gentoo auto-resync : 11:09:2023 - 10:37:57

4 files changed, 56 insertions, 0 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index a2f0a1880c0a..79ec0479774d 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/cluster/Manifest b/sci-chemistry/cluster/Manifest
index f09a5b1b01db..5924d81ba765 100644
--- a/sci-chemistry/cluster/Manifest
+++ b/sci-chemistry/cluster/Manifest
@@ -1,5 +1,7 @@
+AUX 1.3.081231-drop-registers.patch 719 BLAKE2B f2163e354ec7c4406b9d246af0706834e40d4c027ff721b32e7ceb37001a80638b6f913ebe0cb17d0bfd7f954949d66bf57172fcc5dcc06d0347d4d6787b8f94 SHA512 4a74a9aeb8c5bd2c1138210894809a800b385807decc23dd1b7e5264a2e959dbaaab79b1e013dc7e2e36a863347736ddf92e9d4fd565fbc27391aa43107759f9
 AUX 1.3.081231-includes.patch 245 BLAKE2B 6bbe0621d49bc7af8091a5594ebcd52d29d99cc00567eab523186b24c387f5c9af241c7ee53d235c1b56b6a6ea6759d3aeea814e87dd591d585413243be735e2 SHA512 a1261ed2b3f867fe464e1501fa9bc0b1f2909eaf736475e717da95ddbc34ae2938346c0044f7b6d84264a0d85ea5f7b1214caf1c2b12c544876912ff10e2302a
 AUX 1.3.081231-ldflags.patch 842 BLAKE2B 67085c3dd9ca5e97b28481fbf06a0f9b6294bd519eb3639c54b10cd9b11a4c44a48dbfa907cdf9ff8ec68761164e82d415c44ad0c3a551842416759c76d4b7a9 SHA512 9937f88e65ae94595ba2889e7f57d3b295e025d2ebd83817300a7f74a674fab84358e3b7fc9619ba473c586c51bd106e303b096cdb267d8fda05670f7815e9e4
 DIST cluster.1.3.081231.src.tgz 8860 BLAKE2B 4bfc6fe9efa3dbde106ad12df7b23990a748fee5446f16fe4e3cf9232697313bd513366a2283ac732cf0c7306ac65af578155328d0b04e4b5b99536553c9b903 SHA512 af5851ef467458d45ee5f2309c6344ae16145ac371a1b9d0a3d8b5769a18b98877cf7cb65b85f71108d927b0e6c363e06b85a67e7cb2e5e0b41af375cb2db7ac
 EBUILD cluster-1.3.081231-r1.ebuild 656 BLAKE2B a1701e0cae7f246835c39eb48568cced6aac041138994f2362e5759d6bda5c7fbe66bda4f42e1697c5fd7345786de1dc5b94805351f07d9eb42213945fa5737e SHA512 dddfe8c1b7d333f1f472a2788e2a1c82464721a5e3dee622a08012c5c03dc30cbbffe396eef68137253a010030a194ff0454a63b5441bc4a658c653f222bdd7e
+EBUILD cluster-1.3.081231-r2.ebuild 699 BLAKE2B 1678ebcbfed0dbe719bcdbb560c9e370eb30f6828ee9fb5dbb92895151ccf1dfda0ef83ef114889f7467da7a8c571a9c147c2dd2423ae7ee95c8c852c818add6 SHA512 1170ed4dbfdfa23616ee3848046f9224192e09d65e7b899fc73f206df47ae65b2836c221d03a674b931d4c5466f1d7872e76b2e0e81895003df0f4c7e84cf1b7
 MISC metadata.xml 678 BLAKE2B fc060fb969b660db3e27ff534b6c3a8b41b4d8e1f537d99d5858691587541224596210a278945ace78694030934344966bcb580e4e89730c122ad82143269021 SHA512 94cb1c446ec846342fd70008802adde5fad93e183b2aa3b6c10976f9e3bd95d2c34f876d58ea694f143530f45a08fddc918d8d9026929230daceb4e458df1fa3
diff --git a/sci-chemistry/cluster/cluster-1.3.081231-r2.ebuild b/sci-chemistry/cluster/cluster-1.3.081231-r2.ebuild
new file mode 100644
index 000000000000..63f38eed67d2
--- /dev/null
+++ b/sci-chemistry/cluster/cluster-1.3.081231-r2.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Build lists of collections of interacting items"
+HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
+SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz"
+S="${WORKDIR}"/${PN}1.3src
+
+LICENSE="richardson"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+PATCHES=(
+	"${FILESDIR}"/${PV}-ldflags.patch
+	"${FILESDIR}"/${PV}-includes.patch
+	"${FILESDIR}"/${PV}-drop-registers.patch
+)
+
+src_configure() {
+	tc-export CXX
+	default
+}
+
+src_install() {
+	newbin ${PN} molprobity-${PN}
+	dodoc README.cluster
+}
diff --git a/sci-chemistry/cluster/files/1.3.081231-drop-registers.patch b/sci-chemistry/cluster/files/1.3.081231-drop-registers.patch
new file mode 100644
index 000000000000..c00922591faa
--- /dev/null
+++ b/sci-chemistry/cluster/files/1.3.081231-drop-registers.patch
@@ -0,0 +1,23 @@
+Bug: https://bugs.gentoo.org/898132
+--- a/utility.cpp
++++ b/utility.cpp
+@@ -107,8 +107,8 @@ int compArgStr(const char *str, const char *arg, int min) {
+ }
+ 
+ int parseInteger(const char *str, int start, int len) {
+-	register int value = 0;
+-	register char ch;
++	int value = 0;
++	char ch;
+ 	int neg = 0, inside = 0;
+ 
+ 	if (!str || start < 0) { return 0; }
+@@ -136,7 +136,7 @@ int parseInteger(const char *str, int start, int len) {
+ double parseReal(const char *str, int start, int len) {
+    double value = 0.0, scale = 1.0, expscale = 1.0, expfact = 10.0;
+    int expval = 0;
+-   register char ch;
++   char ch;
+    int inside = 0, infract = 0, inexp = 0, insn = 0, esn = 0;
+ 
+    if (!str || start < 0) { return 0; }