proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

4 files changed, 105 insertions, 0 deletions

diff --git a/sci-chemistry/molsketch/files/molsketch-0.2.0-openbabel-231.patch b/sci-chemistry/molsketch/files/molsketch-0.2.0-openbabel-231.patch
new file mode 100644
index 000000000000..41ddf01df5f8
--- /dev/null
+++ b/sci-chemistry/molsketch/files/molsketch-0.2.0-openbabel-231.patch
@@ -0,0 +1,54 @@
+ CMakeLists.txt                        |   12 ++++++------
+ libmolsketch/src/stereocenteritem.cpp |    2 +-
+ 2 files changed, 7 insertions(+), 7 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index a4b5d29..f472b40 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -12,10 +12,10 @@ set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake/modules)
+ # compiler issues are fixed and more warnings are issued. #
+ ###########################################################
+ if (CMAKE_COMPILER_IS_GNUCXX)
+-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-long-long -std=iso9899:1990 -Wundef -Wcast-align")
+-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Werror-implicit-function-declaration -Wchar-subscripts")
+-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -W -Wpointer-arith -Wwrite-strings -Wformat-security")
+-  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wmissing-format-attribute -fno-common")
++#   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-long-long -std=iso9899:1990 -Wundef -Wcast-align")
++#   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Werror-implicit-function-declaration -Wchar-subscripts")
++#   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wall -W -Wpointer-arith -Wwrite-strings -Wformat-security")
++#   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wmissing-format-attribute -fno-common")
+   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wnon-virtual-dtor -Wno-long-long -ansi -Wundef -Wcast-align") 
+   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wchar-subscripts -Wall -W -Wpointer-arith -Wformat-security")
+   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-exceptions -fno-check-new -fno-common")
+@@ -32,7 +32,7 @@ set(CPACK_SOURCE_IGNORE_FILES "/build;/.git")
+ include(CPack)
+ 
+ # Unit testing, mainly useful for developers and so defaults to off
+-option(ENABLE_TESTS "Enable unit testing" ON)
++option(ENABLE_TESTS "Enable unit testing" OFF)
+ if(ENABLE_TESTS)
+   set(QT_USE_QTTEST TRUE)
+   enable_testing()
+@@ -48,7 +48,7 @@ configure_file("${CMAKE_MODULE_PATH}/cmake_uninstall.cmake.in"
+ add_custom_target(uninstall "${CMAKE_COMMAND}" -P "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake")
+ 
+ # Enabling debugging symbols
+-set(CMAKE_BUILD_TYPE Debug)
++# set(CMAKE_BUILD_TYPE Debug)
+ 
+ # Enabling shared libraries
+ set(BUILD_SHARED_LIBS OFF)
+diff --git a/libmolsketch/src/stereocenteritem.cpp b/libmolsketch/src/stereocenteritem.cpp
+index 44a8015..20f2a4a 100644
+--- a/libmolsketch/src/stereocenteritem.cpp
++++ b/libmolsketch/src/stereocenteritem.cpp
+@@ -63,7 +63,7 @@ namespace Molsketch {
+     graphsym.GetSymmetry(symmetry_classes);
+ 
+     //std::vector<unsigned long> atomIds = FindTetrahedralAtoms(obmol, symmetry_classes);
+-    std::vector<OpenBabel::StereogenicUnit> units = FindStereogenicUnits(obmol, symmetry_classes);
++    OpenBabel::OBStereoUnitSet units = FindStereogenicUnits(obmol, symmetry_classes);
+     
+     for (unsigned int i = 0; i < units.size(); ++i) {
+       if (units.at(i).type == OpenBabel::OBStereo::Tetrahedral) {
diff --git a/sci-chemistry/molsketch/files/molsketch-0.3.0-_DEFAULT_SOURCE.patch b/sci-chemistry/molsketch/files/molsketch-0.3.0-_DEFAULT_SOURCE.patch
new file mode 100644
index 000000000000..af3b5ceedac6
--- /dev/null
+++ b/sci-chemistry/molsketch/files/molsketch-0.3.0-_DEFAULT_SOURCE.patch
@@ -0,0 +1,16 @@
+ CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index e3cd0fe..64c18a2 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -19,7 +19,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
+   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wnon-virtual-dtor -Wno-long-long -ansi -Wundef -Wcast-align") 
+   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wchar-subscripts -Wall -W -Wpointer-arith -Wformat-security")
+   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-exceptions -fno-check-new -fno-common")
+-  add_definitions(-D_BSD_SOURCE)
++  add_definitions(-D_DEFAULT_SOURCE)
+ endif (CMAKE_COMPILER_IS_GNUCXX)
+ 
+ # Enable CPack
diff --git a/sci-chemistry/molsketch/files/molsketch-0.3.0-desktop.patch b/sci-chemistry/molsketch/files/molsketch-0.3.0-desktop.patch
new file mode 100644
index 000000000000..fd44e88c7870
--- /dev/null
+++ b/sci-chemistry/molsketch/files/molsketch-0.3.0-desktop.patch
@@ -0,0 +1,19 @@
+ molsketch/src/molsketch.desktop | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/molsketch/src/molsketch.desktop b/molsketch/src/molsketch.desktop
+index a4a5418..4e0a2ef 100644
+--- a/molsketch/src/molsketch.desktop
++++ b/molsketch/src/molsketch.desktop
+@@ -5,9 +5,9 @@ Type=Application
+ Name=molsKetch
+ TryExec=molsketch
+ Exec=molsketch
+-Icon=molsketch.png
++Icon=molsketch
+ DocPath=molsketch/index.html
+-MimeType=chemical/x-cml
++MimeType=chemical/x-cml;
+ Terminal=false
+ Categories=Qt;Education;Science;
+ GenericName=2D molecular structures editor
diff --git a/sci-chemistry/molsketch/files/molsketch-0.3.0-no-quotes.patch b/sci-chemistry/molsketch/files/molsketch-0.3.0-no-quotes.patch
new file mode 100644
index 000000000000..db7be800e385
--- /dev/null
+++ b/sci-chemistry/molsketch/files/molsketch-0.3.0-no-quotes.patch
@@ -0,0 +1,16 @@
+ CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 64c18a2..75c2fb7 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -97,7 +97,7 @@ endif(Qt5Core_FOUND AND Qt5Widgets_FOUND AND Qt5Gui_FOUND AND Qt5PrintSupport_FO
+ if(FORCEQt4)
+ 	add_definitions(-DQTVERSIONSUFFIX="")
+ else(FORCEQt4)
+-	add_definitions(-DQTVERSIONSUFFIX="\\\"-qt5\\\"")
++	add_definitions(-DQTVERSIONSUFFIX="-qt5")
+ endif(FORCEQt4)
+ 
+ # and OpenBabel2