Attachment #198239 for bug #232333

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# $FreeBSD$

PORTNAME=	avogadro
DISTVERSION=	1.2.0
PORTREVISION=	16
CATEGORIES=	science
MASTER_SITES=	SF



# We need to add a RUN_DEPENDS on eigen2, as the cmake file shiped with
# avogadro to use it, contains 'find_package(Eigen2 REQUIRED)'.
USES=		cmake desktop-file-utils eigen:2,build,run gl pkgconfig qt:4
USE_GL=		glu gl
USE_QT=		corelib gui network opengl \
		linguisttools_build moc_build qmake_build rcc_build uic_build
CMAKE_ARGS=	-DENABLE_GLSL=OFF \
		-DQT_MKSPECS_RELATIVE=share/qt4/mkspecs
USE_XORG=	x11
USE_LDCONFIG=	yes

CFLAGS+=	-idirafter ${LOCALBASE}/include/eigen2 \

Lines 1-2 Link Here

(-)science/avogadro/distinfo (-2 / +3 lines)
1	SHA256 (avogadro-1.1.1.tar.bz2) = fe6f7bdea17a27a20be25b70d975145999aae9d90ef320217af2bc4d6e7a0a14	1	TIMESTAMP = 1539715101
2	SIZE (avogadro-1.1.1.tar.bz2) = 11118046	2	SHA256 (avogadro-1.2.0.tar.gz) = 6453e36e8ae3e61655cbe062df6d6fa6b2409122c7b5abc0a6f1d410a181640b
		3	SIZE (avogadro-1.2.0.tar.gz) = 16779635




already try to link against libX11.

Sent upstream: https://github.com/cryos/avogadro/pull/13
--- CMakeLists.txt.orig	2016-06-08 14:19:45 UTC
+++ CMakeLists.txt
@@ -114,7 +114,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
   endif()
   # Set up additional build flags for particular build types. These will be added to CMAKE_CXX_FLAGS,
   # they will not replace them.
-  set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
+#  set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
   set(CMAKE_CXX_FLAGS_RELWITHDEBINFO
     "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} ${CMAKE_CXX_FLAGS_WARN}")
   set(CMAKE_CXX_FLAGS_DEBUG   "-g3 -fno-inline ${CMAKE_CXX_FLAGS_WARN}")
@@ -196,8 +196,8 @@ if(${CMAKE_CXX_COMPILER_ID} MATCHES Inte
     endif()
   endif()
 
-  set(CMAKE_C_FLAGS_RELEASE "-O3 -ipo1 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
-  set(CMAKE_CXX_FLAGS_RELEASE "-O3 -ipo1 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
+#  set(CMAKE_C_FLAGS_RELEASE "-O3 -ipo1 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
+#  set(CMAKE_CXX_FLAGS_RELEASE "-O3 -ipo1 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
 
   set(CMAKE_CXX_FLAGS_RELWITHDEBINFO
     "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} ${CMAKE_CXX_FLAGS_WARN}")
@@ -231,7 +231,11 @@ if(NOT Linguist_FOUND)
   message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations")
 endif()
 
-find_package(Eigen3) # find and setup Eigen3 if available
+if(Q_WS_X11)
+  find_package(X11 REQUIRED) # avogadro/src/main.cpp calls XInitThread().
+endif()
+
+#find_package(Eigen3) # find and setup Eigen3 if available # not ready for Eigen3, see https://github.com/cryos/avogadro/issues/915
 if(NOT EIGEN3_FOUND)
    message(STATUS "Cannot find Eigen3, trying Eigen2")
    find_package(Eigen2 REQUIRED) # Some version is required
@@ -521,7 +525,7 @@ if(UNIX)
     "${CMAKE_CURRENT_SOURCE_DIR}/avogadro.pc.in"
     "${CMAKE_CURRENT_BINARY_DIR}/avogadro.pc" @ONLY)
   set(PC_FILES "${CMAKE_CURRENT_BINARY_DIR}/avogadro.pc")
-  install(FILES ${PC_FILES} DESTINATION ${LIB_INSTALL_DIR}/pkgconfig)
+  install(FILES ${PC_FILES} DESTINATION libdata/pkgconfig)
 endif()
 
 # avopkg

Lines 1-8 Link Here

(-)science/avogadro/files/patch-libavogadro__src__camera.cpp (-5 / +5 lines)
1	--- ./libavogadro/src/camera.cpp.orig 2011-04-25 05:22:18.000000000 +0000	1	--- libavogadro/src/camera.cpp.orig 2016-06-08 14:19:45 UTC
2	+++ ./libavogadro/src/camera.cpp 2012-05-01 21:59:52.241696067 +0000	2	+++ libavogadro/src/camera.cpp
3	@@ -26,6 +26,8 @@	3	@@ -36,6 +36,8 @@
4	#include "glwidget.h"	4	# include <GL/glu.h>
5	#include <avogadro/molecule.h>	5	#endif
6		6
7	+#include <GL/glu.h>	7	+#include <GL/glu.h>
8	+	8	+

Lines 1-8 Link Here

(-)science/avogadro/files/patch-libavogadro__src__glpainter_p.cpp (-5 / +5 lines)
1	--- ./libavogadro/src/glpainter_p.cpp.orig 2011-04-25 05:22:18.000000000 +0000	1	--- libavogadro/src/glpainter_p.cpp.orig 2016-06-08 14:19:45 UTC
2	+++ ./libavogadro/src/glpainter_p.cpp 2012-05-01 21:59:50.998695297 +0000	2	+++ libavogadro/src/glpainter_p.cpp
3	@@ -43,6 +43,8 @@	3	@@ -53,6 +53,8 @@
4	#include <QVarLengthArray>	4	# include <GL/glu.h>
5	#include <Eigen/Geometry>	5	#endif
6		6
7	+#include <GL/glu.h>	7	+#include <GL/glu.h>
8	+	8	+

Lines 1-7 Link Here

(-)science/avogadro/files/patch-libavogadro__src__glwidget.cpp (-4 / +4 lines)
1	--- ./libavogadro/src/glwidget.cpp.orig 2011-04-25 05:22:18.000000000 +0000	1	--- libavogadro/src/glwidget.cpp.orig 2016-06-08 14:19:45 UTC
2	+++ ./libavogadro/src/glwidget.cpp 2012-05-01 22:02:14.170695198 +0000	2	+++ libavogadro/src/glwidget.cpp
3	@@ -64,6 +64,8 @@	3	@@ -84,6 +84,8 @@
4	#include <QMutex>	4	#include <GL/glew.h>
5	#endif	5	#endif
6		6
7	+#include <GL/glu.h>	7	+#include <GL/glu.h>

Lines 1-8 Link Here

(-)science/avogadro/files/patch-libavogadro__src__tools__selectrotatetool.cpp (-5 / +5 lines)
1	--- ./libavogadro/src/tools/selectrotatetool.cpp.orig 2011-04-25 05:22:18.000000000 +0000	1	--- libavogadro/src/tools/selectrotatetool.cpp.orig 2016-06-08 14:19:45 UTC
2	+++ ./libavogadro/src/tools/selectrotatetool.cpp 2012-05-01 22:05:46.053696029 +0000	2	+++ libavogadro/src/tools/selectrotatetool.cpp
3	@@ -44,6 +44,8 @@	3	@@ -57,6 +57,8 @@
4	#include <QComboBox>	4	# include <GL/glu.h>
5	#include <QDebug>	5	#endif
6		6
7	+#include <GL/glu.h>	7	+#include <GL/glu.h>
8	+	8	+

Lines 1-6 Link Here

(-)science/avogadro/files/patch-libavogadro_src_extensions_crystallography_crystallographyextension.cpp (-2 / +2 lines)
1	--- libavogadro/src/extensions/crystallography/crystallographyextension.cpp.orig 2013-12-06 15:50:04 UTC	1	--- libavogadro/src/extensions/crystallography/crystallographyextension.cpp.orig 2016-06-08 14:19:45 UTC
2	+++ libavogadro/src/extensions/crystallography/crystallographyextension.cpp	2	+++ libavogadro/src/extensions/crystallography/crystallographyextension.cpp
3	@@ -51,6 +51,11 @@	3	@@ -53,6 +53,11 @@
4	#include <openbabel/generic.h>	4	#include <openbabel/generic.h>
5	#include <openbabel/mol.h>	5	#include <openbabel/mol.h>
6		6




--- libavogadro/src/extensions/symmetry/libmsym/src/orbital.c.orig	2018-10-16 20:56:21 UTC
+++ libavogadro/src/extensions/symmetry/libmsym/src/orbital.c
@@ -67,13 +67,13 @@ msym_error_t orbitalFromQuantumNumbers(i
         }
         case 2 : {
             //o->v = dpolynomial[m+l];
-            char *d = (signbit(m) == 1 ? "-" : "+");
+            char *d = (signbit((double)m) == 1 ? "-" : "+"); // signbit is misused, see https://github.com/cryos/avogadro/issues/916
             snprintf(o->name, sizeof(o->name), "%dd%d%s",n,abs(m),d);
             break;
         }
         default : {
             char t = 'f' - 3 + l;
-            char *d = (signbit(m) == 1 ? "-" : "+");
+            char *d = (signbit((double)m) == 1 ? "-" : "+"); // signbit is misused, see https://github.com/cryos/avogadro/issues/916
             snprintf(o->name, sizeof(o->name), "%d%c%d%s",n,t,abs(m),d);
         }
     }




bin/avogadro
bin/avopkg
bin/qube
include/avogadro/animation.h
include/avogadro/atom.h
include/avogadro/bond.h

include/avogadro/color.h
include/avogadro/color3f.h
include/avogadro/colorbutton.h
include/avogadro/config.h
include/avogadro/cube.h
include/avogadro/dockextension.h
include/avogadro/dockwidget.h

include/avogadro/toolgroup.h
include/avogadro/undosequence.h
include/avogadro/zmatrix.h
include/libmsym/msym.h
include/libmsym/msym_error.h
lib/avogadro/1_2/AvogadroUse.cmake
lib/avogadro/1_2/cmake/FindEigen2.cmake
lib/avogadro/1_2/cmake/FindEigen3.cmake
lib/avogadro/1_2/cmake/FindGLEW.cmake
lib/avogadro/1_2/colors/atomindexcolor.so
lib/avogadro/1_2/colors/chargecolor.so
lib/avogadro/1_2/colors/customcolor.so
lib/avogadro/1_2/colors/distancecolor.so
lib/avogadro/1_2/colors/residuecolor.so
lib/avogadro/1_2/colors/smartscolor.so
lib/avogadro/1_2/engines/axesengine.so
lib/avogadro/1_2/engines/cartoonengine.so
lib/avogadro/1_2/engines/dipoleengine.so
lib/avogadro/1_2/engines/forceengine.so
lib/avogadro/1_2/engines/hbondengine.so
lib/avogadro/1_2/engines/labelengine.so
lib/avogadro/1_2/engines/polygonengine.so
lib/avogadro/1_2/engines/qtaimengine.so
lib/avogadro/1_2/engines/ribbonengine.so
lib/avogadro/1_2/engines/ringengine.so
lib/avogadro/1_2/engines/simplewireengine.so
lib/avogadro/1_2/engines/sphereengine.so
lib/avogadro/1_2/engines/stickengine.so
lib/avogadro/1_2/engines/surfaceengine.so
lib/avogadro/1_2/engines/wireengine.so
lib/avogadro/1_2/extensions/animationextension.so
lib/avogadro/1_2/extensions/cartesianextension.so
lib/avogadro/1_2/extensions/crystallographyextension.so
lib/avogadro/1_2/extensions/fileimportextension.so
lib/avogadro/1_2/extensions/forcefieldextension.so
lib/avogadro/1_2/extensions/gamessextension.so
lib/avogadro/1_2/extensions/gl2psextension.so
lib/avogadro/1_2/extensions/h2methylextension.so
lib/avogadro/1_2/extensions/hydrogensextension.so
lib/avogadro/1_2/extensions/inputfileextension.so
lib/avogadro/1_2/extensions/insertdnaextension.so
lib/avogadro/1_2/extensions/insertfragmentextension.so
lib/avogadro/1_2/extensions/insertpeptideextension.so
lib/avogadro/1_2/extensions/invertchiralextension.so
lib/avogadro/1_2/extensions/molecularpropextension.so
lib/avogadro/1_2/extensions/networkfetchextension.so
lib/avogadro/1_2/extensions/orbitalextension.so
lib/avogadro/1_2/extensions/orcaextension.so
lib/avogadro/1_2/extensions/povrayextension.so
lib/avogadro/1_2/extensions/propextension.so
%%PYTHON%%lib/avogadro/1_2/extensions/pythonterminal.so
lib/avogadro/1_2/extensions/qtaimextension.so
lib/avogadro/1_2/extensions/selectextension.so
lib/avogadro/1_2/extensions/spectraextension.so
lib/avogadro/1_2/extensions/supercellextension.so
lib/avogadro/1_2/extensions/surfaceextension.so
lib/avogadro/1_2/extensions/swcntbuilderextension.so
lib/avogadro/1_2/extensions/symmetryextension.so
lib/avogadro/1_2/extensions/vibrationextension.so
lib/avogadro/1_2/extensions/vrmlextension.so
lib/avogadro/1_2/tools/aligntool.so
lib/avogadro/1_2/tools/autoopttool.so
lib/avogadro/1_2/tools/autorotatetool.so
lib/avogadro/1_2/tools/bondcentrictool.so
lib/avogadro/1_2/tools/clickmeasuretool.so
lib/avogadro/1_2/tools/drawtool.so
lib/avogadro/1_2/tools/manipulatetool.so
lib/avogadro/1_2/tools/selectrotatetool.so
lib/avogadro/AvogadroConfig.cmake
lib/avogadro/AvogadroConfigVersion.cmake
lib/avogadro/AvogadroTargets-%%CMAKE_BUILD_TYPE%%.cmake
lib/avogadro/AvogadroTargets.cmake
lib/cmake/libmsym/libmsymConfig.cmake
lib/cmake/libmsym/libmsymConfigVersion.cmake
lib/cmake/libmsym/libmsymTargets-%%CMAKE_BUILD_TYPE%%.cmake
lib/cmake/libmsym/libmsymTargets.cmake
lib/libavogadro.so
lib/libavogadro.so.1
lib/libavogadro.so.1.2.0
lib/libavogadro_OpenQube.so
lib/libavogadro_OpenQube.so.0
lib/libavogadro_OpenQube.so.0.1.0
lib/libmsym.a
%%PYTHON%%%%PYTHON_SITELIBDIR%%/Avogadro.so
libdata/pkgconfig/avogadro.pc
man/man1/avogadro.1.gz

%%DATADIR%%/crystals/clays/Al2Si4O12Ca0.5-Montmorillonite.cif
%%DATADIR%%/crystals/clays/Al4KSi2O12-Illite.cif
%%DATADIR%%/crystals/clays/AlSi2O6H-Pyrophyllite.cif
%%DATADIR%%/crystals/clays/Fe2.25Cl0.5H%%PYTHON_VER%%5-Fougerite.cif
%%DATADIR%%/crystals/clays/FeSi2O6H-Nontronite.cif
%%DATADIR%%/crystals/clays/Lepidolite.cif
%%DATADIR%%/crystals/clays/Mg2Al2SiO9H4-Amesite.cif

%%DATADIR%%/i18n/avogadro_eu.qm
%%DATADIR%%/i18n/avogadro_fi.qm
%%DATADIR%%/i18n/avogadro_fr.qm
%%DATADIR%%/i18n/avogadro_fr_CA.qm
%%DATADIR%%/i18n/avogadro_gl.qm
%%DATADIR%%/i18n/avogadro_he.qm
%%DATADIR%%/i18n/avogadro_hi.qm

%%DATADIR%%/i18n/avogadro_sr.qm
%%DATADIR%%/i18n/avogadro_sv.qm
%%DATADIR%%/i18n/avogadro_ta.qm
%%DATADIR%%/i18n/avogadro_te.qm
%%DATADIR%%/i18n/avogadro_th.qm
%%DATADIR%%/i18n/avogadro_tr.qm
%%DATADIR%%/i18n/avogadro_ug.qm

%%DATADIR%%/i18n/libavogadro_sq.qm
%%DATADIR%%/i18n/libavogadro_sr.qm
%%DATADIR%%/i18n/libavogadro_sv.qm
%%DATADIR%%/i18n/libavogadro_th.qm
%%DATADIR%%/i18n/libavogadro_tr.qm
%%DATADIR%%/i18n/libavogadro_ug.qm
%%DATADIR%%/i18n/libavogadro_uk.qm

Return to bug 232333

Lines 2-9 Link Here

(-)science/avogadro/Makefile (-4 / +4 lines)
2	# $FreeBSD$	2	# $FreeBSD$
3		3
4	PORTNAME= avogadro	4	PORTNAME= avogadro
5	PORTVERSION= 1.1.1	5	DISTVERSION= 1.2.0
6	PORTREVISION= 16
7	CATEGORIES= science	6	CATEGORIES= science
8	MASTER_SITES= SF	7	MASTER_SITES= SF
9		8
Lines 20-31 Link Here
20		19
21	# We need to add a RUN_DEPENDS on eigen2, as the cmake file shiped with	20	# We need to add a RUN_DEPENDS on eigen2, as the cmake file shiped with
22	# avogadro to use it, contains 'find_package(Eigen2 REQUIRED)'.	21	# avogadro to use it, contains 'find_package(Eigen2 REQUIRED)'.
23	USES= cmake desktop-file-utils eigen:2,build,run pkgconfig qt:4 tar:bzip2	22	USES= cmake desktop-file-utils eigen:2,build,run gl pkgconfig qt:4
24	USE_GL= glu gl	23	USE_GL= glu gl
25	USE_QT= gui network opengl \	24	USE_QT= corelib gui network opengl \
26	linguisttools_build moc_build qmake_build rcc_build uic_build	25	linguisttools_build moc_build qmake_build rcc_build uic_build
27	CMAKE_ARGS= -DENABLE_GLSL=OFF \	26	CMAKE_ARGS= -DENABLE_GLSL=OFF \
28	-DQT_MKSPECS_RELATIVE=share/qt4/mkspecs	27	-DQT_MKSPECS_RELATIVE=share/qt4/mkspecs
		28	USE_XORG= x11
29	USE_LDCONFIG= yes	29	USE_LDCONFIG= yes
30		30
31	CFLAGS+= -idirafter ${LOCALBASE}/include/eigen2 \	31	CFLAGS+= -idirafter ${LOCALBASE}/include/eigen2 \

Lines 7-22 Link Here

(-)science/avogadro/files/patch-CMakeLists.txt (-3 / +34 lines)
7	already try to link against libX11.	7	already try to link against libX11.
8		8
9	Sent upstream: https://github.com/cryos/avogadro/pull/13	9	Sent upstream: https://github.com/cryos/avogadro/pull/13
10	--- CMakeLists.txt	10	--- CMakeLists.txt.orig 2016-06-08 14:19:45 UTC
11	+++ CMakeLists.txt	11	+++ CMakeLists.txt
12	@@ -230,6 +230,10 @@ if(NOT Linguist_FOUND)	12	@@ -114,7 +114,7 @@ if (CMAKE_COMPILER_IS_GNUCXX)
		13	endif()
		14	# Set up additional build flags for particular build types. These will be added to CMAKE_CXX_FLAGS,
		15	# they will not replace them.
		16	- set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
		17	+# set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
		18	set(CMAKE_CXX_FLAGS_RELWITHDEBINFO
		19	"${CMAKE_CXX_FLAGS_RELWITHDEBINFO} ${CMAKE_CXX_FLAGS_WARN}")
		20	set(CMAKE_CXX_FLAGS_DEBUG "-g3 -fno-inline ${CMAKE_CXX_FLAGS_WARN}")
		21	@@ -196,8 +196,8 @@ if(${CMAKE_CXX_COMPILER_ID} MATCHES Inte
		22	endif()
		23	endif()
		24
		25	- set(CMAKE_C_FLAGS_RELEASE "-O3 -ipo1 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
		26	- set(CMAKE_CXX_FLAGS_RELEASE "-O3 -ipo1 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
		27	+# set(CMAKE_C_FLAGS_RELEASE "-O3 -ipo1 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
		28	+# set(CMAKE_CXX_FLAGS_RELEASE "-O3 -ipo1 -DNDEBUG -DQT_NO_DEBUG_OUTPUT -Wl,-s")
		29
		30	set(CMAKE_CXX_FLAGS_RELWITHDEBINFO
		31	"${CMAKE_CXX_FLAGS_RELWITHDEBINFO} ${CMAKE_CXX_FLAGS_WARN}")
		32	@@ -231,7 +231,11 @@ if(NOT Linguist_FOUND)
13	message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations")	33	message(WARNING " Qt4 Linguist not found, please install it if you want Avogadro translations")
14	endif()	34	endif()
15		35
		36	-find_package(Eigen3) # find and setup Eigen3 if available
16	+if(Q_WS_X11)	37	+if(Q_WS_X11)
17	+ find_package(X11 REQUIRED) # avogadro/src/main.cpp calls XInitThread().	38	+ find_package(X11 REQUIRED) # avogadro/src/main.cpp calls XInitThread().
18	+endif()	39	+endif()
19	+	40	+
20	find_package(Eigen3) # find and setup Eigen3 if available	41	+#find_package(Eigen3) # find and setup Eigen3 if available # not ready for Eigen3, see https://github.com/cryos/avogadro/issues/915
21	if(NOT EIGEN3_FOUND)	42	if(NOT EIGEN3_FOUND)
22	message(STATUS "Cannot find Eigen3, trying Eigen2")	43	message(STATUS "Cannot find Eigen3, trying Eigen2")
		44	find_package(Eigen2 REQUIRED) # Some version is required
		45	@@ -521,7 +525,7 @@ if(UNIX)
		46	"${CMAKE_CURRENT_SOURCE_DIR}/avogadro.pc.in"
		47	"${CMAKE_CURRENT_BINARY_DIR}/avogadro.pc" @ONLY)
		48	set(PC_FILES "${CMAKE_CURRENT_BINARY_DIR}/avogadro.pc")
		49	- install(FILES ${PC_FILES} DESTINATION ${LIB_INSTALL_DIR}/pkgconfig)
		50	+ install(FILES ${PC_FILES} DESTINATION libdata/pkgconfig)
		51	endif()
		52
		53	# avopkg

Line 0 Link Here

(-)science/avogadro/files/patch-libavogadro_src_extensions_symmetry_libmsym_src_orbital.c (+18 lines)
	1	--- libavogadro/src/extensions/symmetry/libmsym/src/orbital.c.orig 2018-10-16 20:56:21 UTC
	2	+++ libavogadro/src/extensions/symmetry/libmsym/src/orbital.c
	3	@@ -67,13 +67,13 @@ msym_error_t orbitalFromQuantumNumbers(i
	4	}
	5	case 2 : {
	6	//o->v = dpolynomial[m+l];
	7	- char *d = (signbit(m) == 1 ? "-" : "+");
	8	+ char *d = (signbit((double)m) == 1 ? "-" : "+"); // signbit is misused, see https://github.com/cryos/avogadro/issues/916
	9	snprintf(o->name, sizeof(o->name), "%dd%d%s",n,abs(m),d);
	10	break;
	11	}
	12	default : {
	13	char t = 'f' - 3 + l;
	14	- char *d = (signbit(m) == 1 ? "-" : "+");
	15	+ char *d = (signbit((double)m) == 1 ? "-" : "+"); // signbit is misused, see https://github.com/cryos/avogadro/issues/916
	16	snprintf(o->name, sizeof(o->name), "%d%c%d%s",n,t,abs(m),d);
	17	}
	18	}

Lines 1-5 Link Here

(-)science/avogadro/pkg-plist (-62 / +77 lines)
1	bin/avogadro	1	bin/avogadro
2	bin/avopkg	2	bin/avopkg
		3	bin/qube
3	include/avogadro/animation.h	4	include/avogadro/animation.h
4	include/avogadro/atom.h	5	include/avogadro/atom.h
5	include/avogadro/bond.h	6	include/avogadro/bond.h
Lines 7-12 Link Here
7	include/avogadro/color.h	8	include/avogadro/color.h
8	include/avogadro/color3f.h	9	include/avogadro/color3f.h
9	include/avogadro/colorbutton.h	10	include/avogadro/colorbutton.h
		11	include/avogadro/config.h
10	include/avogadro/cube.h	12	include/avogadro/cube.h
11	include/avogadro/dockextension.h	13	include/avogadro/dockextension.h
12	include/avogadro/dockwidget.h	14	include/avogadro/dockwidget.h
Lines 46-121 Link Here
46	include/avogadro/toolgroup.h	48	include/avogadro/toolgroup.h
47	include/avogadro/undosequence.h	49	include/avogadro/undosequence.h
48	include/avogadro/zmatrix.h	50	include/avogadro/zmatrix.h
49	lib/avogadro/1_1/AvogadroUse.cmake	51	include/libmsym/msym.h
50	lib/avogadro/1_1/cmake/FindEigen2.cmake	52	include/libmsym/msym_error.h
51	lib/avogadro/1_1/cmake/FindEigen3.cmake	53	lib/avogadro/1_2/AvogadroUse.cmake
52	lib/avogadro/1_1/cmake/FindGLEW.cmake	54	lib/avogadro/1_2/cmake/FindEigen2.cmake
53	lib/avogadro/1_1/colors/atomindexcolor.so	55	lib/avogadro/1_2/cmake/FindEigen3.cmake
54	lib/avogadro/1_1/colors/chargecolor.so	56	lib/avogadro/1_2/cmake/FindGLEW.cmake
55	lib/avogadro/1_1/colors/customcolor.so	57	lib/avogadro/1_2/colors/atomindexcolor.so
56	lib/avogadro/1_1/colors/distancecolor.so	58	lib/avogadro/1_2/colors/chargecolor.so
57	lib/avogadro/1_1/colors/residuecolor.so	59	lib/avogadro/1_2/colors/customcolor.so
58	lib/avogadro/1_1/colors/smartscolor.so	60	lib/avogadro/1_2/colors/distancecolor.so
59	lib/avogadro/1_1/engines/axesengine.so	61	lib/avogadro/1_2/colors/residuecolor.so
60	lib/avogadro/1_1/engines/cartoonengine.so	62	lib/avogadro/1_2/colors/smartscolor.so
61	lib/avogadro/1_1/engines/dipoleengine.so	63	lib/avogadro/1_2/engines/axesengine.so
62	lib/avogadro/1_1/engines/forceengine.so	64	lib/avogadro/1_2/engines/cartoonengine.so
63	lib/avogadro/1_1/engines/hbondengine.so	65	lib/avogadro/1_2/engines/dipoleengine.so
64	lib/avogadro/1_1/engines/labelengine.so	66	lib/avogadro/1_2/engines/forceengine.so
65	lib/avogadro/1_1/engines/polygonengine.so	67	lib/avogadro/1_2/engines/hbondengine.so
66	lib/avogadro/1_1/engines/qtaimengine.so	68	lib/avogadro/1_2/engines/labelengine.so
67	lib/avogadro/1_1/engines/ribbonengine.so	69	lib/avogadro/1_2/engines/polygonengine.so
68	lib/avogadro/1_1/engines/ringengine.so	70	lib/avogadro/1_2/engines/qtaimengine.so
69	lib/avogadro/1_1/engines/simplewireengine.so	71	lib/avogadro/1_2/engines/ribbonengine.so
70	lib/avogadro/1_1/engines/sphereengine.so	72	lib/avogadro/1_2/engines/ringengine.so
71	lib/avogadro/1_1/engines/stickengine.so	73	lib/avogadro/1_2/engines/simplewireengine.so
72	lib/avogadro/1_1/engines/surfaceengine.so	74	lib/avogadro/1_2/engines/sphereengine.so
73	lib/avogadro/1_1/engines/wireengine.so	75	lib/avogadro/1_2/engines/stickengine.so
74	lib/avogadro/1_1/extensions/animationextension.so	76	lib/avogadro/1_2/engines/surfaceengine.so
75	lib/avogadro/1_1/extensions/cartesianextension.so	77	lib/avogadro/1_2/engines/wireengine.so
76	lib/avogadro/1_1/extensions/crystallographyextension.so	78	lib/avogadro/1_2/extensions/animationextension.so
77	lib/avogadro/1_1/extensions/fileimportextension.so	79	lib/avogadro/1_2/extensions/cartesianextension.so
78	lib/avogadro/1_1/extensions/forcefieldextension.so	80	lib/avogadro/1_2/extensions/crystallographyextension.so
79	lib/avogadro/1_1/extensions/gamessextension.so	81	lib/avogadro/1_2/extensions/fileimportextension.so
80	lib/avogadro/1_1/extensions/gl2psextension.so	82	lib/avogadro/1_2/extensions/forcefieldextension.so
81	lib/avogadro/1_1/extensions/h2methylextension.so	83	lib/avogadro/1_2/extensions/gamessextension.so
82	lib/avogadro/1_1/extensions/hydrogensextension.so	84	lib/avogadro/1_2/extensions/gl2psextension.so
83	lib/avogadro/1_1/extensions/inputfileextension.so	85	lib/avogadro/1_2/extensions/h2methylextension.so
84	lib/avogadro/1_1/extensions/insertdnaextension.so	86	lib/avogadro/1_2/extensions/hydrogensextension.so
85	lib/avogadro/1_1/extensions/insertfragmentextension.so	87	lib/avogadro/1_2/extensions/inputfileextension.so
86	lib/avogadro/1_1/extensions/insertpeptideextension.so	88	lib/avogadro/1_2/extensions/insertdnaextension.so
87	lib/avogadro/1_1/extensions/invertchiralextension.so	89	lib/avogadro/1_2/extensions/insertfragmentextension.so
88	lib/avogadro/1_1/extensions/molecularpropextension.so	90	lib/avogadro/1_2/extensions/insertpeptideextension.so
89	lib/avogadro/1_1/extensions/networkfetchextension.so	91	lib/avogadro/1_2/extensions/invertchiralextension.so
90	lib/avogadro/1_1/extensions/orbitalextension.so	92	lib/avogadro/1_2/extensions/molecularpropextension.so
91	lib/avogadro/1_1/extensions/povrayextension.so	93	lib/avogadro/1_2/extensions/networkfetchextension.so
92	lib/avogadro/1_1/extensions/propextension.so	94	lib/avogadro/1_2/extensions/orbitalextension.so
93	%%PYTHON%%lib/avogadro/1_1/extensions/pythonterminal.so	95	lib/avogadro/1_2/extensions/orcaextension.so
94	lib/avogadro/1_1/extensions/qtaimextension.so	96	lib/avogadro/1_2/extensions/povrayextension.so
95	lib/avogadro/1_1/extensions/selectextension.so	97	lib/avogadro/1_2/extensions/propextension.so
96	lib/avogadro/1_1/extensions/spectraextension.so	98	%%PYTHON%%lib/avogadro/1_2/extensions/pythonterminal.so
97	lib/avogadro/1_1/extensions/supercellextension.so	99	lib/avogadro/1_2/extensions/qtaimextension.so
98	lib/avogadro/1_1/extensions/surfaceextension.so	100	lib/avogadro/1_2/extensions/selectextension.so
99	lib/avogadro/1_1/extensions/swcntbuilderextension.so	101	lib/avogadro/1_2/extensions/spectraextension.so
100	lib/avogadro/1_1/extensions/vibrationextension.so	102	lib/avogadro/1_2/extensions/supercellextension.so
101	lib/avogadro/1_1/tools/aligntool.so	103	lib/avogadro/1_2/extensions/surfaceextension.so
102	lib/avogadro/1_1/tools/autoopttool.so	104	lib/avogadro/1_2/extensions/swcntbuilderextension.so
103	lib/avogadro/1_1/tools/autorotatetool.so	105	lib/avogadro/1_2/extensions/symmetryextension.so
104	lib/avogadro/1_1/tools/bondcentrictool.so	106	lib/avogadro/1_2/extensions/vibrationextension.so
105	lib/avogadro/1_1/tools/clickmeasuretool.so	107	lib/avogadro/1_2/extensions/vrmlextension.so
106	lib/avogadro/1_1/tools/drawtool.so	108	lib/avogadro/1_2/tools/aligntool.so
107	lib/avogadro/1_1/tools/manipulatetool.so	109	lib/avogadro/1_2/tools/autoopttool.so
108	lib/avogadro/1_1/tools/selectrotatetool.so	110	lib/avogadro/1_2/tools/autorotatetool.so
		111	lib/avogadro/1_2/tools/bondcentrictool.so
		112	lib/avogadro/1_2/tools/clickmeasuretool.so
		113	lib/avogadro/1_2/tools/drawtool.so
		114	lib/avogadro/1_2/tools/manipulatetool.so
		115	lib/avogadro/1_2/tools/selectrotatetool.so
109	lib/avogadro/AvogadroConfig.cmake	116	lib/avogadro/AvogadroConfig.cmake
110	lib/avogadro/AvogadroConfigVersion.cmake	117	lib/avogadro/AvogadroConfigVersion.cmake
111	lib/avogadro/AvogadroTargets-%%CMAKE_BUILD_TYPE%%.cmake	118	lib/avogadro/AvogadroTargets-%%CMAKE_BUILD_TYPE%%.cmake
112	lib/avogadro/AvogadroTargets.cmake	119	lib/avogadro/AvogadroTargets.cmake
		120	lib/cmake/libmsym/libmsymConfig.cmake
		121	lib/cmake/libmsym/libmsymConfigVersion.cmake
		122	lib/cmake/libmsym/libmsymTargets-%%CMAKE_BUILD_TYPE%%.cmake
		123	lib/cmake/libmsym/libmsymTargets.cmake
113	lib/libavogadro.so	124	lib/libavogadro.so
114	lib/libavogadro.so.1	125	lib/libavogadro.so.1
115	lib/libavogadro.so.1.1.1	126	lib/libavogadro.so.1.2.0
116	lib/libavogadro_OpenQube.so	127	lib/libavogadro_OpenQube.so
117	lib/libavogadro_OpenQube.so.0	128	lib/libavogadro_OpenQube.so.0
118	lib/libavogadro_OpenQube.so.0.1.0	129	lib/libavogadro_OpenQube.so.0.1.0
		130	lib/libmsym.a
119	%%PYTHON%%%%PYTHON_SITELIBDIR%%/Avogadro.so	131	%%PYTHON%%%%PYTHON_SITELIBDIR%%/Avogadro.so
120	libdata/pkgconfig/avogadro.pc	132	libdata/pkgconfig/avogadro.pc
121	man/man1/avogadro.1.gz	133	man/man1/avogadro.1.gz
Lines 190-196 Link Here
190	%%DATADIR%%/crystals/clays/Al2Si4O12Ca0.5-Montmorillonite.cif	202	%%DATADIR%%/crystals/clays/Al2Si4O12Ca0.5-Montmorillonite.cif
191	%%DATADIR%%/crystals/clays/Al4KSi2O12-Illite.cif	203	%%DATADIR%%/crystals/clays/Al4KSi2O12-Illite.cif
192	%%DATADIR%%/crystals/clays/AlSi2O6H-Pyrophyllite.cif	204	%%DATADIR%%/crystals/clays/AlSi2O6H-Pyrophyllite.cif
193	%%DATADIR%%/crystals/clays/Fe2.25Cl0.5H2.75-Fougerite.cif	205	%%DATADIR%%/crystals/clays/Fe2.25Cl0.5H%%PYTHON_VER%%5-Fougerite.cif
194	%%DATADIR%%/crystals/clays/FeSi2O6H-Nontronite.cif	206	%%DATADIR%%/crystals/clays/FeSi2O6H-Nontronite.cif
195	%%DATADIR%%/crystals/clays/Lepidolite.cif	207	%%DATADIR%%/crystals/clays/Lepidolite.cif
196	%%DATADIR%%/crystals/clays/Mg2Al2SiO9H4-Amesite.cif	208	%%DATADIR%%/crystals/clays/Mg2Al2SiO9H4-Amesite.cif
Lines 1068-1073 Link Here
1068	%%DATADIR%%/i18n/avogadro_eu.qm	1080	%%DATADIR%%/i18n/avogadro_eu.qm
1069	%%DATADIR%%/i18n/avogadro_fi.qm	1081	%%DATADIR%%/i18n/avogadro_fi.qm
1070	%%DATADIR%%/i18n/avogadro_fr.qm	1082	%%DATADIR%%/i18n/avogadro_fr.qm
		1083	%%DATADIR%%/i18n/avogadro_fr_CA.qm
1071	%%DATADIR%%/i18n/avogadro_gl.qm	1084	%%DATADIR%%/i18n/avogadro_gl.qm
1072	%%DATADIR%%/i18n/avogadro_he.qm	1085	%%DATADIR%%/i18n/avogadro_he.qm
1073	%%DATADIR%%/i18n/avogadro_hi.qm	1086	%%DATADIR%%/i18n/avogadro_hi.qm
Lines 1092-1097 Link Here
1092	%%DATADIR%%/i18n/avogadro_sr.qm	1105	%%DATADIR%%/i18n/avogadro_sr.qm
1093	%%DATADIR%%/i18n/avogadro_sv.qm	1106	%%DATADIR%%/i18n/avogadro_sv.qm
1094	%%DATADIR%%/i18n/avogadro_ta.qm	1107	%%DATADIR%%/i18n/avogadro_ta.qm
		1108	%%DATADIR%%/i18n/avogadro_te.qm
1095	%%DATADIR%%/i18n/avogadro_th.qm	1109	%%DATADIR%%/i18n/avogadro_th.qm
1096	%%DATADIR%%/i18n/avogadro_tr.qm	1110	%%DATADIR%%/i18n/avogadro_tr.qm
1097	%%DATADIR%%/i18n/avogadro_ug.qm	1111	%%DATADIR%%/i18n/avogadro_ug.qm
Lines 1138-1143 Link Here
1138	%%DATADIR%%/i18n/libavogadro_sq.qm	1152	%%DATADIR%%/i18n/libavogadro_sq.qm
1139	%%DATADIR%%/i18n/libavogadro_sr.qm	1153	%%DATADIR%%/i18n/libavogadro_sr.qm
1140	%%DATADIR%%/i18n/libavogadro_sv.qm	1154	%%DATADIR%%/i18n/libavogadro_sv.qm
		1155	%%DATADIR%%/i18n/libavogadro_th.qm
1141	%%DATADIR%%/i18n/libavogadro_tr.qm	1156	%%DATADIR%%/i18n/libavogadro_tr.qm
1142	%%DATADIR%%/i18n/libavogadro_ug.qm	1157	%%DATADIR%%/i18n/libavogadro_ug.qm
1143	%%DATADIR%%/i18n/libavogadro_uk.qm	1158	%%DATADIR%%/i18n/libavogadro_uk.qm