[med-svn] [Git][med-team/adun-app][master] 11 commits: gcc-10.patch: New; fix FTBFS with GCC 10 (#956981).
Yavor Doganov
gitlab at salsa.debian.org
Tue Jun 16 17:53:09 BST 2020
Yavor Doganov pushed to branch master at Debian Med / adun.app
Commits:
b71dac98 by Yavor Doganov at 2020-06-16T17:04:10+03:00
gcc-10.patch: New; fix FTBFS with GCC 10 (#956981).
- - - - -
1c3a50af by Yavor Doganov at 2020-06-16T17:08:24+03:00
(DEB_LDFLAGS_MAINT_APPEND): Drop -Wl,--as-needed; default as of GCC 9.
- - - - -
f4dab56c by Yavor Doganov at 2020-06-16T17:14:13+03:00
Bump compat level to 13.
- - - - -
1c53f976 by Yavor Doganov at 2020-06-16T17:14:56+03:00
(Build-Depends): Remove gnustep-make.
- - - - -
9d4697e8 by Yavor Doganov at 2020-06-16T17:16:13+03:00
(Depends): Remove obsolete substvar $(gnustep:Depends).
- - - - -
09c02f69 by Yavor Doganov at 2020-06-16T17:33:42+03:00
(Rules-Requires-Root): Set to "no".
- - - - -
a2a202d2 by Yavor Doganov at 2020-06-16T17:40:35+03:00
override_dh_link: Replace dh_gnustep with gsdh_gnustep.
- - - - -
15c39ecc by Yavor Doganov at 2020-06-16T17:51:52+03:00
spelling-errors.patch: Fix more spelling errors.
- - - - -
4f5c45f1 by Yavor Doganov at 2020-06-16T19:26:52+03:00
copyright: Fix Lintian warning "tab-in-license-text".
- - - - -
bccb7260 by Yavor Doganov at 2020-06-16T19:38:25+03:00
Convert the app icon to PNG format; fixes an AppStream error.
- - - - -
1693123f by Yavor Doganov at 2020-06-16T19:52:30+03:00
(Standards-Version): Bump to 4.5.0.
- - - - -
9 changed files:
- debian/UL.desktop
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/patches/gcc-10.patch
- debian/patches/series
- debian/patches/spelling-errors.patch
- debian/rules
Changes:
=====================================
debian/UL.desktop
=====================================
@@ -4,6 +4,6 @@ Name=Adun
Comment=Biomolecular Simulator
Keywords=simulator;molecule;
Version=1.0
-Icon=/usr/lib/GNUstep/Applications/UL.app/Resources/icon.tiff
+Icon=/usr/share/GNUstep/UL.app/UL.png
Categories=Education;Science;Biology;
Exec=UL
=====================================
debian/changelog
=====================================
@@ -1,3 +1,27 @@
+adun.app (0.81-14) UNRELEASED; urgency=medium
+
+ * debian/patches/gcc-10.patch: New; fix FTBFS with GCC 10
+ (Closes: #956981).
+ * debian/patches/spelling-errors.patch: Fix more spelling errors.
+ * debian/patches/series: Update.
+ * debian/rules (DEB_LDFLAGS_MAINT_APPEND): Drop -Wl,--as-needed; default
+ as of GCC 9.
+ (override_dh_link): Replace dh_gnustep with gsdh_gnustep to avoid
+ lintian error "missing-build-dependency-for-dh_-command".
+ (override_dh_auto_install): Convert the app icon to PNG format and
+ install it in /usr/share/GNUstep/UL.app; fixes an AppStream error.
+ * debian/control (Build-Depends): Switch to debhelper-compat; bump
+ compat level to 13. Remove gnustep-make; required version is in
+ buster. Add imagemagick for the icon conversion.
+ (Depends): Remove obsolete substvar $(gnustep:Depends).
+ (Rules-Requires-Root): Set to "no".
+ (Standards-Version): Bump to 4.5.0; no changes needed.
+ * debian/compat: Delete.
+ * debian/UL.desktop: Use the PNG icon.
+ * debian/copyright: Fix Lintian warning "tab-in-license-text".
+
+ -- Yavor Doganov <yavor at gnu.org> Tue, 16 Jun 2020 17:02:59 +0300
+
adun.app (0.81-13) unstable; urgency=medium
* debian/patches/ftbfs-powerpcspe.patch: New; fixes FTBFS on powerpcspe.
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -4,13 +4,14 @@ Uploaders: Andreas Tille <tille at debian.org>,
Yavor Doganov <yavor at gnu.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11),
- gnustep-make (>= 2.7.0-4),
+Build-Depends: debhelper-compat (= 13),
+ imagemagick,
libgnustep-gui-dev,
libsteptalk-dev,
libsqlclient-dev,
libgsl-dev
-Standards-Version: 4.3.0
+Rules-Requires-Root: no
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/adun-app
Vcs-Git: https://salsa.debian.org/med-team/adun-app.git
Homepage: http://wiki.gnustep.org/index.php/Adun
@@ -20,8 +21,7 @@ Architecture: any
Depends: adun-core (= ${binary:Version}),
${shlibs:Depends},
steptalk,
- ${misc:Depends},
- ${gnustep:Depends}
+ ${misc:Depends}
Recommends: gnuplot
Description: Molecular Simulator for GNUstep (GUI)
Adun is a biomolecular simulator that also includes data management and
@@ -34,8 +34,7 @@ Description: Molecular Simulator for GNUstep (GUI)
Package: adun-core
Architecture: any
Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${gnustep:Depends}
+ ${misc:Depends}
Description: Molecular Simulator
Adun is a biomolecular simulator that also includes data management and
analysis capabilities. It was developed at the Computational Biophysics
=====================================
debian/copyright
=====================================
@@ -28,9 +28,9 @@ License: PublicDomain
and the files should be regarded as Public Domain. The according
files in the tango-icon-theme package are:
.
- /usr/share/icons/Tango/32x32/actions/go-next.png byte identical to apply.png
- /usr/share/icons/Tango/32x32/actions/view-refresh.png byte identical to reload.png
- /usr/share/icons/Tango/32x32/actions/document-save.png byte identical to document-save.png
+ /usr/share/icons/Tango/32x32/actions/go-next.png byte identical to apply.png
+ /usr/share/icons/Tango/32x32/actions/view-refresh.png byte identical to reload.png
+ /usr/share/icons/Tango/32x32/actions/document-save.png byte identical to document-save.png
Files: ExternalPackages/StepTalk/Languages/StepTalkSmalltalk/*
ExternalPackages/StepTalk/Frameworks/StepTalk/*
=====================================
debian/patches/gcc-10.patch
=====================================
@@ -0,0 +1,61 @@
+Description: Fix FTBFS with GCC 10.
+Author: Yavor Doganov <yavor at gnu.org>
+Bug-Debian: https://bugs.debian.org/956981
+Forwarded: no
+Last-Update: 2020-06-16
+---
+
+
+--- adun.app.orig/Kernel/AdunKernel/Headers/AdunKernel/AdunDefinitions.h
++++ adun.app/Kernel/AdunKernel/Headers/AdunKernel/AdunDefinitions.h
+@@ -140,7 +140,7 @@
+ \ingroup frameConstants
+ Bitwise OR of all supported floating point exceptions
+ */
+-int AdFloatingPointExceptionMask;
++extern int AdFloatingPointExceptionMask;
+
+ /**
+ \ingroup frameConstants
+--- adun.app.orig/Kernel/main.m
++++ adun.app/Kernel/main.m
+@@ -137,7 +137,7 @@
+ GSPrintf(stdout, @"\tEpsilon: %E.\n", DBL_EPSILON);
+ GSPrintf(stdout, @"\tEpsilon is the smallest number such that '1.0 + epsilon != 1.0' is true.\n\n");
+
+- AdFloatingPointExceptionMask = 0;
++ int AdFloatingPointExceptionMask = 0;
+
+ #ifdef FE_DIVBYZERO
+ AdFloatingPointExceptionMask = AdFloatingPointExceptionMask | FE_DIVBYZERO;
+--- adun.app.orig/Kernel/AdunKernel/Headers/AdunKernel/AdunSmoothedGBTerm.h
++++ adun.app/Kernel/AdunKernel/Headers/AdunKernel/AdunSmoothedGBTerm.h
+@@ -232,7 +232,7 @@
+ @end
+
+ //Contains optimised atomic radii from Nina et al.
+-NSDictionary* generalizedBornRadiiDict;
++extern NSDictionary* generalizedBornRadiiDict;
+
+ #endif
+
+--- adun.app.orig/Kernel/AdunKernel/Framework/AdunSmoothedGBTerm.m
++++ adun.app/Kernel/AdunKernel/Framework/AdunSmoothedGBTerm.m
+@@ -25,6 +25,7 @@
+ #include "AdunKernel/AdunPureNonbondedTerm.h"
+
+ static NSDictionary* coefficients;
++NSDictionary* generalizedBornRadiiDict;
+
+ @implementation AdSmoothedGBTerm
+
+--- adun.app.orig/Kernel/AdunKernel/Framework/AdunConfigurationGenerator.m
++++ adun.app/Kernel/AdunKernel/Framework/AdunConfigurationGenerator.m
+@@ -5,6 +5,7 @@
+ - (void) checkFloatingPointErrors
+ {
+ int raised;
++ int AdFloatingPointExceptionMask = 0;
+ NSMutableDictionary* errorInfo;
+ NSError* error;
+
=====================================
debian/patches/series
=====================================
@@ -9,3 +9,4 @@ invalid-observer.patch
spelling-errors.patch
check-return-value.patch
ftbfs-powerpcspe.patch
+gcc-10.patch
=====================================
debian/patches/spelling-errors.patch
=====================================
@@ -1,7 +1,7 @@
Description: Fix some spelling errors.
Author: Yavor Doganov <yavor at gnu.org>
Forwarded: no
-Last-Update: 2018-01-08
+Last-Update: 2020-06-16
---
--- adun.app.orig/Kernel/AdunKernel/CoreAdditions/AdunFileSystemSimulationStorage.m
@@ -68,6 +68,15 @@ Last-Update: 2018-01-08
[NSException raise: NSInvalidArgumentException
--- adun.app.orig/Kernel/AdunKernel/CoreAdditions/AdunSimulationData.m
+++ adun.app/Kernel/AdunKernel/CoreAdditions/AdunSimulationData.m
+@@ -156,7 +156,7 @@
+ //check the data store is accesible
+ if(![dataStorage isAccessible])
+ {
+- NSWarnLog(@"Simulation data is not accesible raising exception");
++ NSWarnLog(@"Simulation data is not accessible raising exception");
+ error = [dataStorage accessError];
+ exception = [NSException exceptionWithName: NSInternalInconsistencyException
+ reason: @"Unable to access data storage"
@@ -443,7 +443,7 @@
end = NSMaxRange(range);
if(end > (int)[frames numberOfRows])
@@ -115,6 +124,15 @@ Last-Update: 2018-01-08
if(testTemplate == nil)
{
+@@ -443,7 +443,7 @@
+ {
+ *error = AdCreateError(AdunCoreErrorDomain,
+ AdCoreInvalidTemplateError,
+- @"Invalid termplate.",
++ @"Invalid template.",
+ [NSString stringWithFormat: @"Invalid object used for class name - %@", className],
+ @"All class names must be strings.");
+ }
@@ -454,7 +454,7 @@
@@ -135,6 +153,15 @@ Last-Update: 2018-01-08
else
--- adun.app.orig/Kernel/AdunKernel/CoreAdditions/AdunTrajectory.m
+++ adun.app/Kernel/AdunKernel/CoreAdditions/AdunTrajectory.m
+@@ -100,7 +100,7 @@
+ //check the data store is accesible
+ if(![dataStorage isAccessible])
+ {
+- NSWarnLog(@"Simulation data is not accesible raising exception");
++ NSWarnLog(@"Simulation data is not accessible raising exception");
+ error = [dataStorage accessError];
+ exception = [NSException exceptionWithName: NSInternalInconsistencyException
+ reason: @"Unable to access data storage"
@@ -494,7 +494,7 @@
end = NSMaxRange(range);
if(end > (int)[frames numberOfRows])
=====================================
debian/rules
=====================================
@@ -7,7 +7,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
include /usr/share/GNUstep/debian/config.mk
d_app := $(CURDIR)/debian/tmp
-export DEB_LDFLAGS_MAINT_APPEND := -Wl,--no-undefined -Wl,--as-needed \
+export DEB_LDFLAGS_MAINT_APPEND := -Wl,--no-undefined \
-Wl,-rpath,/usr/lib/adun.app
export DEB_CFLAGS_MAINT_APPEND := -fgnu89-inline
# As of GCC 7, the build log gets flooded with warnings for unportable
@@ -54,6 +54,8 @@ override_dh_auto_install:
mkdir -p $(d_app)/usr/share/GNUstep
mv $(d_app)$(GNUSTEP_SYSTEM_APPS)/UL.app/Resources \
$(d_app)/usr/share/GNUstep/UL.app
+ convert UL/Resources/icon.tiff -resize 64x64 \
+ $(d_app)/usr/share/GNUstep/UL.app/UL.png
# Delete empty directories (fixes a lintian warning).
rm -r $(d_app)/usr/include/GNUstep/Framework \
$(d_app)/usr/lib/GNUstep/Tools
@@ -63,7 +65,7 @@ override_dh_auto_install:
chmod -x $(d_app)/usr/lib/GNUstep/Frameworks/ULFramework.framework/Versions/0/Resources/ForceFields/Enzymix/*.ffml
override_dh_link:
- dh_gnustep
+ gsdh_gnustep
dh_link usr/share/GNUstep/UL.app \
$(GNUSTEP_SYSTEM_APPS)/UL.app/Resources
View it on GitLab: https://salsa.debian.org/med-team/adun-app/-/compare/4194661d67b2b1c187eb6f1e4db0165933148efb...1693123ff729eea29ccc14b8d850554b196a9e13
--
View it on GitLab: https://salsa.debian.org/med-team/adun-app/-/compare/4194661d67b2b1c187eb6f1e4db0165933148efb...1693123ff729eea29ccc14b8d850554b196a9e13
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