[med-svn] [Git][med-team/plink][master] 6 commits: Add patch to fix FTBFS with gcc-11 (Closes: #984293)

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / plink


Commits:
d81491db by Nilesh Patra at 2021-10-31T20:58:39+05:30
Add patch to fix FTBFS with gcc-11 (Closes: #984293)

- - - - -
b6f9eeb0 by Nilesh Patra at 2021-10-31T20:58:58+05:30
Bump Standards-Version to 4.6.0 (no changes needed)

- - - - -
bfff5885 by Nilesh Patra at 2021-10-31T20:59:01+05:30
Bump debhelper compatibility level to 13

- - - - -
06e91bb4 by Nilesh Patra at 2021-10-31T20:59:54+05:30
Replace ADTTMP with AUTOPKGTEST_TMP

- - - - -
17b3ecd9 by Nilesh Patra at 2021-10-31T21:01:43+05:30
Add "Rules-Requires-Root: no"

- - - - -
9ec46570 by Nilesh Patra at 2021-10-31T21:02:07+05:30
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/gcc11.patch
- debian/patches/series
- debian/tests/run-sample-analysis


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+plink (1.07+dfsg-4) unstable; urgency=medium
+
+  * Team upload.
+  * Add patch to fix FTBFS with gcc-11 (Closes: #984293)
+  * Bump Standards-Version to 4.6.0 (no changes needed)
+  * Bump debhelper compatibility level to 13
+  * Replace ADTTMP with AUTOPKGTEST_TMP
+  * Add "Rules-Requires-Root: no"
+
+ -- Nilesh Patra <nilesh at debian.org>  Sun, 31 Oct 2021 21:01:46 +0530
+
 plink (1.07+dfsg-3) unstable; urgency=medium
 
   [ Helmut Grohne ]


=====================================
debian/control
=====================================
@@ -6,12 +6,13 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
            Dylan Aïssi <daissi at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                zlib1g-dev
-Standards-Version: 4.4.1
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/med-team/plink
 Vcs-Git: https://salsa.debian.org/med-team/plink.git
 Homepage: http://zzz.bwh.harvard.edu/plink/
+Rules-Requires-Root: no
 
 Package: plink
 Architecture: any


=====================================
debian/patches/gcc11.patch
=====================================
@@ -0,0 +1,46 @@
+Description: Declare operator as const to fix gcc11 FTBFS
+Author: Nilesh Patra <nilesh at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984293
+Last-Update: 2021-10-31
+--- a/plink.h
++++ b/plink.h
+@@ -387,7 +387,7 @@
+   template<>
+     class less<Locus*> {
+     public:
+-    bool operator()(Locus const* p1, Locus const* p2)
++    bool operator()(Locus const* p1, Locus const* p2) const
+       {
+ 
+ 	// Locus comparison based first on distance, 
+--- a/homozyg.cpp
++++ b/homozyg.cpp
+@@ -33,7 +33,7 @@
+   template<>
+   class less<Segment*> {
+   public:
+-  bool operator()(Segment const* s1, Segment const* s2)
++  bool operator()(Segment const* s1, Segment const* s2) const
+   {
+     if      ( s1->start  > s2->start ) return true;
+     else if ( s1->start  < s2->start ) return false;
+@@ -70,7 +70,7 @@
+   template<>
+   class less<Pool*> {
+   public:
+-  bool operator()(Pool const* p1, Pool const* p2)
++  bool operator()(Pool const* p1, Pool const* p2) const
+   {
+ 
+     if      ( p1->segs.size() > p2->segs.size() ) return true; 
+--- a/genogroup.h
++++ b/genogroup.h
+@@ -42,7 +42,7 @@
+   template<> class less<MultiLocusGenotype*> {
+   public:
+     bool operator()(MultiLocusGenotype const* p1, 
+-		    MultiLocusGenotype const* p2) {
++		    MultiLocusGenotype const* p2) const {
+       if (!p1)
+ 	return true;
+       if (!p2)


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 30_endiandetection.patch
 gcc-4.7.patch
 Fix_spelling_error.patch
+gcc11.patch


=====================================
debian/tests/run-sample-analysis
=====================================
@@ -5,11 +5,11 @@
 # Last-Update: 2015-01-24
 
 pkg=plink
-if [ "$ADTTMP" = "" ] ; then
-  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
 fi
-cd $ADTTMP
-cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP
+cd $AUTOPKGTEST_TMP
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
 
 PLINK_TEST='plink1 --noweb --file test'
 
@@ -21,5 +21,5 @@ diff plink.frq expected.plink.frq
 $PLINK_TEST --assoc
 diff plink.assoc expected.plink.assoc
 
-rm -f $ADTTMP/*
+rm -f $AUTOPKGTEST_TMP/*
 



View it on GitLab: https://salsa.debian.org/med-team/plink/-/compare/90d40f887c06a24d3a36ae636ba373f04109e01d...9ec46570f979877494c9c9edf585314c7b69068b

-- 
View it on GitLab: https://salsa.debian.org/med-team/plink/-/compare/90d40f887c06a24d3a36ae636ba373f04109e01d...9ec46570f979877494c9c9edf585314c7b69068b
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