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gnome-chemistry-utils: Update to 0.14.16
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Changelog:
Version 0.14.16:
	GChemPaint:
		* Do not show buttons for non yet implemented tools.

Version 0.14.15:
	GCCV library:
		* Don't use the abs() function on unsigned numbers.
	Other:
		* Updated appdata files.

Version 0.14.14:
	Mozilla plugin:
	* Fix build.

Version 0.14.13:
	GChemPaint:
		* Optional use of Lasem to display maths.
		* Fix rendering with gtk+ >= 3.20.
		* Fix crash with atom charges larger than 1.
		* Fix crash when deleting a bond outside a molecule. [#48256]
	Gnumeric plugin:
		* Add monoisotopicmass function in gnumeric and more.
	Databases:
		* Update names for elements 113, 115, 117 and 118.

Version 0.14.12:
	GChemPaint:
		* Enhanced Chemdraw formats support. [sr #108952]
		* Optional use of Lasem to display maths.
		* Fix rendering with gtk+ >= 3.20.
	GChemCalc:
		* Don't crash on "Ac" string. [#47366]

Version 0.14.11:
	GChemPaint:
		* Fix an infinite loop condition in retrosyntheses alignment.
		* Don't crash when importing an invalid string. [Redhat bug #1285154]
		* Fix drawing when zoomed.
		* Fix various runtime errors.
		* Fix crash when creating a reaction with no product.
		* Enhanced Chemdraw formats support.
		* Fix embedding of a whole molecule inside brackets. [#47224]
	GChemTable:
		* Don't crash when showing an already existing chart.
		[Redhat bug #1302135]
	GCrystal:
		* Fix build with gcc-6. [Redhat bug #1307546]
	GCrystal and GChem3D:
		* Don't crash when rendering to memory (images and print). [#47169]
	Other:
		* Added keywords to desktop files.
		* Updated appdata files.

Version 0.14.10:
	GChemPaint:
		* Fix an object bounds issue.
	Mozilla plugin:
		* Supports the npapi-sdk package as requirement.
	Other:
		* Fixed typos in appdata files.

Version 0.14.9:
	GChemPaint:
		* Ensure that the document size is always updated. [#43091]
	3d viewer and GCrystal:
		* Fix rotation. [#42977] (patch from Toni Andjelkovic)
	All applications:
		* Add appdata files.

Version 0.14.8
	GChemPaint:
		* Fix drawing with Gtk+ >= 3.10.

Version 0.14.7
	GCrystal:
		* Fix crash in dialogs with recent Gtk+.
	Mozilla plugin:
		* Fix crashers for 2D and 3D molecules.

Version 0.14.6
	3d viewer:
		* Avoid empty entries in recent list.
	CGchemPaint:
		* Restore .mol files support.
		* Fix CML import (also affected 3d viewer and >GCrystal).
		* Fix BMP export.
	GCrystal:
		* Fix test order in lines code. [#41261]
	GSpectrum:
		* Fix access to uninitialized data.
		* Don' double free a string.
	GOffice component:
		* Don't crash when editing after saving a GChemPaint object.
	Mozilla plugin:
		* Fix supported mime-types list. (see Debian bug #716961)
	Other:
		* Fix build on FreeBSD (Koop Mast). [#41256]

Version 0.14.5
	GChemPaint:
		* Make adding template work again.

Version 0.14.4
	GChemPaint:
		* Do not use a NULL atom properties. [#40194]

Version 0.14.3
	GChemPaint:
		* Really close the window on delete event.
		* Don't crash when aligning ungrouped objects.
	GChemTable:
		* Fix crash when using masses in a graph.
		* Fix graph behavior after edition.
	All:
		* Make sure to not create a C++ locale from a NULL string.

Version 0.14.2
	GChemPaint:
		* Fix crash when loading some molecules (was introduced in 0.14.1).

Version 0.14.1
	GChemPaint:
		* Do not allow a mesomery destruction when inside a reaction.
		* Fix molecule deletion inside a mesomery.
		* Fix reactant deletion inside a reaction.
		* Don't crash when a mesomery inside a reaction is destroyed.
		* Check molecule consistency when loading, avoids a stack overflow.
		* Enhanced representaion of chiral molecules imported from CML and other
		formats.
		* Fix crash when deleting a cyclic bond.
	GCrystal:
		* Fix row selection operations order in grids.

Version 0.14.0
	GChemPaint:
		* Fix reaction construction.
		* Fix non bonding electron pairs.

Version 0.13.99
	GChemPaint:
		* Fix squiggle bonds period.
		* Allow brackets around a mesomery.
		* Allow a mesomery inside a reaction.
		* Fixed some meomory access issues.
		* Fixed crash when loading a group.
		* Fixed mesomery construction.
		* Fixed crash when ungrouping.

Version 0.13.98
	GChemPaint:
		* Don't freeze after an aborted molecules merge.
		* Initialize the bond order for the Newman projection tool.
		* Don't crash when adding brackets around a fragment.
		* Fix undoing a molecule partial flip.
		* Fix bracket stoichiometry index position after a transform.
		* Fix explicit lone pairs count evaluation.

Version 0.13.92
	GChemCalc
		* Updated the documentation.
	GChemPaint:
		* Fix View::BuildSVG() and View::BuildEPS() which were missing the
		trailing 0.
		* Fix misleading error message while saving.
		* Fix loading of arrows inside a group. [#27032]
	GCrystal:
		* Apply element change to all slected atoms.
		* Updated the documentation.
	GSpectrum:
		* Add "Response factor" as supported unit.
		* Fixed widgets spacing.
		* Updated the documentation.
	GChemTable:
		* Updated the documentation.

Version 0.13.91
	3d viewer:
		* Show all menu items when a molecule is loaded from the command line.
		* Updated user documentation.
	GChemPaint:
		* Don't crash on startup.
	All:
		* Fix localization issues.
		* Fixed modal message boxes behavior.

Version 0.13.90
	3d viewer:
		* Fix import from pdb files. [#36582]
	GCrystal:
		* Fix infinite loop condition. [#36583]
		* Fix atomic radius change issue.
	GChemTable:
		* Fix languages translation.

Version 0.13.7
	GChemPaint:
		* Fixed crash when selecting the alignment item inside a mechanism
		step. [#35626]
	GCrystal:
		* Fixed loading CIF files using uptodate space groups descriptions.
	Other:
		* License is now GPL version 3 (except for the OpenBabel related code).
		* Fix build on big endian machines (Dan Horak). [#36175]
		* Updated API documentation.

Version 0.13.6
	GChemPaint:
		* fixed text position serialization. [#34947]
		* add some support for Newman projections.
		* accept some multisteps reactions.
	Goffice component:
		* Add support for 3D molecular structures.
	Other:
		* Fixed pixmaps installation directory. [#35272]
		* fixed build with ->l,--no-undefined. [patch #7677]

Version 0.13.5
	3d viewer:
		* Import from InChI or SMILES.
		* Export to GChemPaint and GChemCalc.
		* Generates InChI, InChiKey and SMILES.
		* Add access to databases.
	GChemPaint:
		* Brackets inside a molecule accept a stoichiometry coefficient.
	GCrystal:
		* Use multiple selection in atoms and lines dialogs.
	GSpectrum:
		* Allow markup in combo boxes and axes titles.
	Goffice component:
		* Add support for crystal structures.
	Other:
		* Fixed one more OpenGL related crasher.

Version 0.13.4
	All:
		* Ported to Gtk+-3.0.
	GCrystal:
		* Use the new GcrGrid item in atoms, lines and cleavages dialogs.
		* Make these and size dialogs instant apply.
	GChemTable:
		* Use a more complete tip window for elements.

Version 0.13.3
	GChemPaint:
		* Fixed build with gcc-4.6. [#32363]
		* Allow colored atomic symbols on a per-document basis.
		* Brackets tool now working, not perfectly though.
	Other:
		* Don't use POLLRDHUP when not defined. [#32768]
		* Split libgcu so that libgcu itself never calls gtk+ directly.

Version 0.13.2
	GChemPaint:
		* Do not allow document changes using keyboard while
		dragging the mouse. [#31812]
		* Don't add new molecules when undoing a mechanism arrow deletion.
		[#32433]
		* Removed the Wikipedia tool which was obsolete.
		* Reorganized molecule contextual menu with new 3D options
		and databases access.
	Other:
		* OpenBabel support has been moved to a separate process and greatly
		enhanced, specially for 3D export from gchempaint.
		* A lot of bugs have been fixed.

Version 0.13.1
	GSpectrum:
		* Loads NUTS files.
		* Transforms FID to spectrum.

Version 0.13.0
	GChemPaint:
		* New "lasso" tool to allow partial selections.
		* New "brackets" tool (doesn't work yet).
	Other:
		* libgcr: new library for GCrystal.
		* Fixed all bugs discovered in the 0.12 banch.
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ryoon committed Jun 29, 2020
1 parent f8fa971 commit 354ef97
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17 changes: 5 additions & 12 deletions biology/gnome-chemistry-utils/Makefile
Original file line number Diff line number Diff line change
@@ -1,10 +1,9 @@
# $NetBSD: Makefile,v 1.46 2020/06/02 08:23:16 adam Exp $
# $NetBSD: Makefile,v 1.47 2020/06/29 13:04:48 ryoon Exp $
#

DISTNAME= gnome-chemistry-utils-0.12.13
PKGREVISION= 33
DISTNAME= gnome-chemistry-utils-0.14.16
CATEGORIES= biology
MASTER_SITES= http://download-mirror.savannah.gnu.org/releases/gchemutils/0.12/
MASTER_SITES= http://download-mirror.savannah.gnu.org/releases/gchemutils/0.14/
EXTRACT_SUFX= .tar.bz2

MAINTAINER= [email protected]
Expand All @@ -17,25 +16,19 @@ USE_LIBTOOL= yes
USE_TOOLS+= gmake intltool pkg-config msgfmt xgettext msgmerge perl
USE_LANGUAGES= c c++

GCONF_SCHEMAS+= gchemutils.schemas
GCONF_SCHEMAS+= gchempaint-arrows.schemas
GCONF_SCHEMAS+= gcrystal.schemas
GCONF_SCHEMAS+= gchempaint.schemas

BUILDLINK_TRANSFORM+= rm:-DGTK_DISABLE_DEPRECATED
BUILDLINK_TRANSFORM+= rm:-ldl

CONFIGURE_ARGS+= --disable-update-databases

.include "../../devel/GConf/schemas.mk"
.include "../../databases/shared-mime-info/buildlink3.mk"
.include "../../databases/gnome-mime-data/buildlink3.mk"
.include "../../textproc/gnome-doc-utils/buildlink3.mk"
.include "../../mk/omf-scrollkeeper.mk"
.include "../../graphics/gtkglext/buildlink3.mk"
.include "../../misc/goffice0.8/buildlink3.mk"
.include "../../misc/goffice0.10/buildlink3.mk"
.include "../../sysutils/desktop-file-utils/desktopdb.mk"
.include "../../biology/chemical-mime-data/buildlink3.mk"
.include "../../biology/bodr/buildlink3.mk"
.include "../../biology/openbabel/buildlink3.mk"
.include "../../x11/gtk3/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
573 changes: 287 additions & 286 deletions biology/gnome-chemistry-utils/PLIST

Large diffs are not rendered by default.

15 changes: 6 additions & 9 deletions biology/gnome-chemistry-utils/distinfo
Original file line number Diff line number Diff line change
@@ -1,10 +1,7 @@
$NetBSD: distinfo,v 1.7 2015/11/02 18:42:21 agc Exp $
$NetBSD: distinfo,v 1.8 2020/06/29 13:04:48 ryoon Exp $

SHA1 (gnome-chemistry-utils-0.12.13.tar.bz2) = a3d83f281ccd7fdbc98e14e295093287d8648a69
RMD160 (gnome-chemistry-utils-0.12.13.tar.bz2) = 259509c4e9086fc40e91d1f2f93ad5bad9317b8c
SHA512 (gnome-chemistry-utils-0.12.13.tar.bz2) = 70180d9bc51fcef00b979ac0ed573435e17ab626e816a9b0a91cbddf9fb76866c9726802cc741c52fa9243a327d5cd3cdb17e8404916de7447dbd46628adde6d
Size (gnome-chemistry-utils-0.12.13.tar.bz2) = 5399998 bytes
SHA1 (patch-libs_gccv_text.cc) = 798aa83faf31c0e63c88859ccca9ab40c25e5f6d
SHA1 (patch-libs_gcu_loader-error.h) = 8e223394ac6fb6a17cc23439fc2e3bb2e3bc5440
SHA1 (patch-libs_gcu_spectrumdoc.cc) = 6d4d87c128096006fd384fc058c7942b49df8646
SHA1 (patch-programs_crystal_document.cc) = 192b376922d39796780863720459ee3ef025bfed
SHA1 (gnome-chemistry-utils-0.14.16.tar.bz2) = 3ae7d3dfb1a5c9cd119c84a789e6571f44b62da7
RMD160 (gnome-chemistry-utils-0.14.16.tar.bz2) = c4cedcc6aa1cdeae071b3a9a25d3c235f12eb6e7
SHA512 (gnome-chemistry-utils-0.14.16.tar.bz2) = 7ae652edcee9707c731d77f42899dbebb16c058034d234ea95d62351f8d7c1b87a80ebbf37960721585f8d2af2b5017cb072d655a3c2d01a3a2b52fa1a17b34c
Size (gnome-chemistry-utils-0.14.16.tar.bz2) = 6701094 bytes
SHA1 (patch-configure) = 71e51e882eae3ea5920efdfd7f065f497ab2268d
56 changes: 56 additions & 0 deletions biology/gnome-chemistry-utils/patches/patch-configure
Original file line number Diff line number Diff line change
@@ -0,0 +1,56 @@
$NetBSD: patch-configure,v 1.1 2020/06/29 13:04:48 ryoon Exp $

* Use openbabel 3.

--- configure.orig 2016-11-23 13:06:33.000000000 +0000
+++ configure
@@ -19695,12 +19695,12 @@ if test -n "$openbabel_CFLAGS"; then
pkg_cv_openbabel_CFLAGS="$openbabel_CFLAGS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
- { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"openbabel-2.0 >= 2.3.0\""; } >&5
- ($PKG_CONFIG --exists --print-errors "openbabel-2.0 >= 2.3.0") 2>&5
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"openbabel-3 >= 3.0.0\""; } >&5
+ ($PKG_CONFIG --exists --print-errors "openbabel-3 >= 3.0.0") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
- pkg_cv_openbabel_CFLAGS=`$PKG_CONFIG --cflags "openbabel-2.0 >= 2.3.0" 2>/dev/null`
+ pkg_cv_openbabel_CFLAGS=`$PKG_CONFIG --cflags "openbabel-3 >= 3.0.0" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
@@ -19712,12 +19712,12 @@ if test -n "$openbabel_LIBS"; then
pkg_cv_openbabel_LIBS="$openbabel_LIBS"
elif test -n "$PKG_CONFIG"; then
if test -n "$PKG_CONFIG" && \
- { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"openbabel-2.0 >= 2.3.0\""; } >&5
- ($PKG_CONFIG --exists --print-errors "openbabel-2.0 >= 2.3.0") 2>&5
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"openbabel-3 >= 3.0.0\""; } >&5
+ ($PKG_CONFIG --exists --print-errors "openbabel-3 >= 3.0.0") 2>&5
ac_status=$?
$as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
test $ac_status = 0; }; then
- pkg_cv_openbabel_LIBS=`$PKG_CONFIG --libs "openbabel-2.0 >= 2.3.0" 2>/dev/null`
+ pkg_cv_openbabel_LIBS=`$PKG_CONFIG --libs "openbabel-3 >= 3.0.0" 2>/dev/null`
test "x$?" != "x0" && pkg_failed=yes
else
pkg_failed=yes
@@ -19738,14 +19738,14 @@ else
_pkg_short_errors_supported=no
fi
if test $_pkg_short_errors_supported = yes; then
- openbabel_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "openbabel-2.0 >= 2.3.0" 2>&1`
+ openbabel_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "openbabel-3 >= 3.0.0" 2>&1`
else
- openbabel_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "openbabel-2.0 >= 2.3.0" 2>&1`
+ openbabel_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "openbabel-3 >= 3.0.0" 2>&1`
fi
# Put the nasty error message in config.log where it belongs
echo "$openbabel_PKG_ERRORS" >&5

- as_fn_error $? "Package requirements (openbabel-2.0 >= 2.3.0) were not met:
+ as_fn_error $? "Package requirements (openbabel-3 >= 3.0.0) were not met:

$openbabel_PKG_ERRORS

24 changes: 0 additions & 24 deletions biology/gnome-chemistry-utils/patches/patch-libs_gccv_text.cc

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