[med-svn] [Git][med-team/snap][master] 13 commits: Depending on debhelper-compat
Pierre Gruet
gitlab at salsa.debian.org
Thu Aug 6 14:09:53 BST 2020
Pierre Gruet pushed to branch master at Debian Med / snap
Commits:
b0389ce0 by Pierre Gruet at 2020-08-06T10:55:09+02:00
Depending on debhelper-compat
- - - - -
843a1179 by Pierre Gruet at 2020-08-06T10:56:07+02:00
Bumping Standards version to 4.5.0 (Rules-Requires-Root field added)
- - - - -
a6744cd5 by Pierre Gruet at 2020-08-06T10:59:55+02:00
Avoiding multiple definitions error due to gcc-10
- - - - -
0fba0523 by Pierre Gruet at 2020-08-06T11:00:28+02:00
Adding salsa-ci.yml file
- - - - -
c0c80cc5 by Pierre Gruet at 2020-08-06T11:08:08+02:00
Renaming d/NEWS.Debian to d/NEWS
- - - - -
4d7b1ad5 by Pierre Gruet at 2020-08-06T11:22:02+02:00
Changing deprecated ADTTMP variable name in debian/tests/run-unit-test
- - - - -
4f02b27f by Pierre Gruet at 2020-08-06T14:52:46+02:00
Adding Bug- and Repository-related fields in d/upstream/metadata
- - - - -
70aa260d by Pierre Gruet at 2020-08-06T14:53:07+02:00
Updating Forwarded field in headers of patches
Forwarded gcc-10-multiple-definitions.patch
Using Forwarded instead of Forwarded-Upstream in others patches
- - - - -
f836bbf7 by Pierre Gruet at 2020-08-06T14:54:51+02:00
Adding Lintian override for non-advertised repackaging
- - - - -
028ee41c by Pierre Gruet at 2020-08-06T15:01:19+02:00
Adding a Lintian override for a README file in the binary package
- - - - -
41559efa by Pierre Gruet at 2020-08-06T15:02:32+02:00
Updating changelog
- - - - -
4b79ff09 by Pierre Gruet at 2020-08-06T15:03:52+02:00
Trim trailing whitespace.
Changes-By: lintian-brush
Fixes: lintian: trailing-whitespace
See-also: https://lintian.debian.org/tags/trailing-whitespace.html
- - - - -
20852e6d by Pierre Gruet at 2020-08-06T15:04:10+02:00
Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
Changes-By: lintian-brush
- - - - -
20 changed files:
- debian/NEWS.Debian → debian/NEWS
- debian/changelog
- − debian/compat
- debian/control
- debian/patches/build-with-gcc-6.patch
- debian/patches/fix_missing_braces_in_if_statements.patch
- + debian/patches/gcc-10-multiple_definitions.patch
- debian/patches/gcc-8.patch
- debian/patches/hardening.patch
- debian/patches/replace_itoa_with_broken_indentation.patch
- debian/patches/series
- debian/patches/spelling.patch
- debian/patches/unused-but-set-variable.patch
- debian/patches/use-CC.patch
- debian/rules
- + debian/salsa-ci.yml
- + debian/snap.lintian-overrides
- + debian/source/lintian-overrides
- debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/NEWS.Debian → debian/NEWS
=====================================
=====================================
debian/changelog
=====================================
@@ -1,9 +1,22 @@
snap (2013-11-29-10) UNRELEASED; urgency=medium
- * Team upload.
+ [ Dylan Aïssi ]
* d/control: Update homepage (Closes: #927011).
- -- Dylan Aïssi <daissi at debian.org> Sun, 14 Apr 2019 09:09:17 +0200
+ [ Pierre Gruet ]
+ * Avoiding multiple definitions error due to gcc-10 (Closes: #957820)
+ * Depending on debhelper-compat
+ * Bumping Standards version to 4.5.0 (Rules-Requires-Root field added)
+ * Adding salsa-ci.yml file
+ * Renaming d/NEWS.Debian to d/NEWS
+ * Changing deprecated ADTTMP variable name in debian/tests/run-unit-test
+ * Adding Bug- and Repository-related fields in d/upstream/metadata
+ * Adding and documenting Lintian overrides
+ * Trim trailing whitespace.
+ * Remove obsolete field Name from debian/upstream/metadata (already present in
+ machine-readable debian/copyright).
+
+ -- Pierre Gruet <pgtdebian at free.fr> Thu, 06 Aug 2020 15:01:26 +0200
snap (2013-11-29-9) unstable; urgency=medium
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -1,15 +1,17 @@
Source: snap
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>
+ Andreas Tille <tille at debian.org>,
+ Pierre Gruet <pgtdebian at free.fr>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 13),
help2man
-Standards-Version: 4.1.4
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/snap
Vcs-Git: https://salsa.debian.org/med-team/snap.git
Homepage: https://github.com/KorfLab/SNAP
+Rules-Requires-Root: no
Package: snap
Architecture: any
=====================================
debian/patches/build-with-gcc-6.patch
=====================================
@@ -1,7 +1,7 @@
Author: Sascha Steinbiss <satta at tetrinetsucht.de>
Last-Update: Sat, 30 Apr 2016 17:48:14 +0100
Bug-Debian: https://bugs.debian.org/812011
-Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3
+Forwarded: https://github.com/KorfLab/SNAP/issues/3
Description: changing the (likely buggy) behaviour of the zoeHSPCmpQuery and
zoeHSPCmpSbjct functions to do the correct comparisons. This fixes:
error: self-comparison always evaluates to false [-Werror=tautological-compare]
=====================================
debian/patches/fix_missing_braces_in_if_statements.patch
=====================================
@@ -1,7 +1,7 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Wed, 24 Aug 2016 10:43:36 +0200
Bug-Debian: https://bugs.debian.org/835283
-Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3
+Forwarded: https://github.com/KorfLab/SNAP/issues/3
Description: add missing braces
--- a/exonpairs.c
=====================================
debian/patches/gcc-10-multiple_definitions.patch
=====================================
@@ -0,0 +1,21 @@
+Description: Avoiding multiple definitions error due to gcc-10
+Author: Pierre Gruet <pgtdebian at free.fr>
+Bug-Debian: https://bugs.debian.org/957820
+Forwarded: https://github.com/KorfLab/SNAP/issues/7
+Last-Update: 2020-08-06
+
+--- a/Zoe/zoeTools.h
++++ b/Zoe/zoeTools.h
+@@ -40,9 +40,9 @@
+ #include <stdlib.h>
+ #include <string.h>
+
+-const char * zoeFunction;
+-const char * zoeConstructor;
+-const char * zoeMethod;
++extern const char * zoeFunction;
++extern const char * zoeConstructor;
++extern const char * zoeMethod;
+
+ void zoeLibInfo (void);
+ void zoeSetProgramName (const char*);
=====================================
debian/patches/gcc-8.patch
=====================================
@@ -1,6 +1,6 @@
Description: Enlarge too short target string for sprintf
Bug-Debian: https://bugs.debian.org/897864
-Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3
+Forwarded: https://github.com/KorfLab/SNAP/issues/3
Author: Andreas Tille <tille at debian.org>
Last-Update: Mon, 07 May 2018 23:38:54 +0200
=====================================
debian/patches/hardening.patch
=====================================
@@ -1,6 +1,6 @@
Author: Andreas Tille <tille at debian.org>
LastChanged: Fri, 25 Oct 2013 16:39:26 +0200
-Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3
+Forwarded: https://github.com/KorfLab/SNAP/issues/3
Description: Propagate Hardening options
--- a/Makefile
=====================================
debian/patches/replace_itoa_with_broken_indentation.patch
=====================================
@@ -1,6 +1,6 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Wed, 24 Aug 2016 10:43:36 +0200
-Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3
+Forwarded: https://github.com/KorfLab/SNAP/issues/3
Description: itoa implementation had broken indentation - use
sprintf instead
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ replace_itoa_with_broken_indentation.patch
fix_missing_braces_in_if_statements.patch
gcc-8.patch
spelling.patch
+gcc-10-multiple_definitions.patch
=====================================
debian/patches/spelling.patch
=====================================
@@ -1,6 +1,6 @@
Description: Fix spelling
Author: Andreas Tille <tille at debian.org>
-Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3
+Forwarded: https://github.com/KorfLab/SNAP/issues/3
Last-Update: Mon, 07 May 2018 23:38:54 +0200
--- a/Zoe/zoePhasePref.c
=====================================
debian/patches/unused-but-set-variable.patch
=====================================
@@ -1,6 +1,6 @@
Author: Andreas Tille <tille at debian.org>
Date: Tue, 07 Oct 2014 13:31:52 +0200
-Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3
+Forwarded: https://github.com/KorfLab/SNAP/issues/3
Description: When enabling hardening flags by
using debhelper 9 unsused variables should not be assigned.
This patch comments those variables.
=====================================
debian/patches/use-CC.patch
=====================================
@@ -2,7 +2,7 @@ Author: Sascha Steinbiss <satta at tetrinetsucht.de>,
Helmut Grohne <helmut at subdivi.de>
Last-Update: Fri, 8 Dec 2017 22:32:22 +0100
Bug-Debian: https://bugs.debian.org/883891
-Forwarded-Upstream: https://github.com/KorfLab/SNAP/issues/3
+Forwarded: https://github.com/KorfLab/SNAP/issues/3
Description: Do not force gcc explicitly but use $(CC) instead
--- a/Zoe/Makefile
=====================================
debian/rules
=====================================
@@ -7,7 +7,7 @@
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
- dh $@
+ dh $@
override_dh_auto_clean:
touch depend Zoe/depend
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/snap.lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# This README file is related to the purpose of the directory it belongs to.
+package-contains-documentation-outside-usr-share-doc usr/share/snap/HMM/README
=====================================
debian/source/lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# Repackaging is not mandatory, yet this could be considered if there is a new
+# upstream version.
+repackaged-source-not-advertised
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,11 +1,11 @@
#!/bin/sh -e
pkg=snap
-if [ "$ADTTMP" = "" ] ; then
- ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
- trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
-cd $ADTTMP
+cd $AUTOPKGTEST_TMP
snap-hmm /usr/share/snap/HMM/thale /usr/share/doc/${pkg}/examples/DNA/thale.dna.gz
snap-hmm /usr/share/snap/HMM/worm /usr/share/doc/${pkg}/examples/DNA/worm.dna.gz
=====================================
debian/upstream/metadata
=====================================
@@ -1,4 +1,3 @@
-Name: SNAP
Reference:
Author: Ian Korf
Title: Gene finding in novel Genomes
@@ -17,3 +16,7 @@ Registry:
Entry: SNAP
- Name: SciCrunch
Entry: NA
+Bug-Database: https://github.com/KorfLab/SNAP/issues
+Bug-Submit: https://github.com/KorfLab/SNAP/issues/new
+Repository: https://github.com/KorfLab/SNAP.git
+Repository-Browse: https://github.com/KorfLab/SNAP
View it on GitLab: https://salsa.debian.org/med-team/snap/-/compare/244e8a0f43b7b4bf33e1348da1b39fe06bec0c07...20852e6d914be31dbed8c120aacdae3fc5cd72b7
--
View it on GitLab: https://salsa.debian.org/med-team/snap/-/compare/244e8a0f43b7b4bf33e1348da1b39fe06bec0c07...20852e6d914be31dbed8c120aacdae3fc5cd72b7
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