version bump

(Portage version: 2.2.0_alpha186/cvs/Linux x86_64, signed Manifest commit with key E73C35B3)

7 files changed, 954 insertions, 1 deletions

diff --git a/sci-visualization/paraview/ChangeLog b/sci-visualization/paraview/ChangeLog
index 6feba211d16e..dd81cf8bb87e 100644
--- a/sci-visualization/paraview/ChangeLog
+++ b/sci-visualization/paraview/ChangeLog
@@ -1,6 +1,16 @@
 # ChangeLog for sci-visualization/paraview
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-visualization/paraview/ChangeLog,v 1.69 2013/05/29 16:37:35 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-visualization/paraview/ChangeLog,v 1.70 2013/07/01 23:33:28 hasufell Exp $
+
+*paraview-4.0.1 (01 Jul 2013)
+
+  01 Jul 2013; Julian Ospald <hasufell@gentoo.org> +paraview-4.0.1.ebuild,
+  +files/paraview-4.0.1-gcc-4.7.patch,
+  +files/paraview-4.0.1-removesqlite.patch,
+  +files/paraview-4.0.1-vtk-cg-path.patch,
+  +files/paraview-4.0.1-vtknetcd.patch,
+  +files/paraview-4.0.1-xdmf-cstring.patch:
+  version bump
 
   29 May 2013; Justin Lecher <jlec@gentoo.org> paraview-3.98.0.ebuild,
   paraview-3.98.0-r1.ebuild, metadata.xml:
diff --git a/sci-visualization/paraview/files/paraview-4.0.1-gcc-4.7.patch b/sci-visualization/paraview/files/paraview-4.0.1-gcc-4.7.patch
new file mode 100644
index 000000000000..1b941cfa9431
--- /dev/null
+++ b/sci-visualization/paraview/files/paraview-4.0.1-gcc-4.7.patch
@@ -0,0 +1,28 @@
+Description: fix FTBFS with gcc-4.7
+Author: Mathieu Malaterre <malat@debian.org>
+Origin: http://anonscm.debian.org/gitweb/?p=collab-maint/vtk.git;a=commitdiff;h=428e763c995bb303805e07da70c1a34fc103d208
+Reviewed-by: Anton Gladky <gladky.anton@gmail.com>
+Last-Update: 2012-05-08
+
+--- a/VTK/Rendering/FreeType/vtkFreeTypeTools.cxx
++++ b/VTK/Rendering/FreeType/vtkFreeTypeTools.cxx
+@@ -35,6 +35,8 @@
+ using namespace ftgl;
+ #endif
+ 
++#include <stdint.h>
++
+ // Print debug info
+ #define VTK_FTFC_DEBUG 0
+ #define VTK_FTFC_DEBUG_CD 0
+--- a/VTK/Rendering/FreeType/vtkFreeTypeUtilities.cxx
++++ b/VTK/Rendering/FreeType/vtkFreeTypeUtilities.cxx
+@@ -36,6 +36,8 @@
+ using namespace ftgl;
+ #endif
+ 
++#include <stdint.h>
++
+ // Print debug info
+ 
+ #define VTK_FTFC_DEBUG 0
diff --git a/sci-visualization/paraview/files/paraview-4.0.1-removesqlite.patch b/sci-visualization/paraview/files/paraview-4.0.1-removesqlite.patch
new file mode 100644
index 000000000000..be495b4fbb3a
--- /dev/null
+++ b/sci-visualization/paraview/files/paraview-4.0.1-removesqlite.patch
@@ -0,0 +1,517 @@
+Description: Import patch from VTK to remove sqlite
+Author: Mathieu Malaterre <mathieu.malaterre@gmail.com>
+Last-Update: Mon Feb 11 14:58:03 UTC 2013
+
+remove the internal copy of sqlite (vtksqlite)
+http://patch-tracker.debian.org/patch/series/view/paraview/3.14.1-7/removesqlite.patch
+
+--- VTK/IO/SQL/vtkSQLiteDatabase.cxx
++++ VTK/IO/SQL/vtkSQLiteDatabase.cxx
+@@ -29,7 +29,7 @@
+ #include <vtksys/ios/fstream>
+ #include <vtksys/ios/sstream>
+ 
+-#include <vtksqlite/vtk_sqlite3.h>
++#include <sqlite3.h>
+ 
+ vtkStandardNewMacro(vtkSQLiteDatabase);
+ 
+@@ -307,15 +307,15 @@
+       }
+     }
+ 
+-  int result = vtk_sqlite3_open(this->DatabaseFileName, & (this->SQLiteInstance));
++  int result = sqlite3_open(this->DatabaseFileName, & (this->SQLiteInstance));
+ 
+-  if (result != VTK_SQLITE_OK)
++  if (result != SQLITE_OK)
+     {
+     vtkDebugMacro(<<"SQLite open() failed.  Error code is "
+                   << result << " and message is "
+-                  << vtk_sqlite3_errmsg(this->SQLiteInstance) );
++                  << sqlite3_errmsg(this->SQLiteInstance) );
+ 
+-    vtk_sqlite3_close(this->SQLiteInstance);
++    sqlite3_close(this->SQLiteInstance);
+     return false;
+     }
+   else
+@@ -334,8 +334,8 @@
+     }
+   else
+     {
+-    int result = vtk_sqlite3_close(this->SQLiteInstance);
+-    if (result != VTK_SQLITE_OK)
++    int result = sqlite3_close(this->SQLiteInstance);
++    if (result != SQLITE_OK)
+       {
+       vtkWarningMacro(<< "Close(): SQLite returned result code " << result);
+       }
+@@ -374,7 +374,7 @@
+   if (!status)
+     {
+     vtkErrorMacro(<< "GetTables(): Database returned error: "
+-                  << vtk_sqlite3_errmsg(this->SQLiteInstance) );
++                  << sqlite3_errmsg(this->SQLiteInstance) );
+     query->Delete();
+     return this->Tables;
+     }
+@@ -403,7 +403,7 @@
+   if (!status)
+     {
+     vtkErrorMacro(<< "GetRecord(" << table << "): Database returned error: "
+-                  << vtk_sqlite3_errmsg(this->SQLiteInstance) );
++                  << sqlite3_errmsg(this->SQLiteInstance) );
+     query->Delete();
+     return NULL;
+     }
+@@ -467,10 +467,10 @@
+ // ----------------------------------------------------------------------
+ bool vtkSQLiteDatabase::HasError()
+ {
+-  return (vtk_sqlite3_errcode(this->SQLiteInstance)!=VTK_SQLITE_OK);
++  return (sqlite3_errcode(this->SQLiteInstance)!=SQLITE_OK);
+ }
+ 
+ const char* vtkSQLiteDatabase::GetLastErrorText()
+ {
+-  return vtk_sqlite3_errmsg(this->SQLiteInstance);
++  return sqlite3_errmsg(this->SQLiteInstance);
+ }
+--- VTK/IO/SQL/vtkSQLiteQuery.cxx
++++ VTK/IO/SQL/vtkSQLiteQuery.cxx
+@@ -25,7 +25,7 @@
+ #include "vtkVariant.h"
+ #include "vtkVariantArray.h"
+ 
+-#include <vtksqlite/vtk_sqlite3.h>
++#include <sqlite3.h>
+ 
+ #include <assert.h>
+ 
+@@ -43,7 +43,7 @@
+ {
+   this->Statement = NULL;
+   this->InitialFetch = true;
+-  this->InitialFetchResult=VTK_SQLITE_DONE;
++  this->InitialFetchResult=SQLITE_DONE;
+   this->LastErrorText = NULL;
+   this->TransactionInProgress = false;
+ }
+@@ -61,7 +61,7 @@
+     {
+     if (this->Database != NULL)
+       {
+-      vtk_sqlite3_finalize(this->Statement);
++      sqlite3_finalize(this->Statement);
+       this->Statement = NULL;
+       }
+     }
+@@ -131,8 +131,8 @@
+   if (this->Statement)
+     {
+     vtkDebugMacro(<<"Finalizing old statement");
+-    int finalizeStatus = vtk_sqlite3_finalize(this->Statement);
+-    if (finalizeStatus != VTK_SQLITE_OK)
++    int finalizeStatus = sqlite3_finalize(this->Statement);
++    if (finalizeStatus != SQLITE_OK)
+       {
+       vtkWarningMacro(<<"SetQuery(): Finalize returned unexpected code "
+                       << finalizeStatus);
+@@ -151,19 +151,19 @@
+       return false;
+       }
+ 
+-    vtk_sqlite3 *db = dbContainer->SQLiteInstance;
++    sqlite3 *db = dbContainer->SQLiteInstance;
+     const char *unused_statement;
+ 
+-    int prepareStatus = vtk_sqlite3_prepare_v2(db,
++    int prepareStatus = sqlite3_prepare_v2(db,
+                                                this->Query,
+                                                static_cast<int>(strlen(this->Query)),
+                                                &this->Statement,
+                                                &unused_statement);
+ 
+-    if (prepareStatus != VTK_SQLITE_OK)
++    if (prepareStatus != SQLITE_OK)
+       {
+-      this->SetLastErrorText(vtk_sqlite3_errmsg(db));
+-      vtkWarningMacro(<<"SetQuery(): vtk_sqlite3_prepare_v2() failed with error message "
++      this->SetLastErrorText(sqlite3_errmsg(db));
++      vtkWarningMacro(<<"SetQuery(): sqlite3_prepare_v2() failed with error message "
+                     << this->GetLastErrorText()
+                     << " on statement: '"
+                     << this->Query << "'");
+@@ -194,31 +194,31 @@
+     }
+   else
+     {
+-    vtk_sqlite3_reset(this->Statement);
++    sqlite3_reset(this->Statement);
+     }
+ 
+   vtkDebugMacro(<<"Execute(): Query ready to execute.");
+ 
+   this->InitialFetch = true;
+-  int result = vtk_sqlite3_step(this->Statement);
++  int result = sqlite3_step(this->Statement);
+   this->InitialFetchResult = result;
+ 
+-  if (result == VTK_SQLITE_DONE)
++  if (result == SQLITE_DONE)
+     {
+     this->SetLastErrorText(NULL);
+     this->Active = true;
+     return true;
+     }
+-  else if (result != VTK_SQLITE_ROW)
++  else if (result != SQLITE_ROW)
+     {
+     vtkSQLiteDatabase *dbContainer =
+       vtkSQLiteDatabase::SafeDownCast(this->Database);
+     assert(dbContainer != NULL);
+ 
+-    vtk_sqlite3 *db = dbContainer->SQLiteInstance;
++    sqlite3 *db = dbContainer->SQLiteInstance;
+ 
+-    this->SetLastErrorText(vtk_sqlite3_errmsg(db));
+-    vtkDebugMacro(<< "Execute(): vtk_sqlite3_step() returned error message "
++    this->SetLastErrorText(sqlite3_errmsg(db));
++    vtkDebugMacro(<< "Execute(): sqlite3_step() returned error message "
+                   << this->GetLastErrorText());
+     this->Active = false;
+     return false;
+@@ -239,7 +239,7 @@
+     }
+   else
+     {
+-    return vtk_sqlite3_column_count(this->Statement);
++    return sqlite3_column_count(this->Statement);
+     }
+ }
+ 
+@@ -259,7 +259,7 @@
+     }
+   else
+     {
+-    return vtk_sqlite3_column_name(this->Statement, column);
++    return sqlite3_column_name(this->Statement, column);
+     }
+ }
+ 
+@@ -279,22 +279,22 @@
+     }
+   else
+     {
+-    switch (vtk_sqlite3_column_type(this->Statement, column))
++    switch (sqlite3_column_type(this->Statement, column))
+       {
+-      case VTK_SQLITE_INTEGER:
++      case SQLITE_INTEGER:
+         return VTK_INT;
+-      case VTK_SQLITE_FLOAT:
++      case SQLITE_FLOAT:
+         return VTK_FLOAT;
+-      case VTK_SQLITE_TEXT:
++      case SQLITE_TEXT:
+         return VTK_STRING;
+-      case VTK_SQLITE_BLOB:
++      case SQLITE_BLOB:
+         return VTK_STRING; // until we have a BLOB type of our own
+-      case VTK_SQLITE_NULL:
++      case SQLITE_NULL:
+         return VTK_VOID; // ??? what makes sense here?
+       default:
+       {
+       vtkErrorMacro(<<"GetFieldType(): Unknown data type "
+-                    << vtk_sqlite3_column_type(this->Statement, column)
++                    << sqlite3_column_type(this->Statement, column)
+                     <<" from SQLite.");
+       return VTK_VOID;
+       }
+@@ -315,7 +315,7 @@
+     {
+     vtkDebugMacro(<<"NextRow(): Initial fetch being handled.");
+     this->InitialFetch = false;
+-    if (this->InitialFetchResult == VTK_SQLITE_DONE)
++    if (this->InitialFetchResult == SQLITE_DONE)
+       {
+       return false;
+       }
+@@ -326,12 +326,12 @@
+     }
+   else
+     {
+-    int result = vtk_sqlite3_step(this->Statement);
+-    if (result == VTK_SQLITE_DONE)
++    int result = sqlite3_step(this->Statement);
++    if (result == SQLITE_DONE)
+       {
+       return false;
+       }
+-    else if (result == VTK_SQLITE_ROW)
++    else if (result == SQLITE_ROW)
+       {
+       return true;
+       }
+@@ -339,8 +339,8 @@
+       {
+       vtkSQLiteDatabase *dbContainer = vtkSQLiteDatabase::SafeDownCast( this->Database );
+       assert(dbContainer != NULL);
+-      vtk_sqlite3 *db = dbContainer->SQLiteInstance;
+-      this->SetLastErrorText(vtk_sqlite3_errmsg(db));
++      sqlite3 *db = dbContainer->SQLiteInstance;
++      this->SetLastErrorText(sqlite3_errmsg(db));
+       vtkErrorMacro(<<"NextRow(): Database returned error code "
+                     << result << " with the following message: "
+                     << this->GetLastErrorText());
+@@ -366,33 +366,33 @@
+     }
+   else
+     {
+-    switch (vtk_sqlite3_column_type(this->Statement, column))
++    switch (sqlite3_column_type(this->Statement, column))
+       {
+-      case VTK_SQLITE_INTEGER:
+-        return vtkVariant(vtk_sqlite3_column_int(this->Statement, column));
++      case SQLITE_INTEGER:
++        return vtkVariant(sqlite3_column_int(this->Statement, column));
+ 
+-      case VTK_SQLITE_FLOAT:
+-        return vtkVariant(vtk_sqlite3_column_double(this->Statement, column));
++      case SQLITE_FLOAT:
++        return vtkVariant(sqlite3_column_double(this->Statement, column));
+ 
+-      case VTK_SQLITE_TEXT:
++      case SQLITE_TEXT:
+       {
+       vtksys_ios::ostringstream str;
+-      str << vtk_sqlite3_column_text(this->Statement, column);
++      str << sqlite3_column_text(this->Statement, column);
+       return vtkVariant(vtkStdString(str.str()));
+       }
+ 
+-      case VTK_SQLITE_BLOB:
++      case SQLITE_BLOB:
+       {
+       // This is a hack ... by passing the BLOB to vtkStdString with an explicit
+       // byte count, we ensure that the string will store all of the BLOB's bytes,
+       // even if there are NULL values.
+ 
+       return vtkVariant(vtkStdString(
+-        static_cast<const char*>(vtk_sqlite3_column_blob(this->Statement, column)),
+-        vtk_sqlite3_column_bytes(this->Statement, column)));
++        static_cast<const char*>(sqlite3_column_blob(this->Statement, column)),
++        sqlite3_column_bytes(this->Statement, column)));
+       }
+ 
+-      case VTK_SQLITE_NULL:
++      case SQLITE_NULL:
+       default:
+         return vtkVariant();
+       }
+@@ -423,11 +423,11 @@
+   vtkSQLiteDatabase *dbContainer = vtkSQLiteDatabase::SafeDownCast( this->Database );
+   assert(dbContainer != NULL);
+ 
+-  vtk_sqlite3 *db = dbContainer->SQLiteInstance;
++  sqlite3 *db = dbContainer->SQLiteInstance;
+   char *errorMessage = NULL;
+-  int result = vtk_sqlite3_exec(db, BEGIN_TRANSACTION, NULL, NULL, &errorMessage);
++  int result = sqlite3_exec(db, BEGIN_TRANSACTION, NULL, NULL, &errorMessage);
+ 
+-  if (result == VTK_SQLITE_OK)
++  if (result == SQLITE_OK)
+     {
+     this->TransactionInProgress = true;
+     this->SetLastErrorText(NULL);
+@@ -451,7 +451,7 @@
+ {
+   if (this->Statement)
+     {
+-    vtk_sqlite3_finalize(this->Statement);
++    sqlite3_finalize(this->Statement);
+     this->Statement = NULL;
+     }
+ 
+@@ -463,11 +463,11 @@
+ 
+   vtkSQLiteDatabase *dbContainer = vtkSQLiteDatabase::SafeDownCast( this->Database );
+   assert(dbContainer != NULL);
+-  vtk_sqlite3 *db = dbContainer->SQLiteInstance;
++  sqlite3 *db = dbContainer->SQLiteInstance;
+   char *errorMessage = NULL;
+-  int result = vtk_sqlite3_exec(db, COMMIT_TRANSACTION, NULL, NULL, &errorMessage);
++  int result = sqlite3_exec(db, COMMIT_TRANSACTION, NULL, NULL, &errorMessage);
+ 
+-  if (result == VTK_SQLITE_OK)
++  if (result == SQLITE_OK)
+     {
+     this->TransactionInProgress = false;
+     this->SetLastErrorText(NULL);
+@@ -499,11 +499,11 @@
+ 
+   vtkSQLiteDatabase *dbContainer = vtkSQLiteDatabase::SafeDownCast( this->Database );
+   assert(dbContainer != NULL);
+-  vtk_sqlite3 *db = dbContainer->SQLiteInstance;
++  sqlite3 *db = dbContainer->SQLiteInstance;
+   char *errorMessage = NULL;
+-  int result = vtk_sqlite3_exec(db, ROLLBACK_TRANSACTION, NULL, NULL, &errorMessage);
++  int result = sqlite3_exec(db, ROLLBACK_TRANSACTION, NULL, NULL, &errorMessage);
+ 
+-  if (result == VTK_SQLITE_OK)
++  if (result == SQLITE_OK)
+     {
+     this->TransactionInProgress = false;
+     this->SetLastErrorText(NULL);
+@@ -647,11 +647,11 @@
+   if (this->Active)
+     {
+     this->Active = false;
+-    vtk_sqlite3_reset(this->Statement);
++    sqlite3_reset(this->Statement);
+     }
+-  int status = vtk_sqlite3_bind_int(this->Statement, index+1, value);
++  int status = sqlite3_bind_int(this->Statement, index+1, value);
+ 
+-  if (status != VTK_SQLITE_OK)
++  if (status != SQLITE_OK)
+     {
+     vtksys_ios::ostringstream errormessage;
+     errormessage << "sqlite_bind_int returned error: " << status;
+@@ -676,11 +676,11 @@
+   if (this->Active)
+     {
+     this->Active = false;
+-    vtk_sqlite3_reset(this->Statement);
++    sqlite3_reset(this->Statement);
+     }
+-  int status = vtk_sqlite3_bind_int(this->Statement, index+1, static_cast<vtk_sqlite_int64>(value));
++  int status = sqlite3_bind_int(this->Statement, index+1, static_cast<sqlite_int64>(value));
+ 
+-  if (status != VTK_SQLITE_OK)
++  if (status != SQLITE_OK)
+     {
+     vtksys_ios::ostringstream errormessage;
+     errormessage << "sqlite_bind_int64 returned error: " << status;
+@@ -705,12 +705,12 @@
+   if (this->Active)
+     {
+     this->Active = false;
+-    vtk_sqlite3_reset(this->Statement);
++    sqlite3_reset(this->Statement);
+     }
+ 
+-  int status = vtk_sqlite3_bind_double(this->Statement, index+1, value);
++  int status = sqlite3_bind_double(this->Statement, index+1, value);
+ 
+-  if (status != VTK_SQLITE_OK)
++  if (status != SQLITE_OK)
+     {
+     vtksys_ios::ostringstream errormessage;
+     errormessage << "sqlite_bind_double returned error: " << status;
+@@ -734,12 +734,12 @@
+   if (this->Active)
+     {
+     this->Active = false;
+-    vtk_sqlite3_reset(this->Statement);
++    sqlite3_reset(this->Statement);
+     }
+ 
+-  int status = vtk_sqlite3_bind_text(this->Statement, index+1, value, length, VTK_SQLITE_TRANSIENT);
++  int status = sqlite3_bind_text(this->Statement, index+1, value, length, SQLITE_TRANSIENT);
+ 
+-  if (status != VTK_SQLITE_OK)
++  if (status != SQLITE_OK)
+     {
+     vtksys_ios::ostringstream errormessage;
+     errormessage << "sqlite_bind_text returned error: " << status;
+@@ -763,17 +763,17 @@
+   if (this->Active)
+     {
+     this->Active = false;
+-    vtk_sqlite3_reset(this->Statement);
++    sqlite3_reset(this->Statement);
+     }
+ 
+   int status =
+-    vtk_sqlite3_bind_blob(this->Statement,
++    sqlite3_bind_blob(this->Statement,
+                           index+1,
+                           data,
+                           length,
+-                          VTK_SQLITE_TRANSIENT);
++                          SQLITE_TRANSIENT);
+ 
+-  if (status != VTK_SQLITE_OK)
++  if (status != SQLITE_OK)
+     {
+     vtksys_ios::ostringstream errormessage;
+     errormessage << "sqlite_bind_blob returned error: " << status;
+@@ -797,12 +797,12 @@
+   if (this->Active)
+     {
+     this->Active = false;
+-    vtk_sqlite3_reset(this->Statement);
++    sqlite3_reset(this->Statement);
+     }
+ 
+-  int status = vtk_sqlite3_clear_bindings(this->Statement);
++  int status = sqlite3_clear_bindings(this->Statement);
+ 
+-  if (status != VTK_SQLITE_OK)
++  if (status != SQLITE_OK)
+     {
+     vtksys_ios::ostringstream errormessage;
+     errormessage << "sqlite_clear_bindings returned error: " << status;
+--- VTK/IO/SQL/vtkSQLiteDatabase.h
++++ VTK/IO/SQL/vtkSQLiteDatabase.h
+@@ -49,7 +49,7 @@
+ class vtkSQLQuery;
+ class vtkSQLiteQuery;
+ class vtkStringArray;
+-struct vtk_sqlite3;
++struct sqlite3;
+ 
+ class VTKIOSQL_EXPORT vtkSQLiteDatabase : public vtkSQLDatabase
+ {
+@@ -147,7 +147,7 @@
+   virtual bool ParseURL(const char* url);
+ 
+ private:
+-  vtk_sqlite3 *SQLiteInstance;
++  sqlite3 *SQLiteInstance;
+ 
+   // We want this to be private, a user of this class
+   // should not be setting this for any reason
+--- VTK/IO/SQL/vtkSQLiteQuery.h
++++ VTK/IO/SQL/vtkSQLiteQuery.h
+@@ -47,7 +47,7 @@
+ class vtkSQLiteDatabase;
+ class vtkVariant;
+ class vtkVariantArray;
+-struct vtk_sqlite3_stmt;
++struct sqlite3_stmt;
+ 
+ class VTKIOSQL_EXPORT vtkSQLiteQuery : public vtkSQLQuery
+ {
+@@ -155,7 +155,7 @@
+   vtkSQLiteQuery(const vtkSQLiteQuery &); // Not implemented.
+   void operator=(const vtkSQLiteQuery &); // Not implemented.
+ 
+-  vtk_sqlite3_stmt *Statement;
++  sqlite3_stmt *Statement;
+   bool InitialFetch;
+   int InitialFetchResult;
+   char *LastErrorText;
+--- VTK/ThirdParty/sqlite/CMakeLists.txt
++++ VTK/ThirdParty/sqlite/CMakeLists.txt
+@@ -1,4 +1,4 @@
+-set(vtksqlite_THIRD_PARTY 1)
+-set(vtksqlite_LIBRARIES vtksqlite)
++#set(vtksqlite_THIRD_PARTY 1)
++set(vtksqlite_LIBRARIES sqlite3)
+ vtk_module_export_info()
+-add_subdirectory(vtksqlite)
++#add_subdirectory(vtksqlite)
diff --git a/sci-visualization/paraview/files/paraview-4.0.1-vtk-cg-path.patch b/sci-visualization/paraview/files/paraview-4.0.1-vtk-cg-path.patch
new file mode 100644
index 000000000000..58ddde97d4fb
--- /dev/null
+++ b/sci-visualization/paraview/files/paraview-4.0.1-vtk-cg-path.patch
@@ -0,0 +1,36 @@
+--- ParaView-3.98.0-src/VTK/CMake/FindCg.cmake
++++ ParaView-3.98.0-src/VTK/CMake/FindCg.cmake
+@@ -82,6 +82,7 @@
+     FIND_PROGRAM( CG_COMPILER cgc
+       /usr/bin
+       /usr/local/bin
++      /opt/nvidia-cg-toolkit/bin
+       DOC "The Cg Compiler"
+       )
+     GET_FILENAME_COMPONENT(CG_COMPILER_DIR "${CG_COMPILER}" PATH)
+@@ -89,6 +90,7 @@
+     FIND_PATH( CG_INCLUDE_PATH Cg/cg.h
+       /usr/include
+       /usr/local/include
++      /opt/nvidia-cg-toolkit/include
+       ${CG_COMPILER_SUPER_DIR}/include
+       DOC "The directory where Cg/cg.h resides"
+       )
+@@ -98,6 +100,8 @@
+       /usr/lib
+       /usr/local/lib64
+       /usr/local/lib
++      /opt/nvidia-cg-toolkit/lib64
++      /opt/nvidia-cg-toolkit/lib
+       ${CG_COMPILER_SUPER_DIR}/lib64
+       ${CG_COMPILER_SUPER_DIR}/lib
+       DOC "The Cg runtime library"
+@@ -108,6 +112,8 @@
+       /usr/lib
+       /usr/local/lib64
+       /usr/local/lib
++      /opt/nvidia-cg-toolkit/lib64
++      /opt/nvidia-cg-toolkit/lib
+       ${CG_COMPILER_SUPER_DIR}/lib64
+       ${CG_COMPILER_SUPER_DIR}/lib
+       DOC "The Cg runtime library"
diff --git a/sci-visualization/paraview/files/paraview-4.0.1-vtknetcd.patch b/sci-visualization/paraview/files/paraview-4.0.1-vtknetcd.patch
new file mode 100644
index 000000000000..a478b7dfc2d4
--- /dev/null
+++ b/sci-visualization/paraview/files/paraview-4.0.1-vtknetcd.patch
@@ -0,0 +1,79 @@
+adapted from debian patch need to be applied after paraview-3.14.1-removesqlite.patch
+
+--- ParaView-3.98.0-src/VTK/ThirdParty/netcdf/CMakeLists.txt
++++ ParaView-3.98.0-src/VTK/ThirdParty/netcdf/CMakeLists.txt
+@@ -1,8 +1,8 @@
+-set(vtknetcdf_THIRD_PARTY 1)
+-set(vtknetcdf_LIBRARIES vtkNetCDF vtkNetCDF_cxx)
+-set(vtknetcdf_INCLUDE_DIRS
+-  ${vtknetcdf_SOURCE_DIR}/vtknetcdf/include
+-  ${vtknetcdf_BINARY_DIR}/vtknetcdf
+-  )
++#set(vtknetcdf_THIRD_PARTY 1)
++set(vtknetcdf_LIBRARIES netcdf netcdf_c++)
++#set(vtknetcdf_INCLUDE_DIRS
++#  ${vtknetcdf_SOURCE_DIR}/vtknetcdf/include
++#  ${vtknetcdf_BINARY_DIR}/vtknetcdf
++#  )
+ vtk_module_export_info()
+-add_subdirectory(vtknetcdf)
++#add_subdirectory(vtknetcdf)
+--- ParaView-3.98.0-src/VTK/ThirdParty/netcdf/vtk_netcdf.h
++++ ParaView-3.98.0-src/VTK/ThirdParty/netcdf/vtk_netcdf.h
+@@ -16,6 +16,6 @@
+ #define __vtk_netcdf_h
+ 
+ /* Use the netcdf library configured for VTK.  */
+-#include <vtknetcdf/include/netcdf.h>
++#include <netcdf.h>
+ 
+ #endif
+--- ParaView-3.98.0-src/VTK/ThirdParty/netcdf/vtk_netcdfcpp.h
++++ ParaView-3.98.0-src/VTK/ThirdParty/netcdf/vtk_netcdfcpp.h
+@@ -16,6 +16,6 @@
+ #define __vtk_netcdfcpp_h
+ 
+ /* Use the netcdf library configured for VTK.  */
+-#include <vtknetcdf/cxx/netcdfcpp.h>
++#include <netcdfcpp.h>
+ 
+ #endif
+--- ParaView-3.98.0-src/VTK/ThirdParty/exodusII/vtkexodusII/test/CMakeLists.txt
++++ ParaView-3.98.0-src/VTK/ThirdParty/exodusII/vtkexodusII/test/CMakeLists.txt
+@@ -21,7 +21,7 @@
+   )
+ 
+ add_executable(ExoIICTests ${ExoIICTests})
+-target_link_libraries(ExoIICTests vtkCommon vtkexoIIc vtkNetCDF)
++target_link_libraries(ExoIICTests vtkCommon vtkexoIIc netcdf)
+ 
+ set(TestsToRun ${ExoIICTests})
+ remove(TestsToRun ExoIICTests.cxx)
+--- ParaView-3.98.0-src/VTK/ThirdParty/exodusII/vtkexodusII/CMakeLists.txt
++++ ParaView-3.98.0-src/VTK/ThirdParty/exodusII/vtkexodusII/CMakeLists.txt
+@@ -241,7 +241,7 @@
+ 
+ 
+ VTK_ADD_LIBRARY(vtkexoIIc ${cbind_SRCS})
+-TARGET_LINK_LIBRARIES(vtkexoIIc vtkNetCDF)
++TARGET_LINK_LIBRARIES(vtkexoIIc netcdf)
+ 
+ IF(NOT VTK_INSTALL_NO_DEVELOPMENT)
+ #  INSTALL_FILES(${VTK_INSTALL_INCLUDE_DIR}/vtkexodus2 .h
+--- ParaView-3.98.0-src/VTK/IO/NetCDF/CMakeLists.txt
++++ ParaView-3.98.0-src/VTK/IO/NetCDF/CMakeLists.txt
+@@ -10,5 +10,5 @@
+ 
+ vtk_module_library(vtkIONetCDF ${Module_SRCS})
+ 
+-target_link_libraries(vtkIONetCDF vtkNetCDF_cxx)
++target_link_libraries(vtkIONetCDF netcdf netcdf_c++)
+ set_target_properties(vtkIONetCDF PROPERTIES LINK_INTERFACE_LIBRARIES "")
+--- ParaView-3.98.0-src/VTK/IO/ParallelNetCDF/CMakeLists.txt
++++ ParaView-3.98.0-src/VTK/IO/ParallelNetCDF/CMakeLists.txt
+@@ -8,4 +8,4 @@
+ 
+ vtk_module_library(vtkIOParallelNetCDF ${Module_SRCS})
+ 
+-target_link_libraries(vtkIOParallelNetCDF vtkNetCDF_cxx)
++target_link_libraries(vtkIOParallelNetCDF netcdf netcdf_c++)
diff --git a/sci-visualization/paraview/files/paraview-4.0.1-xdmf-cstring.patch b/sci-visualization/paraview/files/paraview-4.0.1-xdmf-cstring.patch
new file mode 100644
index 000000000000..665f40ad4fa7
--- /dev/null
+++ b/sci-visualization/paraview/files/paraview-4.0.1-xdmf-cstring.patch
@@ -0,0 +1,12 @@
+gcc header fix
+
+--- ParaView-3.98.0-src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfObject.h
++++ ParaView-3.98.0-src/VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/XdmfObject.h
+@@ -82,6 +82,7 @@
+ # ifdef UNIX
+ #  include "sys/file.h"
+ #  include "strings.h"
++#  include <cstring>
+ #  define STRCASECMP strcasecmp
+ #  define STRNCASECMP strncasecmp
+ #  define STRCMP strcmp
diff --git a/sci-visualization/paraview/paraview-4.0.1.ebuild b/sci-visualization/paraview/paraview-4.0.1.ebuild
new file mode 100644
index 000000000000..a5df7de36a74
--- /dev/null
+++ b/sci-visualization/paraview/paraview-4.0.1.ebuild
@@ -0,0 +1,271 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-visualization/paraview/paraview-4.0.1.ebuild,v 1.1 2013/07/01 23:33:28 hasufell Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_6 python2_7 )
+inherit eutils multilib versionator python-single-r1 cmake-utils
+
+MAIN_PV=$(get_major_version)
+MAJOR_PV=$(get_version_component_range 1-2)
+MY_P="ParaView-v${PV}-source"
+
+DESCRIPTION="ParaView is a powerful scientific data visualization application"
+HOMEPAGE="http://www.paraview.org"
+SRC_URI="http://www.paraview.org/files/v${MAJOR_PV}/${MY_P}.tgz"
+RESTRICT="mirror"
+
+LICENSE="paraview GPL-2"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+IUSE="boost cg coprocessing development doc examples ffmpeg mpi mysql nvcontrol plugins python qt4 sqlite tcl test tk"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+RDEPEND="
+	dev-libs/expat
+	dev-libs/libxml2:2
+	dev-libs/protobuf
+	media-libs/freetype
+	media-libs/libpng:0
+	media-libs/libtheora
+	media-libs/tiff
+	sci-libs/hdf5[mpi=]
+	~sci-libs/netcdf-4.1.3[cxx,hdf5]
+	sys-libs/zlib
+	virtual/jpeg
+	virtual/opengl
+	>=x11-libs/gl2ps-1.3.8
+	x11-libs/libX11
+	x11-libs/libXext
+	x11-libs/libXmu
+	x11-libs/libXt
+	coprocessing? (
+		plugins? (
+			dev-python/PyQt4
+			dev-qt/qtgui:4
+		)
+	)
+	ffmpeg? ( virtual/ffmpeg )
+	mpi? ( virtual/mpi[cxx,romio] )
+	mysql? ( virtual/mysql )
+	python? (
+		${PYTHON_DEPS}
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+		dev-python/mpi4py
+		dev-python/numpy[${PYTHON_USEDEP}]
+		dev-python/sip[${PYTHON_USEDEP}]
+		dev-python/twisted
+		net-zope/zope-interface[${PYTHON_USEDEP}]
+		mpi? ( dev-python/mpi4py )
+		qt4? ( dev-python/PyQt4[opengl,webkit,${PYTHON_USEDEP}] )
+	)
+	qt4? (
+		dev-qt/qtgui:4
+		dev-qt/qtopengl:4
+		dev-qt/qthelp:4[compat]
+		dev-qt/qtsql:4
+		dev-qt/qtwebkit:4
+	)
+	sqlite? ( dev-db/sqlite )
+	tcl? ( dev-lang/tcl )
+	tk? ( dev-lang/tk )"
+DEPEND="${RDEPEND}
+	${PYTHON_DEPS}
+	boost? ( >=dev-libs/boost-1.40.0[mpi?,${PYTHON_USEDEP}] )
+	doc? ( app-doc/doxygen )"
+
+S=${WORKDIR}/${MY_P}
+
+pkg_setup() {
+	python-single-r1_pkg_setup
+	PVLIBDIR=$(get_libdir)/${PN}-${MAJOR_PV}
+}
+
+src_prepare() {
+	# see patch headers for description
+	epatch "${FILESDIR}"/${P}-xdmf-cstring.patch \
+		"${FILESDIR}"/${P}-removesqlite.patch \
+		"${FILESDIR}"/${P}-gcc-4.7.patch \
+		"${FILESDIR}"/${P}-vtknetcd.patch \
+		"${FILESDIR}"/${P}-vtk-cg-path.patch
+
+	# lib64 fixes
+	sed -i \
+		-e "s:/usr/lib:${EPREFIX}/usr/$(get_libdir):g" \
+		 VTK/ThirdParty/xdmf2/vtkxdmf2/libsrc/CMakeLists.txt || die
+	sed -i \
+		-e "s:\/lib\/python:\/$(get_libdir)\/python:g" \
+		 VTK/ThirdParty/xdmf2/vtkxdmf2/CMake/setup_install_paths.py || die
+	sed -i \
+		-e "s:lib/paraview-:$(get_libdir)/paraview-:g" \
+		CMakeLists.txt \
+		Plugins/SciberQuestToolKit/CMakeLists.txt \
+		ParaViewConfig.cmake.in \
+		CoProcessing/PythonCatalyst/vtkCPPythonScriptPipeline.cxx \
+		ParaViewCore/ClientServerCore/Core/vtkProcessModuleInitializePython.h || die
+
+	# no proper switch
+	use nvcontrol || {
+		sed -i \
+			-e '/VTK_USE_NVCONTROL/s#1#0#' \
+			VTK/Rendering/OpenGL/CMakeLists.txt || die
+	}
+}
+
+src_configure() {
+	# TODO: use system protobuf, jsoncpp
+	# VTK_USE_SYSTEM_QTTESTING
+	# PARAVIEW_USE_SYSTEM_AUTOBAHN
+	local mycmakeargs=(
+		-DPV_INSTALL_LIB_DIR="${PVLIBDIR}"
+		-DCMAKE_INSTALL_PREFIX="${EPREFIX}"/usr
+		-DEXPAT_INCLUDE_DIR="${EPREFIX}"/usr/include
+		-DEXPAT_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libexpat.so
+		-DOPENGL_gl_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libGL.so
+		-DOPENGL_glu_LIBRARY="${EPREFIX}"/usr/$(get_libdir)/libGLU.so
+		-DBUILD_SHARED_LIBS=ON
+		-DVTK_USE_SYSTEM_EXPAT=ON
+		-DVTK_USE_SYSTEM_FREETYPE=ON
+		-DVTK_USE_SYSTEM_GL2PS=ON
+		-DVTK_USE_SYSTEM_HDF5=ON
+		-DVTK_USE_SYSTEM_JPEG=ON
+		-DVTK_USE_SYSTEM_LIBXML2=ON
+		-DVTK_USE_SYSTEM_OGGTHEORA=ON
+		-DVTK_USE_SYSTEM_PNG=ON
+		-DVTK_USE_SYSTEM_PROTOBUF=OFF
+		-DVTK_USE_SYSTEM_TIFF=ON
+		-DVTK_USE_SYSTEM_XDMF2=OFF
+		-DVTK_USE_SYSTEM_ZLIB=ON
+		-DPARAVIEW_USE_SYSTEM_MPI4PY=ON
+		-DPARAVIEW_USE_SYSTEM_ZOPE=ON
+		-DPARAVIEW_USE_SYSTEM_TWISTED=ON
+		-DCMAKE_VERBOSE_MAKEFILE=ON
+		-DCMAKE_COLOR_MAKEFILE=TRUE
+		-DVTK_USE_OFFSCREEN=TRUE
+		-DCMAKE_USE_PTHREADS=ON
+		-DVTK_USE_FFMPEG_ENCODER=OFF
+		-DPROTOC_LOCATION=$(type -P protoc)
+		-DVTK_Group_StandAlone=ON
+		# force this module due to incorrect build system deps
+		# wrt bug 460528
+		-DModule_vtkUtilitiesProcessXML=ON
+		)
+
+	# TODO: XDMF_USE_MYSQL?
+	# VTK_WRAP_JAVA
+	mycmakeargs+=(
+		$(cmake-utils_use development PARAVIEW_INSTALL_DEVELOPMENT_FILES)
+		$(cmake-utils_use qt4 PARAVIEW_BUILD_QT_GUI)
+		$(cmake-utils_use qt4 Module_vtkGUISupportQtOpenGL)
+		$(cmake-utils_use qt4 Module_vtkGUISupportQtSQL)
+		$(cmake-utils_use qt4 Module_vtkGUISupportQtWebkit)
+		$(cmake-utils_use qt4 Module_vtkRenderingQt)
+		$(cmake-utils_use qt4 Module_vtkViewsQt)
+		$(cmake-utils_use qt4 VTK_Group_ParaViewQt)
+		$(cmake-utils_use qt4 VTK_Group_Qt)
+		$(cmake-utils_use !qt4 PQWIDGETS_DISABLE_QTWEBKIT)
+		$(cmake-utils_use boost Module_vtkInfovisBoost)
+		$(cmake-utils_use boost Module_vtkInfovisBoostGraphAlg)
+		$(cmake-utils_use mpi PARAVIEW_USE_MPI)
+		$(cmake-utils_use mpi PARAVIEW_USE_MPI_SSEND)
+		$(cmake-utils_use mpi PARAVIEW_USE_ICE_T)
+		$(cmake-utils_use mpi VTK_Group_MPI)
+		$(cmake-utils_use mpi VTK_XDMF_USE_MPI)
+		$(cmake-utils_use mpi XDMF_BUILD_MPI)
+		$(cmake-utils_use python PARAVIEW_ENABLE_PYTHON)
+		$(cmake-utils_use python VTK_Group_ParaViewPython)
+		$(cmake-utils_use python XDMF_WRAP_PYTHON)
+		$(cmake-utils_use python Module_vtkPython)
+		$(cmake-utils_use python Module_pqPython)
+		$(cmake-utils_use python Module_vtkWrappingPythonCore)
+		$(cmake-utils_use python Module_vtkPVPythonSupport)
+		$(cmake-utils_use python Module_AutobahnPython)
+		$(cmake-utils_use python Module_Twisted)
+		$(cmake-utils_use python Module_ZopeInterface)
+		$(cmake-utils_use python Module_vtkmpi4py)
+		$(cmake-utils_use python Module_pqPython)
+		$(cmake-utils_use doc BUILD_DOCUMENTATION)
+		$(cmake-utils_use doc PARAVIEW_BUILD_WEB_DOCUMENTATION)
+		$(cmake-utils_use examples BUILD_EXAMPLES)
+		$(cmake-utils_use cg VTK_USE_CG_SHADERS)
+		$(cmake-utils_use mysql Module_vtkIOMySQL)
+		$(cmake-utils_use sqlite Module_vtksqlite)
+		$(cmake-utils_use coprocessing PARAVIEW_ENABLE_CATALYST)
+		$(cmake-utils_use ffmpeg PARAVIEW_ENABLE_FFMPEG)
+		$(cmake-utils_use ffmpeg VTK_USE_FFMPEG_ENCODER)
+		$(cmake-utils_use ffmpeg Module_vtkIOFFMPEG)
+		$(cmake-utils_use tk VTK_Group_Tk)
+		$(cmake-utils_use tk VTK_USE_TK)
+		$(cmake-utils_use tk Module_vtkRenderingTk)
+		$(cmake-utils_use tcl Module_vtkTclTk)
+		$(cmake-utils_use tcl Module_vtkWrappingTcl)
+		$(cmake-utils_use test BUILD_TESTING)
+		)
+
+	if use qt4 ; then
+		mycmakeargs+=( -DVTK_INSTALL_QT_DIR=/${PVLIBDIR}/plugins/designer )
+		if use python ; then
+			# paraview cannot guess sip directory properly
+			mycmakeargs+=( -DSIP_INCLUDE_DIR="${EPREFIX}$(python_get_includedir)" )
+		fi
+	fi
+
+	# TODO: MantaView VaporPlugin VRPlugin
+	mycmakeargs+=(
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_AdiosReader)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_AnalyzeNIfTIIO)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_ArrowGlyph)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_EyeDomeLighting)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_ForceTime)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_GMVReader)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_H5PartReader)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_Moments)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_NonOrthogonalSource)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_PacMan)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_PointSprite)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_PrismPlugin)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_QuadView)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SLACTools)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SciberQuestToolKit)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SierraPlotTools)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_SurfaceLIC)
+		$(cmake-utils_use plugins PARAVIEW_BUILD_PLUGIN_UncertaintyRendering)
+		# these are always needed for plugins
+		$(cmake-utils_use plugins Module_vtkFiltersFlowPaths)
+		$(cmake-utils_use plugins Module_vtkPVServerManagerApplication)
+		)
+
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile
+}
+
+src_install() {
+	cmake-utils_src_install
+
+	# set up the environment
+	echo "LDPATH=${EPREFIX}/usr/${PVLIBDIR}" > "${T}"/40${PN}
+	echo "PYTHONPATH="${EPREFIX}"/usr/${PVLIBDIR}:/usr/${PVLIBDIR}/site-packages" >> "${T}"/40${PN}
+	doenvd "${T}"/40${PN}
+
+	newicon "${S}"/Applications/ParaView/pvIcon.png paraview.png
+	make_desktop_entry paraview "Paraview" paraview
+
+	use python && python_optimize "${D}"/usr/$(get_libdir)/${PN}-${MAJOR_PV}
+}
+
+pkg_postinst() {
+	# with Qt4.5 there seem to be issues reading data files
+	# under certain locales. Setting LC_ALL=C should fix these.
+	echo
+	elog "If you experience data corruption during parsing of"
+	elog "data files with paraview please try setting your"
+	elog "locale to LC_ALL=C."
+	elog "If you plan to use paraview component from an existing shell"
+	elog "you should run env-update and . /etc/profile first"
+	echo
+}