEPORT64 */
-+#undef USEPORT64
-+
- /* Version number of package */
- #undef VERSION
- 
-diff --git a/configure.in b/configure.in
-index dfc3817..a86da05 100755
---- a/configure.in
-+++ b/configure.in
-@@ -1,7 +1,7 @@
- dnl Process this file with autoconf to produce a configure script.
- AC_INIT(configure.in,minuit/minuit/minuit/d506cm.inc)
- AM_INIT_AUTOMAKE(simpson,2.0.0)
--AM_CONFIG_HEADER(config.h)
-+AC_CONFIG_HEADER(config.h)
- 
- builtin(include,div.m4)
- dnl Checks for host-type.
-@@ -10,7 +10,7 @@ BINDISTDIR=simpson-$VERSION-$host
- AC_SUBST(BINDISTDIR)
- 
- dnl Checks for programs.
--AC_ISC_POSIX
-+AC_SEARCH_LIBS([strerror],[cposix])
- AC_PROG_CC
- AC_PROG_CXX
- AM_PROG_LIBTOOL
-@@ -21,7 +21,7 @@ AC_HEADER_STDC
- AC_PROG_LIBTOOL
- AC_PROG_INSTALL
- AC_PROG_LN_S
--AC_PROG_RANLIB
-+#AC_PROG_RANLIB
- AC_CHECK_PROGS(TAR, gtar tar)
- AC_CHECK_PROGS(F77, g77 f77)
- 
-@@ -30,17 +30,17 @@ AC_CHECK_LIB(m, sqrt)
- AC_CHECK_LIB(g2c, log, have_g2c=1, have_g2c=0)
- if test "$have_g2c" = 1; then
-   LIBG2C=-lg2c
--  AC_CHECK_LIB(g2c, pow_di, AC_DEFINE(HAVE_POW_DI))
-+  AC_CHECK_LIB(g2c, pow_di, AC_DEFINE([HAVE_POW_DI],,[#undef HAVE_POW_DI]))
- fi
- AC_CHECK_LIB(f2c, log, have_f2c=1, have_f2c=0)
- if test "$have_f2c" = 1; then
-   LIBG2C=-lf2c
--  AC_CHECK_LIB(f2c, pow_di, AC_DEFINE(HAVE_POW_DI))
-+  AC_CHECK_LIB(f2c, pow_di, AC_DEFINE([HAVE_POW_DI],,[#undef HAVE_POW_DI]))
- fi
- AC_CHECK_LIB(gfortran, log, have_gfortran=1, have_gfortran=0)
- if test "$have_gfortran" = 1; then
-   LIBG2C=-lgfortran
--  AC_CHECK_LIB(gfortran, pow_di, AC_DEFINE(HAVE_POW_DI))
-+  AC_CHECK_LIB(gfortran, pow_di, AC_DEFINE([HAVE_POW_DI],,[#undef HAVE_POW_DI]))
- fi
- AC_SUBST(LIBG2C)
- AC_CHECK_LIB(g2c, main)
-@@ -61,14 +61,14 @@ AC_SUBST(LIB_SOCKET)
- 
- 
- LIBLAPACK=""
--AC_CHECK_LIB(lapack, zgeev, have_lapack=1, have_lapack=0)
-+AC_CHECK_LIB(lapack, zgeev_, have_lapack=1, have_lapack=0)
- if test "$have_lapack" = 1; then
-   LIBLAPACK=-llapack
- fi
- AC_SUBST(LIBLAPACK)
- 
- LIBBLAS=
--AC_CHECK_LIB(blas, cscal, have_blas=1, have_blas=0)
-+AC_CHECK_LIB(blas, cscal_, have_blas=1, have_blas=0)
- if test "$have_blas" = 1; then
-   LIBBLAS=-lblas
- fi
-@@ -85,7 +85,7 @@ if test "$have_fexit" = 0; then
-   AC_CHECK_LIB(gfortran, f_exit, have_fexit=1, have_fexit=0)
- fi
- if test "$have_fexit" = 1; then
--  AC_DEFINE(HAVE_F_EXIT)
-+  AC_DEFINE(HAVE_F_EXIT,,[#undef HAVE_F_EXIT])
- fi
- 
- AC_CHECK_LIB(g2c, pow_di, have_powdi=1, have_powdi=0)
-@@ -96,11 +96,11 @@ if test "$have_powdi" = 0; then
-   AC_CHECK_LIB(gfortran, pow_di, have_powdi=1, have_powdi=0)
- fi
- if test "$have_fexit" = 1; then
--  AC_DEFINE(HAVE_F_EXIT)
-+  AC_DEFINE([HAVE_F_EXIT],,[#undef HAVE_F_EXIT])
- fi
- 
- dnl Checks for header files.
--#AC_STDC_HEADERS
-+#AC_HEADER_STDC
- #AC_CHECK_HEADERS(malloc.h)
-          
- dnl Checks for typedefs, structures, and compiler characteristics.
-@@ -113,7 +113,7 @@ dnl Checks for library functions.
- AC_TYPE_SIGNAL
- AC_FUNC_VPRINTF
- AC_CHECK_FUNCS(strstr strtod strtol)
--AC_CHECK_FUNC(getline, AC_DEFINE(HAVE_GETLINE))                                 
-+AC_CHECK_FUNC(getline, AC_DEFINE([HAVE_GETLINE],,[#undef HAVE_GETLINE]))                                 
- 
- dnl Use -Wall if we have gcc.
- changequote(,)dnl
-@@ -124,7 +124,13 @@ if test "x$GCC" = "xyes"; then
-   esac
- fi
- changequote([,])dnl
--AC_CYGWIN
-+
-+AC_CANONICAL_HOST
-+case $host_os in
-+  *cygwin* ) CYGWIN=yes;;
-+	 * ) CYGWIN=no;;
-+esac
-+
- AC_OBJEXT
- AC_EXEEXT
- 
-@@ -133,14 +139,14 @@ SC_PATH_TCLCONFIG
- SC_LOAD_TCLCONFIG
- SC_PUBLIC_TCL_HEADERS
- 
--AC_ARG_WITH(tklib, [  --with-tklib            Build with Tk support], enable_tk="no", enable_tk="yes")
-+AC_ARG_ENABLE([tklib], AS_HELP_STRING([--enable-tklib],[Build with Tk support]))
- 
--if test x$enable_tk = xyes; then  
-+AS_IF([test "x$enable_tklib" = "xyes"], [
-   AC_DEFINE([ENABLE_TK], 1, [Compile with Tk support])
-   SC_PATH_TKCONFIG
-   SC_LOAD_TKCONFIG
-   SC_PUBLIC_TK_HEADERS
--fi
-+])
- 
- SUBDIR_ADD=""
- 
-@@ -186,51 +192,42 @@ fi
- AC_ARG_ENABLE(serverlog, [  --enable-serverlog      Enable server logging], enable_serverlog="yes", enable_serverlog="no")
- 
- if test x"${enable_serverlog}" = xyes; then
--  AC_DEFINE([SERVER_LOGGING], 1, [Enable serverlogging])
-+  AC_DEFINE([SERVER_LOGGING], 1, [#undef SERVER_LOGGING])
- fi
- 
- 
--AC_ARG_ENABLE(parallel, [  --enable-parallel       Create multithreaded code], enable_parallel="yes", enable_parallel="no")
-+AC_ARG_ENABLE([parallel], AS_HELP_STRING([--enable-parallel],[Create multithreaded code]))
- 
--if test x"${enable_parallel}" = xyes; then
-+AS_IF([test "x$enable_parallel" = "xyes"], [
-   AC_DEFINE([PARALLEL], 1, [Make the code multithreaded])
--fi
-+])
- 
- 
- 
- 
--AC_ARG_WITH(simplot,[  --without-simplot       Do not compile the SIMPLOT program], simplot="no", simplot="yes")
-+AC_ARG_ENABLE([simplot], AS_HELP_STRING([--enable-simplot],[Do not compile the SIMPLOT program]))
- 
--if test x$simplot = xyes; then
-+AS_IF([test "x$enable_simplot" = "xyes"], [
- 
--    AM_PATH_GTK(1.2.0, ,
--      if test x"${ac_cv_cygwin}" = x"yes" ; then
--      AC_MSG_ERROR(Cannot find GTK: Is gtk-config in path?
--      
--   Optionally use './configure --without-simplot' and compile simplot
--   manually with the makefile 'simplot/Makefile.win32' configured properly.
--   )
--      else
--      AC_MSG_ERROR(Cannot find GTK: Is gtk-config in path?)
--      fi
--    )
-+	PKG_PROG_PKG_CONFIG
-+	PKG_CHECK_MODULES([GTK], [gtk+])
-     dnl Set PACKAGE_DATA_DIR in config.h.
-     if test "x${datadir}" = 'x${prefix}/share'; then
-       if test "x${prefix}" = "xNONE"; then
--        AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${ac_default_prefix}/share/${PACKAGE}")
-+        AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${ac_default_prefix}/share/${PACKAGE}",[#undef PACKAGE_DATA_DIR])
-       else
--        AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${prefix}/share/${PACKAGE}")
-+        AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${prefix}/share/${PACKAGE}",[#undef PACKAGE_DATA_DIR])
-       fi
-     else
--      AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${datadir}/${PACKAGE}")
-+      AC_DEFINE_UNQUOTED(PACKAGE_DATA_DIR, "${datadir}/${PACKAGE}",[#undef PACKAGE_DATA_DIR])
-     fi
- 
-     dnl Set PACKAGE_SOURCE_DIR in config.h.
-     packagesrcdir=`cd $srcdir && pwd`
--    AC_DEFINE_UNQUOTED(PACKAGE_SOURCE_DIR, "${packagesrcdir}")
-+    AC_DEFINE_UNQUOTED(PACKAGE_SOURCE_DIR, "${packagesrcdir}",[#undef PACKAGE_SOURCE_DIR])
- 
-     SUBDIR_ADD="${SUBDIR_ADD} simplot"
--fi
-+])
- 
- if test -z "$TARGET"; then
-   test -f ./config.guess && TARGET=`sh ./config.guess` 2>/dev/null
-@@ -241,17 +238,26 @@ else
- your target specification; this may cause problems later on...)
- fi
- 
--case $TARGET in
-+AC_CANONICAL_HOST
-+case $host in
- mips-dec-*)	REVERSEBYTES="yes";;
- i386-*)		REVERSEBYTES="yes";;
- i486-*)		REVERSEBYTES="yes";;
- i586-*)		REVERSEBYTES="yes";;
- i686-*)		REVERSEBYTES="yes";;
-+x86_64-*)	REVERSEBYTES="yes"; USEPORT64="yes";;
- *)		REVERSEBYTES="no";;
- esac
-+
-+echo "host is $host"
- echo "Reverse byte order...$REVERSEBYTES"
-+
- if test x$REVERSEBYTES = xyes; then
--  AC_DEFINE_UNQUOTED(REVERSEBYTES, 1)
-+  AC_DEFINE_UNQUOTED([REVERSEBYTES], 1,[#undef REVERSEBYTES])
-+fi
-+# if building on 64bits architecture then change the default port to 3264
-+if test x$USEPORT64 = xyes; then
-+  AC_DEFINE([USEPORT64], 1,[#undef USEPORT64])
- fi
- 
- 
-@@ -268,7 +274,7 @@ if test x$minuit = xyes; then
-       AC_MSG_WARN(You must have a Fortran compiler to compile minuit) 
-     fi
-     SUBDIR_ADD="${SUBDIR_ADD} minuit"
--    AC_DEFINE_UNQUOTED(ENABLE_MINUIT, 1)
-+    AC_DEFINE_UNQUOTED([ENABLE_MINUIT], 1, [#undef ENABLE_MINUIT ])
-     MINUIT_LIB="../minuit/minuit/code/libminuit.a"
- fi
- 
-@@ -276,19 +282,20 @@ AC_ARG_WITH(simmol,   [  --without-simmol         Build with simmol], enable_sim
- 
- if test x$enable_simmol = xyes; then
-   SUBDIR_ADD="${SUBDIR_ADD} simmol"
--  AC_DEFINE_UNQUOTED(ENABLE_SIMMOL,1)
-+  AC_DEFINE_UNQUOTED(ENABLE_SIMMOL,1,[#undef ENABLE_SIMMOL])
- fi
-+AM_CONDITIONAL([ENABLE_SIMBIO], [test x$enable_simmol = xyes])
- 
- AC_ARG_WITH(secureserver,   [  --without-secureserver  Do not overrule dangerous tcl-commands], secure="no", secure="yes")
- 
- if test x$secure = xyes; then
--    AC_DEFINE_UNQUOTED(SECURE_SERVER, 1)
-+    AC_DEFINE_UNQUOTED(SECURE_SERVER, 1,[#undef SECURE_SERVER])
- fi
- 
- AC_ARG_WITH(pivotphasing,   [  --with-pivotphasing     Enable vnmr pivot phasing], pivot="yes", pivot="no")
- 
- if test x$pivot = xyes; then
--    AC_DEFINE_UNQUOTED(PIVOT_PHASE, 1)
-+    AC_DEFINE_UNQUOTED(PIVOT_PHASE, 1,[#undef PIVOT_PHASE])
- fi
- 
- AC_SUBST(SUBDIR_ADD)
-@@ -296,9 +303,8 @@ AC_SUBST(MINUIT_LIB)
- AC_SUBST(GD_LIB)
- AC_SUBST(BUILDLIBSIMPSON)
- 
--AC_OUTPUT([Makefile 
-+AC_CONFIG_FILES([Makefile 
- 	   cryst/Makefile
--	   f2c/Makefile
- 	   simpson/Makefile
- 	   simplot/Makefile
- 	   simmol/Makefile
-@@ -309,5 +315,6 @@ AC_OUTPUT([Makefile
- 	   gd1.4/Makefile
- 	   vnmrtools/Makefile
- 	   ])
-+AC_OUTPUT
- 
- 
-diff --git a/simmol/Makefile.am b/simmol/Makefile.am
-index 4d61920..632feba 100644
---- a/simmol/Makefile.am
-+++ b/simmol/Makefile.am
-@@ -1,7 +1,7 @@
- INCLUDES = $(TCL_INCLUDES) -I../minuit
- LIBS = $(TCL_LIBS)
--CFLAGS=-g -O2 -Wall -DNO_CONST
--CXXFLAGS=-g -O0 -Wall -DNO_CONST
-+AM_CFLAGS=-g -O2 -Wall -DNO_CONST
-+AM_CXXFLAGS=-g -O0 -Wall -DNO_CONST
- bin_PROGRAMS = simmol
- noinst_LIBRARIES = libsimmol.a
- 
-diff --git a/simmol/backbone.cc b/simmol/backbone.cc
-index 88261e0..c3cf714 100644
---- a/simmol/backbone.cc
-+++ b/simmol/backbone.cc
-@@ -23,10 +23,10 @@
- #include <fstream>
- #include <math.h>
- #include <stdlib.h>
--#include <fstream.h>
- #include <ctype.h>
- #include "euler.h"
- #include "molecule.h"
-+using namespace std;
- 
- /* The distances in atomtype.h must be multiplied with 0.004
-    to be converted to Aangstroems */
-diff --git a/simmol/commands.cc b/simmol/commands.cc
-index 8650e1e..d6d3a18 100644
---- a/simmol/commands.cc
-+++ b/simmol/commands.cc
-@@ -31,6 +31,7 @@
- #include "descriptor.h"
- #include "vector3.h"
- #include "molecule.h"
-+using namespace std;
- 
- 
- int tclMload(ClientData data,Tcl_Interp* interp,int argc, char *argv[])
-diff --git a/simmol/complx.h b/simmol/complx.h
-index 631ab10..09a5450 100644
---- a/simmol/complx.h
-+++ b/simmol/complx.h
-@@ -24,7 +24,8 @@
- #define __COMPLX_H
- 
- #include <math.h>
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- 
- #ifdef DEFINE_MATHCONST
- #define M_E             2.7182818284590452354
-diff --git a/simmol/descriptor.cc b/simmol/descriptor.cc
-index 468be77..8e315b4 100644
---- a/simmol/descriptor.cc
-+++ b/simmol/descriptor.cc
-@@ -21,9 +21,10 @@
-     Descriptor is the internal list of allocated molecules.
- */
- 
--#include <iostream.h>
-+#include <iostream>
- #include <stdlib.h>
- #include "descriptor.h"
-+using namespace std;
- 
- Descriptor desc;
- 
-diff --git a/simmol/elements.cc b/simmol/elements.cc
-index 817212f..ca321ba 100644
---- a/simmol/elements.cc
-+++ b/simmol/elements.cc
-@@ -19,7 +19,7 @@
-     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA  
- */
- #include <iomanip>
--#include <iostream.h>
-+#include <iostream>
- #include <math.h>
- #include <ctype.h>
- #include <stdlib.h>
-@@ -29,6 +29,7 @@
- #include "elements.h"
- #include "tensors.h"
- #include "jcouplings.h"
-+using namespace std;
- 
- 
- int Atom::getsecondary_structuretype()
-@@ -94,7 +95,7 @@ Atom::Atom(const vector<double>& p) : plane(0)
- 
- ostream& operator << (ostream& out, const Atom& atom)
- {
--  char *p;
-+  const char *p;
-   static int atomno = 1;
-   int flags;
-   
-diff --git a/simmol/geomview.cc b/simmol/geomview.cc
-index e0e8eef..831d316 100644
---- a/simmol/geomview.cc
-+++ b/simmol/geomview.cc
-@@ -20,12 +20,13 @@
-     
- */
- 
--#include <iostream.h>
-+#include <iostream>
- #include <stdlib.h>
- #include <math.h>
- #include <ctype.h>
- #include "euler.h"
- #include "geomview.h"
-+using namespace std;
- 
- const char *Geomview_begin = 
- "(backcolor \"World\" 1.000000 1.000000 1.000000)\n"
-diff --git a/simmol/geomview.h b/simmol/geomview.h
-index a08d65a..8f78659 100644
---- a/simmol/geomview.h
-+++ b/simmol/geomview.h
-@@ -34,8 +34,9 @@
- #include "container.h"
- #endif
- 
--#include <iostream.h>
--#include <fstream.h>
-+#include <iostream>
-+#include <fstream>
-+using namespace std;
- 
- /* Writes a OOGL object to a file
- 
-diff --git a/simmol/libsimmol.cc b/simmol/libsimmol.cc
-index e11bd90..84cf942 100644
---- a/simmol/libsimmol.cc
-+++ b/simmol/libsimmol.cc
-@@ -20,12 +20,13 @@
-     
- */
- 
--#include <iostream.h> 
-+#include "config.h"
-+#include <iostream> 
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
- #include <tcl.h>
--#include "config.h"
-+using namespace std;
- 
- extern void RegisterCommands_commands(Tcl_Interp* interp);
- extern void RegisterCommands_primitives(Tcl_Interp* interp);
-diff --git a/simmol/main.cc b/simmol/main.cc
-index 0e0c615..f7f724f 100644
---- a/simmol/main.cc
-+++ b/simmol/main.cc
-@@ -20,12 +20,13 @@
-     
- */
- 
--#include <iostream.h> 
-+#include "config.h"
-+#include <iostream> 
- #include <stdio.h>
- #include <stdlib.h>
- #include <string.h>
- #include <tcl.h>
--#include "config.h"
-+using namespace std;
- 
- extern void RegisterCommands_commands(Tcl_Interp* interp);
- extern void RegisterCommands_primitives(Tcl_Interp* interp);
-diff --git a/simmol/make.cc b/simmol/make.cc
-index 3e94d66..c3c4bd2 100644
---- a/simmol/make.cc
-+++ b/simmol/make.cc
-@@ -19,12 +19,11 @@
-     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
- */
- 
--#include <iomanip.h>
-+#include <iomanip>
- #include <strstream>
- #include <fstream>
- #include <math.h>
- #include <stdlib.h>
--#include <fstream.h>
- #include <ctype.h>
- #include <tcl.h>
- #include <string.h>
-@@ -35,6 +34,7 @@
- #include "tensors.h"
- #include "jcouplings.h"
- 
-+using namespace std;
- 
- #define Cos(a) cos((a)*M_PI/360.0)
- #define Sin(a) sin((a)*M_PI/360.0)
-diff --git a/simmol/matrix.h b/simmol/matrix.h
-index a997a61..a58fc56 100644
---- a/simmol/matrix.h
-+++ b/simmol/matrix.h
-@@ -23,8 +23,10 @@
- #ifndef __MATRIX_H	 
- #define __MATRIX_H
- 
--#include <iostream.h>
-+#include <iostream>
-+#include <stdlib.h>
- #include <memory.h>
-+using namespace std;
- 
- 
- template <class T> class matrix {
-diff --git a/simmol/molecule.cc b/simmol/molecule.cc
-index 0500162..c75ad52 100644
---- a/simmol/molecule.cc
-+++ b/simmol/molecule.cc
-@@ -19,12 +19,11 @@
-     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
- */
- 
--#include <iomanip.h>
-+#include <iomanip>
- #include <strstream>
- #include <fstream>
- #include <math.h>
- #include <stdlib.h>
--#include <fstream.h>
- #include <ctype.h>
- #include <tcl.h>
- #include <string.h>
-@@ -34,6 +33,7 @@
- #include "descriptor.h"
- #include "tensors.h"
- #include "jcouplings.h"
-+using namespace std;
- 
- 
- #define Cos(a) cos((a)*M_PI/360.0)
-diff --git a/simmol/primitives.cc b/simmol/primitives.cc
-index 195af7f..df876a5 100644
---- a/simmol/primitives.cc
-+++ b/simmol/primitives.cc
-@@ -28,6 +28,7 @@
- #include "vector3.h"
- #include "euler.h"
- #include "matrix.h"
-+using namespace std;
- 
- #define TYPE_FLOAT  3
- #define TYPE_VECTOR 1
-diff --git a/simmol/spinsys.cc b/simmol/spinsys.cc
-index f811b24..06b4c75 100644
---- a/simmol/spinsys.cc
-+++ b/simmol/spinsys.cc
-@@ -24,12 +24,13 @@
- */
- 
- #include <stdlib.h>
--#include <iostream.h>
--#include <iomanip.h>
-+#include <iostream>
-+#include <iomanip>
- #include <string.h>
- #include <stdio.h>
- #include <assert.h>
- #include "spinsys.h"
-+using namespace std;
- 
- Hash::Hash(int _nlist=101) : nlist(_nlist), curr(0), nnames(0)
- { 
-diff --git a/simmol/spinsys.h b/simmol/spinsys.h
-index d863af0..4dcea0a 100644
---- a/simmol/spinsys.h
-+++ b/simmol/spinsys.h
-@@ -26,8 +26,9 @@
- #ifndef __SPINSYS_H
- #define __SPINSYS_H
- 
--#include <iostream.h>
-+#include <iostream>
- #include <stdio.h>
-+using namespace std;
- 
- #include "atomtype.h"
- const int MAX_NUC_LEN = 16;
-diff --git a/simmol/vector3.cc b/simmol/vector3.cc
-index f13c5ea..0376e90 100644
---- a/simmol/vector3.cc
-+++ b/simmol/vector3.cc
-@@ -20,10 +20,11 @@
-     
- */
- 
--#include <iostream.h>
-+#include <iostream>
- #include <stdlib.h>
- #include <math.h>
- #include "vector3.h"
-+using namespace std;
- 
- double norm(const vector<double>& v)
- {
-diff --git a/simplot/Makefile.am b/simplot/Makefile.am
-index a36f260..4b34100 100644
---- a/simplot/Makefile.am
-+++ b/simplot/Makefile.am
-@@ -1,6 +1,6 @@
- INCLUDES = @GTK_CFLAGS@ -I../simpson
- 
--CFLAGS=@CFLAGS_STATIC@ @CFLAGS@
-+AM_CFLAGS=@CFLAGS_STATIC@ @CFLAGS@
- LIBS=@LIBS@ @LIBS_STATIC@ $(BZLIB)
- 
- EXTRA_DIST = simplot.glade Makefile.win32 Makefile.osx
-diff --git a/simpson/Makefile.am b/simpson/Makefile.am
-index b19a781..c4caed9 100644
---- a/simpson/Makefile.am
-+++ b/simpson/Makefile.am
-@@ -1,8 +1,8 @@
--INCLUDES = -I../f2c $(TCL_INCLUDES) -I../minuit
-+INCLUDES = -I${incudedir}/f2c $(TCL_INCLUDES) -I../minuit
- TCLSRC=csafit.tcl ftools.tcl main.tcl misc.tcl simpson.tcl rfshapes.tcl
- simbio_TCLSRC=csafit.tcl ftools.tcl misc.tcl simpson.tcl rfshapes.tcl simbio_main.tcl
- 
--CFLAGS=@CFLAGS@ -DNO_CONST
-+AM_CFLAGS=@CFLAGS@ -DNO_CONST
- LIBS=@LIBS@ $(LIB_SOCKET) $(LIBLAPACK) $(LIBBLAS)
- 
- EXTRA_LTLIBRARIES=libsimpson.la
-@@ -52,18 +52,18 @@ simbio_SOURCES = cm.h defs.h ham.h matrix.h sim.h cryst.h tclcmd.h \
-   atom.h rfshapes.h rfshapes.c OCroutines.h OCroutines.c rfprof.c
- 
- simpson_LDADD =  $(GD_LIB) $(LIBG2C) \
--  ../f2c/libf2c.a  $(TCL_LIB_SPEC) $(MINUIT_LIB) -lm
-+  -lf2c  $(TCL_LIB_SPEC) $(MINUIT_LIB) -lm
- 
- simbio_LIBS = @LIBS@ @LIBS_STATIC@
- simbio_LDADD =  $(GD_LIB) \
--  ../f2c/libf2c.a  $(TCL_LIB_SPEC) $(MINUIT_LIB) \
-+  -lf2c  $(TCL_LIB_SPEC) $(MINUIT_LIB) \
-   ../simmol/libsimmol.a -lm $(TK_LIB_SPEC) $(OPENGL_LIB) $(LIBG2C) 
- 
- libsimpson_la_SOURCES = $(simpson_SOURCES) 
- libsimpson_la_CFLAGS = -DLIBSIMPSON
- libsimpson_la_LDFLAGS = -release $(VERSION)
--libsimpson_la_LIBADD = ../gd1.4/libgd.a \
--  ../f2c/libf2c.a ../minuit/minuit/code/libminuit.a
-+libsimpson_la_LIBADD = $(GD_LIB) \
-+  -lf2c -lminuit
- 
- simdps_SOURCES = simdps.c simdpstcl.c
- simdps_LDADD = $(TCL_LIB_SPEC) -lm
-diff --git a/simpson/simpson.c b/simpson/simpson.c
-index e613806..c9975d9 100644
---- a/simpson/simpson.c
-+++ b/simpson/simpson.c
-@@ -85,7 +85,11 @@ void putbits(char *bits,int e)
- 
- #ifndef DISABLE_NETWORK
- 
-+#ifdef USEPORT64
-+#define DEFAULT_PORT 3264
-+#else
- #define DEFAULT_PORT 3265
-+#endif
- #define SIMPSON_ID 15273
- 
- #ifndef STDIN_FILENO
-diff --git a/vnmrtools/Makefile.am b/vnmrtools/Makefile.am
-index 79bb7c5..61084aa 100644
---- a/vnmrtools/Makefile.am
-+++ b/vnmrtools/Makefile.am
-@@ -1,4 +1,4 @@
--EXTRA_DIST = README.vnmrtools create2d create2dph rt2d rt2dph savefid savespe
-+EXTRA_DIST = create2d create2dph rt2d rt2dph savefid savespe
- LIBS= @LIBS@ -lm
- bin_SCRIPTS = create2d create2dph rt2d rt2dph savefid savespe README.vnmrtools
- 
diff --git a/sci-chemistry/simpson/files/3.0.1-gentoo.patch b/sci-chemistry/simpson/files/3.0.1-gentoo.patch
new file mode 100644
index 000000000..61d170f89
--- /dev/null
+++ b/sci-chemistry/simpson/files/3.0.1-gentoo.patch
@@ -0,0 +1,28 @@
+diff --git a/Makefile b/Makefile
+index c5f6fcf..25e328f 100644
+--- a/Makefile
++++ b/Makefile
+@@ -7,8 +7,9 @@ C_OBJS = *.o
+ #INCLUDES = -IC:/Tcl/include -I../CBLAS/src
+ #LIBRARIES = -lm *.dll
+ # LINUX:
+-INCLUDES = -I/usr/include/tcl8.5
+-LIBRARIES = -lm -lgslcblas -llapack -ltcl8.5
++INCLUDES = -I@GENTOO_PORTAGE_EPREFIX@/usr/include/
++BLASLIBS = `pkg-config --libs cblas lapack`
++LIBRARIES = -lm ${BLASLIBS} -ltcl
+ 
+ FLAGS = -c -O3
+ CC = gcc
+@@ -16,9 +17,9 @@ RM = rm
+ TAR = tar
+ 
+ simpson: $(C_OBJS)
+-	$(CC) $(LIBRARIES) $(C_OBJS) -o simpson 
++	$(CC) $(LDFLAGS) -o simpson $(C_OBJS) $(LIBRARIES)
+ $(C_OBJS):
+-	$(CC) $(FLAGS) $(INCLUDES) *.c
++	$(CC) $(CFLAGS) $(INCLUDES) -c *.c
+ clean:
+ 	$(RM) -f *.o simpson
+ dist:
diff --git a/sci-chemistry/simpson/files/3.0.1-type.patch b/sci-chemistry/simpson/files/3.0.1-type.patch
new file mode 100644
index 000000000..3f6cc7023
--- /dev/null
+++ b/sci-chemistry/simpson/files/3.0.1-type.patch
@@ -0,0 +1,110 @@
+diff --git a/OCroutines.c b/OCroutines.c
+index eef6849..60ef56c 100644
+--- a/OCroutines.c
++++ b/OCroutines.c
+@@ -11,6 +11,7 @@
+ #include "iodata.h"
+ #include "tclutil.h"
+ #include "B0inhom.h"
++#include "defs_blas_lapack.h"
+ 
+ /* global variable holding all OC parameters */
+ OCoptPars OCpar;
+diff --git a/contour.c b/contour.c
+index ec5a223..87ae8ee 100644
+--- a/contour.c
++++ b/contour.c
+@@ -242,7 +242,8 @@ DEFINE_CMD(FContour)
+   double lowcolor[3], highcolor[3], xmin, xmax, ymin, ymax;
+   double *levels, x1, y1, x2, y2, cl, r1, r2, fmax;
+   double *xpos, *ypos, **z, iratio, jratio, nlowcolor[3], nhighcolor[3];
+-  char outputfile[256], **av;
++  char outputfile[256];
++  const char **av;
+   FILE *file;
+   FD *fdp;
+   Point *p, **pp;
+diff --git a/ftools.c b/ftools.c
+index 682e475..3c150d6 100644
+--- a/ftools.c
++++ b/ftools.c
+@@ -1434,7 +1434,8 @@ int tclFRms(ClientData data,Tcl_Interp* interp,int argc, char *argv[])
+   double2 *vec,*vec2;
+   double v1,v2;
+   int part;
+-  char **par,**par2,*range;
++  char *range;
++  const char **par,**par2;
+   int i,i1,i2,npar,npar2;
+   double sumrms,sumint;
+ 
+diff --git a/ham.c b/ham.c
+index 5be9dd1..5d36bdc 100644
+--- a/ham.c
++++ b/ham.c
+@@ -34,6 +34,7 @@
+ #include "cm_new.h"
+ #include "ham.h"
+ #include "defs.h"
++#include "defs_blas_lapack.h"
+ 
+ /*
+   Allocation strategy:
+diff --git a/matrix_new.c b/matrix_new.c
+index c0aaad2..2f3f370 100644
+--- a/matrix_new.c
++++ b/matrix_new.c
+@@ -24,6 +24,7 @@
+ 
+ #include <stdlib.h>
+ #include <stdio.h>
++#include <string.h>
+ #include "complx.h"
+ #include "matrix_new.h"
+ 
+diff --git a/new_direct.c b/new_direct.c
+index 24502f2..cc5fd68 100644
+--- a/new_direct.c
++++ b/new_direct.c
+@@ -1,4 +1,5 @@
+ #include "new_direct.h"
++#include "defs_blas_lapack.h"
+ 
+ /* make visible global variable pulse */
+ extern Pulse* puls;
+diff --git a/pulse.c b/pulse.c
+index f40787c..335d225 100644
+--- a/pulse.c
++++ b/pulse.c
+@@ -43,6 +43,7 @@
+ #include "OCroutines.h"
+ #include "B0inhom.h"
+ #include "relax.h"
++#include "defs_blas_lapack.h"
+ 
+ /*
+   tpropstart_usec : the time when the propagator was reset last time
+diff --git a/wigner.c b/wigner.c
+index bacf4b8..1644aaf 100644
+--- a/wigner.c
++++ b/wigner.c
+@@ -27,6 +27,7 @@
+ #include <math.h>
+ #include "complx.h"
+ #include <stdio.h>
++#include <stdlib.h>
+ #include "defs.h"
+ #include "matrix_new.h"
+ //#include "defs_blas_lapack.h"
+diff --git a/zte.c b/zte.c
+index 77dcb87..6025fa4 100644
+--- a/zte.c
++++ b/zte.c
+@@ -2,6 +2,7 @@
+ #include <stdlib.h>
+ #include "cm_new.h"
+ #include "pulse.h"
++#include "tclutil.h"
+ 
+ typedef struct _ZTEstruct {
+    mv_complx *rho0, *sigma;