CVS commit: pkgsrc/biology/plink

["Thomas Klausner" <wiz%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wiz
Date:           Sat Jan  3 11:45:59 UTC 2026

Modified Files:
        pkgsrc/biology/plink: distinfo
Added Files:
        pkgsrc/biology/plink/patches: patch-genogroup.h patch-homozyg.cpp
            patch-plink.h

Log Message:
plink: fix build on NetBSD-current


To generate a diff of this commit:
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/plink/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/plink/patches/patch-genogroup.h \
    pkgsrc/biology/plink/patches/patch-homozyg.cpp \
    pkgsrc/biology/plink/patches/patch-plink.h

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/plink/distinfo
diff -u pkgsrc/biology/plink/distinfo:1.5 pkgsrc/biology/plink/distinfo:1.6
--- pkgsrc/biology/plink/distinfo:1.5   Tue Oct 26 10:03:42 2021
+++ pkgsrc/biology/plink/distinfo       Sat Jan  3 11:45:59 2026
@@ -1,9 +1,12 @@
-$NetBSD: distinfo,v 1.5 2021/10/26 10:03:42 nia Exp $
+$NetBSD: distinfo,v 1.6 2026/01/03 11:45:59 wiz Exp $
 
 BLAKE2s (plink-1.07-src.zip) = a2eee6b172743e83087cf48b4c4586651a7b1cbe50aad75ddd5fd1133af2aaa6
 SHA512 (plink-1.07-src.zip) = 493f9f32ecd9eb20c5d11dc8ac98c47a9e695059cec3d1ad6f17465b71609577032368c0fee0d3d564e9451c3c07761e444717bec0f4628caefc587fceb1f6c3
 Size (plink-1.07-src.zip) = 2257297 bytes
 SHA1 (patch-Makefile) = cb01e12cea61d1fe41f352759481277284d9c187
 SHA1 (patch-elf.cpp) = ab0bfdda3c84b4f3891f53a95bacaafa5d016bd9
+SHA1 (patch-genogroup.h) = ec44d9837b1071dad809daca381b94cfc2602fb8
+SHA1 (patch-homozyg.cpp) = aa35863c609839306fc0f5dd097294ca1dafc073
 SHA1 (patch-idhelp.cpp) = 3321f343a02bf7cfd253f12f24c8abfb2ef9ec3a
+SHA1 (patch-plink.h) = 909bcd58b19fac713e2bfb6395fe999fdc43e6ff
 SHA1 (patch-sets.cpp) = cd317b6b3775682e60e93f1d35955007d71b90b0

Added files:

Index: pkgsrc/biology/plink/patches/patch-genogroup.h
diff -u /dev/null pkgsrc/biology/plink/patches/patch-genogroup.h:1.1
--- /dev/null   Sat Jan  3 11:45:59 2026
+++ pkgsrc/biology/plink/patches/patch-genogroup.h      Sat Jan  3 11:45:59 2026
@@ -0,0 +1,16 @@
+$NetBSD: patch-genogroup.h,v 1.1 2026/01/03 11:45:59 wiz Exp $
+
+Fix
+error: static assertion failed: comparison object must be invocable as const
+
+--- genogroup.h.orig   2026-01-03 11:44:09.583290253 +0000
++++ genogroup.h
+@@ -42,7 +42,7 @@ namespace std {
+   template<> class less<MultiLocusGenotype*> {
+   public:
+     bool operator()(MultiLocusGenotype const* p1, 
+-                  MultiLocusGenotype const* p2) {
++                  MultiLocusGenotype const* p2) const {
+       if (!p1)
+       return true;
+       if (!p2)
Index: pkgsrc/biology/plink/patches/patch-homozyg.cpp
diff -u /dev/null pkgsrc/biology/plink/patches/patch-homozyg.cpp:1.1
--- /dev/null   Sat Jan  3 11:45:59 2026
+++ pkgsrc/biology/plink/patches/patch-homozyg.cpp      Sat Jan  3 11:45:59 2026
@@ -0,0 +1,25 @@
+$NetBSD: patch-homozyg.cpp,v 1.1 2026/01/03 11:45:59 wiz Exp $
+
+Fix
+error: static assertion failed: comparison object must be invocable as const 
+
+--- homozyg.cpp.orig   2009-10-10 16:00:21.000000000 +0000
++++ homozyg.cpp
+@@ -33,7 +33,7 @@ namespace std
+   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 @@ namespace std
+   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; 
Index: pkgsrc/biology/plink/patches/patch-plink.h
diff -u /dev/null pkgsrc/biology/plink/patches/patch-plink.h:1.1
--- /dev/null   Sat Jan  3 11:45:59 2026
+++ pkgsrc/biology/plink/patches/patch-plink.h  Sat Jan  3 11:45:59 2026
@@ -0,0 +1,16 @@
+$NetBSD: patch-plink.h,v 1.1 2026/01/03 11:45:59 wiz Exp $
+
+Fix
+error: static assertion failed: comparison object must be invocable as const 
+
+--- plink.h.orig       2026-01-03 11:39:25.306972822 +0000
++++ plink.h
+@@ -387,7 +387,7 @@ namespace std
+   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,