gentoo auto-resync : 10:05:2024 - 00:01:13

4 files changed, 22 insertions, 2 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index ed0811dd1d57..90ea37bf4b0d 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest
index 79c67879328d..4b622aa2a7dc 100644
--- a/sci-biology/hmmer/Manifest
+++ b/sci-biology/hmmer/Manifest
@@ -1,9 +1,10 @@
 AUX hmmer-2.3.2-fix-build-system-destdir.patch 825 BLAKE2B 46264f43ed43a567c1f650710e1485942eb48a0b7ed3860424f00ca06cf04f9e923318c5df3d56eb312ed773bf2d42e22880b4ac6c2f81ac6c65bf2cebf44008 SHA512 f7eb3de5cbb1bf58b4ae4514e020ea059ad6a267e6f425494d8b444ac1bab056bc4709fed7f2793e68720b057ca1ac8c6dbca907125712d18dc05b77e37b1c3f
+AUX hmmer-2.3.2-fix-missing-include-in-configure.patch 526 BLAKE2B 5b382c4d827a3287349d4f4f4969e9d46339ccb065fd5f9eedcd855b8f830d3625c42a7df5f40476c16d00113038ebb658d510135e42b337d00f2fcfee7ac36d SHA512 aac277e7a8f5eed78b72b841f520f6792d327b7f2cc2173e526ce33fb25069d674f9875997fb0bf8e585cd9a645e88501e30f22aa43bacb29127fc380efc40de
 AUX hmmer-2.3.2-fix-perl-shebangs.patch 2457 BLAKE2B 1afca014901d79416dac2c1d41e20371ef970aa3691a6b414e9a96adf8331c619753df7a42e1d9af63aab12a3fc8b8c7d2251129dd581bfb33a0d7c3e50970b2 SHA512 9597d77b3101c091bb1d005f36229cb6bedaf496a15da472495bb688fdb2750c94a38adc1236f3d90b0085caa78f61bddb350d51e0d3cc8dfa96edcdd5e2e5b9
 AUX hmmer-3.1_beta2-fix-perl-shebangs.patch 8605 BLAKE2B c0c78fed780b43df960dc24914e5dabe161243cec015deaf058d7eebf79c5e1633ded4f1305bb37b9766d74588009142fd58886e67810940e9601ef138647c21 SHA512 ce2c91c2d34d49dd5082a97ca0543bf3a176c792b4efd0cb37561114fc572b41d6cd546e16267283d33138ad54e2bb0c9c912c8fa1142e558a5452e9e72da2ff
 AUX hmmer-3.1_beta2-makefile.patch 3679 BLAKE2B e258b23bda9d0515891f1d571b94f9ef48499f25ce6cb52c3d1bcd0a28bc527f335cb25ece944afb33e4824438315cc9986243fb13e07eb128d7859e0a77f4b1 SHA512 bebd36deee48d4a043a1d84233ccbc93de8e44b5f7f57bf24a551b53a6f3dbfb3166861555755744d0abb4fce871d7c19fa8887c08115b7d8f61ca5ad38c3cc6
 DIST hmmer-2.3.2.tar.gz 1024933 BLAKE2B 34fdc7b24b28d653022c80a63b2fd8376c15c961e1550a04cb310943d165575a2721cc5e4cb516335f57414f8621b7e62c4e30ee1f107bb714e40c59ed37d418 SHA512 5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7
 DIST hmmer-3.1b2.tar.gz 5965253 BLAKE2B 38d1d6fb43aa814c0e3ddc551469ebd6b967f181c45df3802598f31abef10998595218167555a8862c0d2caa9118d9a7f1c22b673b6d596665f797ba903093f5 SHA512 64c8a840cb62160a1c13a20e64f42d297edb7969425d5047eefd8ee9f992d66612d62843523e8f33a2c38568ce1b0a9df23dd1d3ecf6773007f6db12d4cc4771
-EBUILD hmmer-2.3.2-r5.ebuild 1843 BLAKE2B ecea0f3370698641b3ddc5c572f9386bacc2547fab72889d79fd910052edd14bd4a2447b8a9183290a5c0be4f313735bbab8e1bd67d1c4275a6d036fe2fae3dc SHA512 3109f304c6f48b7d924eeadd416fa3e9c3e662f2380b4ce1da283d80a47de9fda4585966e8f29c47dd89914e7e03bf0f9966f828d45a13befb0f035e89cb2978
+EBUILD hmmer-2.3.2-r6.ebuild 1902 BLAKE2B caf57622e095891b70b95838ded043a530c0160e53da84dc1d93ecdd7c65e08ee7abb05c98c835c64d6aea4d9b064f511e34cd1d5cee2c33493a957e31b5991f SHA512 c68017cec913425eed52350638bf1f9408f1fb65e1ada8209da60acb533944e1ec3b6ffd035692844d53ac069999023b54da937f7fa6d51c3e212220bf8950c9
 EBUILD hmmer-3.1_beta2-r1.ebuild 1140 BLAKE2B a5a0a26f2461edc08101505fa600383952501083111e828b4a0484a2c895acb63b3784247ea3a9b4fb10a13089a84f09f9721b4835cbb7b5479f0877e62c84aa SHA512 65889b5afe47d60abdd7ebb4d098510e8f25979e442df2a88d6327ab2fffc6d056fa6f96f32c0d37614473bc961c1e60fc3e194e535c5b6816b3c420816c5ea9
 MISC metadata.xml 262 BLAKE2B adaacf2ac22ce09f8b1b68f538773c1e2101156181ff302eca2ce1280ee5d45db4eb302a8eee1bbead5e55942443dd16ef924cfbfdc95a1658dc6a9f460468a2 SHA512 ac924b6b530d96645f173d40f7a2bf0e3abbf49048ebf7fadcea3dd553cd25504f0e68a103395de1fb59a2e5e11497dcead601be01cc6f0295ccbc4155f67e3f
diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch
new file mode 100644
index 000000000000..37683d425edb
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-2.3.2-fix-missing-include-in-configure.patch
@@ -0,0 +1,18 @@
+--- a/squid/configure	2024-05-08 09:21:15.751063495 -0000
++++ b/squid/configure	2024-05-08 09:22:50.491502934 -0000
+@@ -2493,6 +2493,7 @@
+ cat confdefs.h >>conftest.$ac_ext
+ cat >>conftest.$ac_ext <<_ACEOF
+ /* end confdefs.h.  */
++#include <stdlib.h>
+ int
+ main ()
+ {
+@@ -3500,6 +3501,7 @@
+ cat >>conftest.$ac_ext <<_ACEOF
+ /* end confdefs.h.  */
+ #include <ctype.h>
++#include <stdlib.h>
+ #if ((' ' & 0x0FF) == 0x020)
+ # define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+ # define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
index b305820faff3..74a8a151b0c4 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r5.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -20,6 +20,7 @@ BDEPEND="test? ( dev-lang/perl )"
 PATCHES=(
 	"${FILESDIR}/${P}-fix-perl-shebangs.patch"
 	"${FILESDIR}/${P}-fix-build-system-destdir.patch"
+	"${FILESDIR}/${P}-fix-missing-include-in-configure.patch"
 )
 
 src_configure() {