[med-svn] [Git][med-team/autodock-vina][master] 10 commits: unenforce-standard-c++.patch: new: do not enforce std=c++11.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Jan 3 18:01:14 GMT 2026
Étienne Mollier pushed to branch master at Debian Med / autodock-vina
Commits:
d979e5c4 by Étienne Mollier at 2026-01-03T18:35:37+01:00
unenforce-standard-c++.patch: new: do not enforce std=c++11.
- - - - -
cc116b97 by Étienne Mollier at 2026-01-03T18:36:12+01:00
d/rules: fix compilation flags setting.
- - - - -
4a366bce by Étienne Mollier at 2026-01-03T18:45:44+01:00
d/rules: pass -std=c++14 to compiler flags.
Closes: #1110595
- - - - -
3e265271 by Étienne Mollier at 2026-01-03T18:53:32+01:00
d/control: drop redundant Priority: optional.
- - - - -
8178eaf6 by Étienne Mollier at 2026-01-03T18:53:57+01:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
ab9ec91d by Étienne Mollier at 2026-01-03T18:54:29+01:00
d/control: declare compliance to standards version 4.7.3.
- - - - -
855c739e by Étienne Mollier at 2026-01-03T18:56:48+01:00
fortify.patch: update: ensure LDFLAGS are not erased.
- - - - -
021ade60 by Étienne Mollier at 2026-01-03T18:57:08+01:00
d/watch: convert to v5 Github template.
- - - - -
b5c9e6eb by Étienne Mollier at 2026-01-03T18:57:40+01:00
d/{clean,rules}: move files cleanup to d/clean.
- - - - -
406309d6 by Étienne Mollier at 2026-01-03T19:00:29+01:00
d/changelog: ready for upload to unstable.
- - - - -
8 changed files:
- debian/changelog
- + debian/clean
- debian/control
- debian/patches/fortify.patch
- debian/patches/series
- + debian/patches/unenforce-standard-c++.patch
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+autodock-vina (1.2.7-2) unstable; urgency=medium
+
+ * unenforce-standard-c++.patch: new: do not enforce std=c++11.
+ * fortify.patch: update: ensure LDFLAGS are not erased.
+ * d/rules: fix compilation flags setting.
+ * d/rules: pass -std=c++14 to compiler flags. (Closes: #1110595)
+ * d/control: drop redundant Priority: optional.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/control: declare compliance to standards version 4.7.3.
+ * d/watch: convert to v5 Github template.
+ * d/{clean,rules}: move files cleanup to d/clean.
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 03 Jan 2026 18:58:21 +0100
+
autodock-vina (1.2.7-1) unstable; urgency=medium
* New upstream version 1.2.7
=====================================
debian/clean
=====================================
@@ -0,0 +1,2 @@
+build/linux/release/*.o
+build/linux/release/vina*
=====================================
debian/control
=====================================
@@ -5,15 +5,13 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>,
Étienne Mollier <emollier at debian.org>
Section: science
-Priority: optional
Build-Depends: debhelper-compat (= 13),
libboost-all-dev,
debhelper
-Standards-Version: 4.7.2
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/autodock-vina
Vcs-Git: https://salsa.debian.org/med-team/autodock-vina.git
Homepage: https://vina.scripps.edu
-Rules-Requires-Root: no
Package: autodock-vina
Architecture: any
=====================================
debian/patches/fortify.patch
=====================================
@@ -1,4 +1,5 @@
Description: propagate _FORTIFY_SOURCE macro definition.
+ The patch also includes a later change to avoid erasing LDFLAGS.
Author: Étienne Mollier <emollier at debian.org>
Forwarded: not-needed
Last-Update: 2025-03-02
@@ -6,12 +7,15 @@ Last-Update: 2025-03-02
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- autodock-vina.orig/build/makefile_common
+++ autodock-vina/build/makefile_common
-@@ -12,7 +12,7 @@
+@@ -12,9 +12,9 @@
# -pedantic fails on Mac with Boost 1.41 (syntax problems in their headers)
#CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
-CC = ${GPP} ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
+CC = ${GPP} $(CPPFLAGS) ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
- LDFLAGS = -L$(BASE)/lib -L.
+-LDFLAGS = -L$(BASE)/lib -L.
++LDFLAGS += -L$(BASE)/lib -L.
+ # test if boost_thread-mt exists, this is
+ # necessary as some versions of boost only
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ remove_static.patch
do_not_link_against_unneeded_libs.patch
annoying_static_removed_was_in_for_a_reason_questionmark.patch
fortify.patch
+unenforce-standard-c++.patch
=====================================
debian/patches/unenforce-standard-c++.patch
=====================================
@@ -0,0 +1,33 @@
+Description: unenforce the standard C++ version.
+ This change allows setting the standard C++ version level from the
+ d/rules file. Therefore, this is not really intended for use upstream.
+ Note that not enforcing the standard in this package will result in
+ sticking to C++ 2003, which guaranteed to fail to build from source
+ with newer Boost library versions at this point in time (2026).
+Author: Étienne Mollier <emollier at debian.org>
+Bug: https://github.com/ccsb-scripps/AutoDock-Vina/issues/406
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1110595
+Last-Update: 2026-01-03
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- autodock-vina.orig/build/linux/release/Makefile
++++ autodock-vina/build/linux/release/Makefile
+@@ -3,7 +3,7 @@
+ BOOST_INCLUDE = $(BASE)/include
+ C_PLATFORM=-pthread
+ GPP=g++
+-C_OPTIONS= -O3 -DNDEBUG -std=c++11
++C_OPTIONS= -O3 -DNDEBUG
+ BOOST_LIB_VERSION=
+
+ include ../../makefile_common
+--- autodock-vina.orig/build/python/setup.py
++++ autodock-vina/build/python/setup.py
+@@ -277,7 +277,6 @@
+
+ # Source: https://stackoverflow.com/questions/9723793/undefined-reference-to-boostsystemsystem-category-when-compiling
+ vina_compiler_options = [
+- "-std=c++11",
+ "-Wno-long-long",
+ "-pedantic",
+ '-DBOOST_ERROR_CODE_HEADER_ONLY'
=====================================
debian/rules
=====================================
@@ -3,18 +3,13 @@
# Authors: Yask Gupta <yask.gupta87 at gmail.com>, Andreas Tille <tille at debian.org>
# License: GPL
-export DEB_BUILD_MAINT_OPTIONS = hardening=+all
-
-CFLAGS+=-fpermissive -DBOOST_FILESYSTEM_VERSION=3 --lto
-CXXFLAGS+=-fpermissive -DBOOST_FILESYSTEM_VERSION=3 --lto
-LDFLAGS+=--lto -g
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all optimize=+lto
+export DEB_CXXFLAGS_MAINT_APPEND = -fpermissive -DBOOST_FILESYSTEM_VERSION=3 -std=c++14
+# Workaround erroneous use of CFLAGS for CXX compilers.
+export DEB_CFLAGS_MAINT_APPEND = $(DEB_CXXFLAGS_MAINT_APPEND)
%:
dh $@
override_dh_auto_build:
- $(MAKE) BASE=/usr -C build/linux/release CLFAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" LDFLAGS="$(LDFLAGS)"
-
-override_dh_clean:
- dh_clean
- rm -f build/linux/release/*.o build/linux/release/vina*
+ $(MAKE) BASE=/usr -C build/linux/release
=====================================
debian/watch
=====================================
@@ -1,4 +1,5 @@
-version=4
+Version: 5
-opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/ccsb-scripps/AutoDock-Vina/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
+Template: Github
+Owner: ccsb-scripps
+Project: AutoDock-Vina
View it on GitLab: https://salsa.debian.org/med-team/autodock-vina/-/compare/029988d69cdd9b381aa86696f017c25cc0a0698f...406309d6ab39515104572637155c171ee24f8545
--
View it on GitLab: https://salsa.debian.org/med-team/autodock-vina/-/compare/029988d69cdd9b381aa86696f017c25cc0a0698f...406309d6ab39515104572637155c171ee24f8545
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