[gentoo-commits] gentoo-x86 commit in sci-chemistry/pdb2pqr/files: pdb2pqr-1.8.0-automagic.patch pdb2pqr-1.8.0-ldflags.patch

[gentoo-commits] gentoo-x86 commit in sci-chemistry/pdb2pqr/files: pdb2pqr-1.8.0-automagic.patch pdb2pqr-1.8.0-ldflags.patch

[Justin Lecher (jlec)]

jlec        14/10/24 10:54:05

  Added:                pdb2pqr-1.8.0-automagic.patch
                        pdb2pqr-1.8.0-ldflags.patch
  Log:
  sci-chemistry/pdb2pqr: Version Bump
  
  (Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

Revision  Changes    Path
1.1                  sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-automagic.patch?rev=1.1&content-type=text/plain

Index: pdb2pqr-1.8.0-automagic.patch
===================================================================
diff -Naur pdb2pqr-1.4.0/configure.ac pdb2pqr-1.4.0.new/configure.ac
--- pdb2pqr-1.4.0/configure.ac	2009-04-02 10:53:56.000000000 -0400
+++ pdb2pqr-1.4.0.new/configure.ac	2009-09-24 19:36:47.000000000 -0400
@@ -255,38 +255,6 @@
 
   # Test for Numeric install
   AC_MSG_CHECKING([whether you defined Numeric or Numpy])
-  if (test -n "${NUMERIC}") ; then
-    AC_MSG_RESULT([yes])
-    NUMERIC_INC=`find ${NUMERIC} -iname "arrayobject.h" | tail -n1`
-    if test "$NUMERIC_INC" = ""; then
-      AC_MSG_ERROR([Please check your NUMERIC path.  arrayobject.h cannot be found in ${NUMERIC}])
-    fi
-    NUMERIC_INC=`dirname ${NUMERIC_INC}`
-    NUMERIC_LIB=`find ${NUMERIC} -iname "Numeric.pth" | tail -n1`
-    if test "${NUMERIC_LIB}" = ""; then
-      AC_MSG_ERROR([Please check your NUMERIC path.  Numeric.pth cannot be found in ${NUMERIC}])
-    fi
-    NUMERIC_NAME=`cat ${NUMERIC_LIB}`
-    NUMERIC_LIB=`dirname ${NUMERIC_LIB}`
-    NUMERIC_LIB=${NUMERIC_LIB}/${NUMERIC_NAME}
-    if test "${PACKAGE_PATH}" = ""; then
-      PACKAGE_PATH=${NUMERIC_LIB}
-    else
-      PACKAGE_PATH="${PACKAGE_PATH}:${NUMERIC_LIB}"
-    fi
-    PY_NUMERIC="-I${NUMERIC_INC} "
-    PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
-  else
-    AC_MSG_RESULT([no])	
-    AC_MSG_CHECKING([for Numeric include files])
-    if test -f $PY_PREFIX/include/python$PY_VERSION/Numeric/arrayobject.h; then
-      PY_NUMERIC="-I$PY_PREFIX/include/python$PY_VERSION/Numeric"   
-      AC_MSG_RESULT([$PY_NUMERIC])
-      PY_CFLAGS="$PY_CFLAGS $PY_NUMERIC"
-    else
-      AC_MSG_RESULT([no])
-    fi
-  fi
 
   # If failed, test for numpy
   AC_MSG_CHECKING([whether you defined numpy])
@@ -457,29 +425,14 @@
   HAVE_PDB2PQR_OPAL=1
 fi
 
-if test "$PDB2PQR_OPAL_URL" != ""; then 
+if test "$PDB2PQR_OPAL_URL" != "no"; then 
   HAVE_PDB2PQR_OPAL=1
   if test -d $PY_PREFIX/lib/python$PY_VERSION/site-packages/ZSI ; then
     echo ZSI is installed
   else
     #  need to install ZSI
-    echo Installing ZSI.  This might take a while...
-    cd contrib/ZSI-2.1-a1 
-    if test `whoami` = "root"; then
-      $py_path setup.py install
-    else
-      zsi_install="true"
-      mkdir -p ${prefix}lib/python$PY_VERSION/site-packages
-      export PYTHONPATH=${prefix}lib/python$PY_VERSION/site-packages
-      $py_path setup.py install --prefix=${prefix}
-      if test -d ${prefix}ZSI ; then
-        echo ZSI is installed
-      else
-        cp -r ./build/lib/ZSI ${prefix}ZSI
-      fi
-      PYTHONPATH=""
-    fi 
-    cd ../..
+    echo Missing ZSI
+    exit 1
   fi
 fi  
 



1.1                  sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pdb2pqr/files/pdb2pqr-1.8.0-ldflags.patch?rev=1.1&content-type=text/plain

Index: pdb2pqr-1.8.0-ldflags.patch
===================================================================
 pdb2pka/Makefile.am           | 2 +-
 pdb2pka/substruct/Makefile.am | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pdb2pka/Makefile.am b/pdb2pka/Makefile.am
index 75f6ffd..e40a2f6 100644
--- a/pdb2pka/Makefile.am
+++ b/pdb2pka/Makefile.am
@@ -16,7 +16,7 @@ SUBDIRS          = substruct
 
 noinst_PROGRAMS         = _pMC_mult.so
 _pMC_mult_so_SOURCES     = pMC_mult.cpp pMC_mult_wrap.cpp  
-_pMC_mult_so_LINK        = $(CXX) -o $@ $(PY_SHARED)
+_pMC_mult_so_LINK        = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED)
 _pMC_mult_so_LDADD       = $(PY_LDFLAGS)
 
 #all:
diff --git a/pdb2pka/substruct/Makefile.am b/pdb2pka/substruct/Makefile.am
index b1638a0..ae95e94 100644
--- a/pdb2pka/substruct/Makefile.am
+++ b/pdb2pka/substruct/Makefile.am
@@ -15,7 +15,7 @@ CLEANFILES       = Algorithms.so
 
 noinst_PROGRAMS          = Algorithms.so
 Algorithms_so_SOURCES     = Algorithms.cpp  
-Algorithms_so_LINK        = $(CXX) -o $@ $(PY_SHARED)
+Algorithms_so_LINK        = $(CXX) $(LDFLAGS) -o $@ $(PY_SHARED)
 Algorithms_so_LDADD       = $(PY_LDFLAGS)
 
 distclean-local: clean-local