openbabel: update to 3.1.1.

common/shlibs

@@ -2787,8 +2787,8 @@ libMonoPosixHelper.so mono-4.0.1.44_2
 libMonoSupportW.so mono-4.0.1.44_2
 libmono-btls-shared.so mono-5.2.0.215_1
 libxcb-xrm.so.0 xcb-util-xrm-1.0_1
-libinchi.so.0 openbabel-2.3.2_1
-libopenbabel.so.5 openbabel-2.4.1_1
+libinchi.so.0 openbabel-3.1.1_1
+libopenbabel.so.7 openbabel-3.1.1_1
 libcourier-unicode.so.7 courier-unicode-2.2.2_1
 libzstd.so.1 libzstd-1.0.0_1
 libudis86.so.0 udis86-1.7.2_4

srcpkgs/openbabel/patches/c0570bfe.patch

@@ -0,0 +1,36 @@
+From c0570bfeb2d7e0a6a6de1f257cf28e7f3cac8739 Mon Sep 17 00:00:00 2001
+From: Sam James <sam@gentoo.org>
+Date: Sun, 12 Jun 2022 11:23:59 +0100
+Subject: [PATCH] CMake: fix time check typo (fixes build failure w/ GCC 12)
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+Without this fixed check, we get a build failure with GCC 12:
+```
+/var/tmp/portage/sci-chemistry/openbabel-3.1.1_p20210225/work/openbabel-08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b/include/openbabel/obutil.h:65:14: error: ‘clock’ was not declared in this scope; did you mean ‘clock_t’?
+   65 |       start= clock();
+      |              ^~~~~
+      |              clock_t
+```
+
+Bug: https://bugs.gentoo.org/851510
+---
+ src/config.h.cmake | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/src/config.h.cmake b/src/config.h.cmake
+index 1c59c67699..26e5dde94f 100644
+--- a/src/config.h.cmake
++++ b/src/config.h.cmake
+@@ -182,8 +182,8 @@
+ #define OB_MODULE_PATH "@OB_MODULE_PATH@"
+ 
+ #ifndef TIME_WITH_SYS_TIME
+-  #ifdef HAVE_SYS_TIME
+-    #ifdef HAVE_TIME
++  #ifdef HAVE_SYS_TIME_H
++    #ifdef HAVE_TIME_H
+       #define TIME_WITH_SYS_TIME 1
+     #else
+       #define TIME_WITH_SYS_TIME 0

srcpkgs/openbabel/patches/unsigned_char.patch

@@ -1,33 +0,0 @@
-https://github.com/openbabel/openbabel/commit/ee11c98a655296550710db1207b294f00e168216
-
---- a/src/formats/pngformat.cpp	2016-09-21 21:55:37.000000000 +0200
-+++ b/src/formats/pngformat.cpp		2018-01-04 08:22:33.377616730 +0100
-@@ -218,7 +218,7 @@
-     _count=0;
-     _hasInputPngFile=true;
-   }
--  const char pngheader[] = {-119,80,78,71,13,10,26,10,0};
-+  const unsigned char pngheader[] = {137,80,78,71,13,10,26,10,0};
-   char readbytes[9];
-   ifs.read(readbytes, 8);
- 
---- a/src/formats/yasaraformat.cpp	2016-09-21 21:55:37.000000000 +0200
-+++ b/src/formats/yasaraformat.cpp	2018-01-04 09:00:45.636003936 +0100
-@@ -472,7 +472,7 @@
- 
-   //  bool hetatom;
-   char buffer[32],/*resname[4],*/atomname[5];
--  char double1[8]={0,0,0,0,0,0,-16,0x3f};
-+  unsigned char double1[8]={0,0,0,0,0,0,0xf,0x3f};
-   //   char *str;
-   int i,j,/*m,q,*/pos;
-   int /*resno,chainNum,link,linktype,*/atoms,element,links/*,chain*/;
-@@ -500,7 +500,7 @@
-   mem_set(buffer,0,8);
-   for (i=0;i<4;i++)
-   { for (j=0;j<4;j++)
--    { if (i==j) ofs.write(double1,8);
-+    { if (i==j) ofs.write((char*)double1,8);
-       else ofs.write(buffer,8); } }
-   storeint32le(buffer,MOB_INFOEND);
-   storeint32le(&buffer[4],MOB_INFOENDSIZE);

srcpkgs/openbabel/template

@@ -1,7 +1,7 @@
 # Template file for 'openbabel'
 pkgname=openbabel
-version=2.4.1
-revision=7
+version=3.1.1
+revision=1
 _ver=${version//./-}
 wrksrc=${pkgname}-${pkgname}-${_ver}
 build_style=cmake
@@ -13,7 +13,7 @@ maintainer="Diogo Leal <diogo@diogoleal.com>"
 license="GPL-2.0-only"
 homepage="http://openbabel.org"
 distfiles="https://github.com/openbabel/openbabel/archive/openbabel-${_ver}.tar.gz"
-checksum=594c7f8a83f3502381469d643f7b185882da1dd4bc2280c16502ef980af2a776
+checksum=c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02
 
 openbabel-devel_package() {
 	depends="${sourcepkg}>=${version}_${revision}"