gentoo auto-resync : 15:06:2023 - 13:38:09

12 files changed, 35 insertions, 45 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index cd753c56e371..06fbd6eaaa58 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/givaro/Manifest b/sci-libs/givaro/Manifest
index cefda44ddebf..295520ad1be9 100644
--- a/sci-libs/givaro/Manifest
+++ b/sci-libs/givaro/Manifest
@@ -1,5 +1,6 @@
 AUX givaro-4.1.1-fix-pc-libdir.patch 549 BLAKE2B f564256b81f1e2ef42bca171fce581e603887905dcf7fe8c881e59aae82d062767efdb096598f92bca09e9127c98fe023e9c034b5b38ef4ca575da9e877ca334 SHA512 927b1a15c834ba2c1cab37e1fdac1ab1c347cba7aba98be652e2ed4468d2a0627cc7f4820561655d1a223c02f8eaba7cc2911acb9998fc853dc20590fb1c74ef
 AUX givaro-4.1.1-gcc-10.patch 1035 BLAKE2B 460371ff8e628e1945a29d9c6d2b718c7d98b07b023540bc49a439cd941a19191db44536a1514495014084a85028debfb4e714d6d9efd9ae7c7c12687d5f8400 SHA512 3e154b3cf6c11a106f78778eeaaf0c2cfe81e25d18f623b5b071b306f1221c8513f27f87ab3e3684a8b3f18138dfbb516c33691dbb854072a35a0be21ac0bc48
+AUX givaro-4.1.1-gcc-13.patch 667 BLAKE2B d51ce9ce832d6d3e31410207bd77d3efa56e87a3a3c0cebb4dd16387a41647f59f5e6cd768b763909c54e2de06ed73ed0cc3dd8be0eb4809d6a77ecf201eafdf SHA512 e414c98aea642b705cf692c06371512713d1a8210cebfbfe80d26d48a18d6fb42726a6d9cf161390b66c7b424965fc3280ca2811b13a20b1fd986f346e3ae6df
 DIST givaro-4.1.1.tar.gz 1008358 BLAKE2B 246fd1a263174f58d96dd66fa79e6113368b6c318c33d68858a339bd9cb778dfda84636c683ee9d02f2ac72ccff8ac22d395b92741448a8ed2ce08c041ac8ba9 SHA512 7ad15ac24f55ad65c9c5d0d48ff4388d0494e75dc7b66d1e139195cd086ff2371259bdb5df940fead1db2fd378bb76289f2327a8d6f41575d99d424a74cf644c
-EBUILD givaro-4.1.1-r3.ebuild 1900 BLAKE2B 8cbdeb653e6b381b48e18cf671e595feaaf2b43dd818d8fff3f4870e4ab530dd11a7abfe6b234ecb4df5df8c35e58372eb80c1e74e49b7d9ed3274337898e145 SHA512 69a160fb4b74cc6f93542a4daf85507cad29d649a3523b3e9856b7e88700f2a291de682963696477dca0371f4dc0827fe14ab41a6a92b84c4542c46c551a378f
+EBUILD givaro-4.1.1-r3.ebuild 1941 BLAKE2B cc0533f6ee0b414a015ecd2a9b9b89d3405bf36086174ab9dff808c51028dc4772daabce90569e13ef51f306dc4bf64a72e10cc873fba09a1369ea941202dbb4 SHA512 74e8d84e900a1eaffe96d56e774377038a39d44b81ee34f32bd22e0a8211b715ac4769063ae84a22719d9b783ff022bca4d46c66ccf34f3ecac4b175e9ae87cf
 MISC metadata.xml 769 BLAKE2B b407b31de2f554fdf554b2d77c2dd0b1bbf39f36b29fdf565f50362153798c60bcfecf0411247eec556ff6ddc92af0c49e11a9b242b5e3e7b7dcc1066527d08c SHA512 063ccc3fcd55f3d7033fd23efe5095d83784d0e60cca2e1092e534fe06d0e69d5d340a0a25547bddc2962d2906c14a2c996852e2c198124ed007ecdfde4fff2e
diff --git a/sci-libs/givaro/files/givaro-4.1.1-gcc-13.patch b/sci-libs/givaro/files/givaro-4.1.1-gcc-13.patch
new file mode 100644
index 000000000000..15178289ca84
--- /dev/null
+++ b/sci-libs/givaro/files/givaro-4.1.1-gcc-13.patch
@@ -0,0 +1,23 @@
+From c7744bb133496cd7ac04688f345646d505e1bf52 Mon Sep 17 00:00:00 2001
+From: "Benjamin A. Beasley" <code@musicinmybrain.net>
+Date: Thu, 19 Jan 2023 09:12:22 -0500
+Subject: [PATCH] Add missing #include <cstdint> for (u)int64_t
+
+Fixes failure to compile on GCC 13.
+---
+ src/library/poly1/givdegree.h | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/library/poly1/givdegree.h b/src/library/poly1/givdegree.h
+index 3753a425..eb85a0dd 100644
+--- a/src/library/poly1/givdegree.h
++++ b/src/library/poly1/givdegree.h
+@@ -19,6 +19,8 @@
+ #ifndef __GIVARO_poly1degree_H
+ #define __GIVARO_poly1degree_H
+ 
++#include <cstdint>
++
+ #include <iostream>
+ 
+ namespace Givaro {
diff --git a/sci-libs/givaro/givaro-4.1.1-r3.ebuild b/sci-libs/givaro/givaro-4.1.1-r3.ebuild
index 86922d8736ca..e072eb6ffbe7 100644
--- a/sci-libs/givaro/givaro-4.1.1-r3.ebuild
+++ b/sci-libs/givaro/givaro-4.1.1-r3.ebuild
@@ -30,6 +30,7 @@ DOCS=( AUTHORS ChangeLog README.md )
 
 PATCHES=(
 	"${FILESDIR}/givaro-4.1.1-gcc-10.patch"
+	"${FILESDIR}/givaro-4.1.1-gcc-13.patch"
 	"${FILESDIR}/givaro-4.1.1-fix-pc-libdir.patch"
 )
 
diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
index 457e00faaaec..179bc0d2bb85 100644
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@@ -1,7 +1,6 @@
 AUX hdf5-1.12.2-configure-clang16.patch 1239 BLAKE2B 76641263e8cdf1f694a0b23c9787e9c1a0e86e30079507beb25caf2c1b89a2e431f7456321e89a39a6ec1d06c5a51a941f9ae5c85a7e3e24462c0eabd41911e3 SHA512 b664f6e464ec824bad46a8e58b571a46b10bcdcc8eae39b878d239b169685b2d1bba6c0ce295f8a690b94f016731176f500b568ef9f0cd2fe0df290ffb6dc298
 AUX hdf5-1.12.2-no-messing-ldpath.patch 1086 BLAKE2B 77aba02cd8f3663883fa5cf91b3f77067163f58ec4270d22e2c4e1a5b9b1cc138a2e9dd1c7a44331165c69d6c7a0427fe2708bae63958b416a9f26c799de7443 SHA512 8b8aa080cb6feded376900cf9f4b1f1bbe98550b37e9ae8ad660419f732e686aae2ff6eac37e7810ee438a0e9c1b7a37d24f5db8590cce0c91f482ec7b873527
 AUX hdf5-1.12.2-no-strip-symbols.patch 434 BLAKE2B c8d96cb95d3444c18349d72b7fd59f76b4af3d0c5422a7c31161b8f98afacb322b042b8f5751b581565b351148fd0f4003379349b6ca964f5957cd9e19ebdebc SHA512 6b593a8bbbd4a4e9b97e8b3324ad90024b2c09c669d2f6e21a0d23adb66bbbec34afc5961bf97bc6f913492e33610a4b5aeca6a7a4ef9f7605ce5b69fbba6527
-AUX hdf5-1.14.0-fix-include-path.patch 1319 BLAKE2B b9be1c2c8675feb1dd202849ae1d38bc9d62aec11bbd207d4fff6670a50eecc670b481edd840fe9281a1b54b3cda40917717a3ccd913a843d119f5ebcbca9870 SHA512 e0eaedf03edb1add0fbd55a105d7731a98762ae09ec5c2e3d861fdfddd51292b979d54be54eaed1d7ae7806cfcbaac80bf208fa8a3d01c7ad18d5ddd4f585792
 AUX hdf5-1.8.13-no-messing-ldpath.patch 1141 BLAKE2B d7d186e4c00acb9fd3d44beb1d8c3c4da0c373f88b3fdf21e1f89b169b747d49572239385228687cfc10380bdceb9ca6d1ac0d5f5154cb7a328f8a2d509fb28d SHA512 e43021ceb83909ab06ba378363c192aa0f1b34cc7c2b121f5000e215516dbdea1b825a53ac4023073bf4870a5c3452c22f5535391d95af45ad63a309e1ffa5a4
 AUX hdf5-1.8.9-mpicxx.patch 494 BLAKE2B 148d87af064e2ba28c918c8db39ece0782a179803e4c38c5cd5eaba81a673bb8aa3699a48e80a7ae2d4579ac0261cc21d5509e46661ada9a69f444a58eb45ecd SHA512 8b4c39e40591860652547ea8ff205230da7d67488233e911cbcb3416eab561f2529c65bc5e7c9c812bf4298812346f47f9209e5f69f7e8f66ad587306a5b477b
 AUX hdf5-1.8.9-static_libgfortran.patch 429 BLAKE2B 9e1c544a453c09b3498a7d9d3e8090c928571776934c4dd6b426cbdb2783ed8f47185d6ee0c73ede6b4f14e27459ef5e1412112e9d897daa2dc57f1ad5fb0b24 SHA512 af97c54469a90bf3b0e8ec1218d4ca95822ac0cbc7120114979fc467fe3114743c74f4d4e16f0c10b1cd82d40880ef482f6fd34e1effc7c621b981ad466204f9
diff --git a/sci-libs/hdf5/files/hdf5-1.14.0-fix-include-path.patch b/sci-libs/hdf5/files/hdf5-1.14.0-fix-include-path.patch
deleted file mode 100644
index 4530f1fa6d2e..000000000000
--- a/sci-libs/hdf5/files/hdf5-1.14.0-fix-include-path.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-https://bugs.gentoo.org/904515
-https://github.com/HDFGroup/hdf5/issues/2422
-https://github.com/HDFGroup/hdf5/issues/2621
-https://github.com/HDFGroup/hdf5/pull/2667
-https://github.com/HDFGroup/hdf5/commit/b77cb393b884c1dbdaffb300aa8c4967d9ba7fb0
-
-From b77cb393b884c1dbdaffb300aa8c4967d9ba7fb0 Mon Sep 17 00:00:00 2001
-From: jhendersonHDF <jhenderson@hdfgroup.org>
-Date: Tue, 11 Apr 2023 14:31:25 -0500
-Subject: [PATCH] Fix improper include of build directory (#2422, #2621)
- (#2667)
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -3012,8 +3012,7 @@ SUBFILING_VFD=no
- HAVE_MERCURY="no"
- 
- ## Always include subfiling directory so public header files are available
--CPPFLAGS="$CPPFLAGS -I$ac_abs_confdir/src/H5FDsubfiling"
--AM_CPPFLAGS="$AM_CPPFLAGS -I$ac_abs_confdir/src/H5FDsubfiling"
-+H5_CPPFLAGS="$H5_CPPFLAGS -I$ac_abs_confdir/src/H5FDsubfiling"
- 
- AC_MSG_CHECKING([if the subfiling I/O virtual file driver (VFD) is enabled])
- 
-@@ -3061,8 +3060,7 @@ if test "X$SUBFILING_VFD" = "Xyes"; then
-     mercury_dir="$ac_abs_confdir/src/H5FDsubfiling/mercury"
-     mercury_inc="$mercury_dir/src/util"
- 
--    CPPFLAGS="$CPPFLAGS -I$mercury_inc"
--    AM_CPPFLAGS="$AM_CPPFLAGS -I$mercury_inc"
-+    H5_CPPFLAGS="$H5_CPPFLAGS -I$mercury_inc"
- 
-     HAVE_STDATOMIC_H="yes"
-     AC_CHECK_HEADERS([stdatomic.h],,[HAVE_STDATOMIC_H="no"])
diff --git a/sci-libs/m4ri/Manifest b/sci-libs/m4ri/Manifest
index b8a53b47913c..64de8ef5334d 100644
--- a/sci-libs/m4ri/Manifest
+++ b/sci-libs/m4ri/Manifest
@@ -1,3 +1,3 @@
 DIST m4ri-20200125.tar.gz 511132 BLAKE2B 637dbf7f17b84dc5fc91c9d8f501fa223cfacd687cb953ce3b9c4716e9a6d39318ef168c2ec8a4b5eeb469a4b46abbcd8802aaf694991d82deb20c832843c3ab SHA512 212ea58a93b792c1901f62411b06cd1a2ee60b3506c987e45ded73c146f2fa6baf5461b1dcabf31a5771ab5a44eab050d64714f7a5fca3df2d141d0d80c6c51a
-EBUILD m4ri-20200125.ebuild 1271 BLAKE2B bce89bfd944cbf457222e13ed2d5b726a0ad12e23704b2cd0b4d4b00671b33693d4bf5756e4f6b760decc59050b8fe1c12984fb2365827bb0407dcd12d4af77b SHA512 6a48cfbf4e8b6e944d3881d09921eaf32963dbfa1ad52d09e243a8079af3820cf5042292ffd785fbef691a981dea0b4bf42aebec5db4027ba4bded632dc33148
-MISC metadata.xml 1190 BLAKE2B 57ec862b1b1d29fedbdb9f75fd560e24fa0494afc168ae9894219aeccc890fc77f6909a2f9b241122b51bb438bf6774b8d1b77444051095d18e1dbe62a5a5f0e SHA512 f756e8d2a9c5bf44763933eb09c00a058b88d88120553809618f5c927e39a7fe8c19fd7342206eea97474a6d596959493a8390bff39ad032890dfa2d4a49a7e5
+EBUILD m4ri-20200125.ebuild 1268 BLAKE2B 5d22b54401ac58a895d4d1e341a3297b52afcfe5fd66fee56a0083e7737301fae1273bfb1bcd2f377999d94a663cf39aa5686332d50e1a1a126c2d0256bbd7b7 SHA512 a7286abf7010d66f76966c12074eb5a3b7bab2f361106e8984430a20e0a118a3665839515ae50d4b8027a73291e11044e477739e02a6c89c92270707e4dce661
+MISC metadata.xml 1187 BLAKE2B b5428f60e018c6503ec91f9a13949c6e3571c94474d234317e416fa81e2370d473db9ecb5a1c73306e071673c27b02d57feae552b12f9ce791b426d7a8a488a4 SHA512 a984f783b8bb1971663a75ac655aba7e0a4ddbdb8db6d01105bb6a75711d8e83c9b598076207e1a9619198cca0ed901a5aef64a5443b6efe89a28c2571cdfa71
diff --git a/sci-libs/m4ri/m4ri-20200125.ebuild b/sci-libs/m4ri/m4ri-20200125.ebuild
index 3b265a53a4ce..adf6e85765c9 100644
--- a/sci-libs/m4ri/m4ri-20200125.ebuild
+++ b/sci-libs/m4ri/m4ri-20200125.ebuild
@@ -6,7 +6,7 @@ EAPI=7
 inherit flag-o-matic toolchain-funcs
 
 DESCRIPTION="Method of four russian for inversion (M4RI)"
-HOMEPAGE="https://bitbucket.org/malb/m4ri"
+HOMEPAGE="https://github.com/malb/m4ri"
 SRC_URI="https://bitbucket.org/malb/${PN}/downloads/${P}.tar.gz"
 
 LICENSE="GPL-2+"
diff --git a/sci-libs/m4ri/metadata.xml b/sci-libs/m4ri/metadata.xml
index 189a75d32cd2..b31730792145 100644
--- a/sci-libs/m4ri/metadata.xml
+++ b/sci-libs/m4ri/metadata.xml
@@ -28,6 +28,6 @@
   </longdescription>
 
   <upstream>
-    <remote-id type="bitbucket">malb/m4ri</remote-id>
+    <remote-id type="github">malb/m4ri</remote-id>
   </upstream>
 </pkgmetadata>
diff --git a/sci-libs/m4rie/Manifest b/sci-libs/m4rie/Manifest
index 2a4cbcdf75d6..d9629d53b750 100644
--- a/sci-libs/m4rie/Manifest
+++ b/sci-libs/m4rie/Manifest
@@ -1,4 +1,4 @@
 AUX m4rie-20200115-link-libm.patch 654 BLAKE2B af7ff7b56c14078817b6a12a8184c81e1547a0c75b682d7398a040645be7e392ce3f923be56110bbf282f0ed729aa5ea2fadb23d6815aa96370d99ba29f7b2b6 SHA512 6d85c998f0f2f85c9f3cb77861318eab31b38bcb88ff3133fc3bbef0492fcb412e832d92f5d76c63aa3c979cd21e55164a2a53bc08c67da6f22bd1d27d08e883
 DIST m4rie-20200115.tar.gz 500702 BLAKE2B d8b1506ef9902def6577851a97dd6f7da986dce39b3250f9f9b66f9caf8f811568b7975165fb75b6b8ab3c9faf65d890f7c2254725224266f1250a0bcf18a464 SHA512 22c990cf06de9ac790f82f48e498b2bfc87fdf6834257f4e4a4c44e2446b4226438d21692d654008b58df36d8da746bba04dcf1a3d50e34ccf8c678efd5b642b
-EBUILD m4rie-20200115-r1.ebuild 932 BLAKE2B 7843792f14c62881b34ffd565116b552d42050dd9b77fb9bcbd688943d212c233a76e23c99a9e7a7dee9538f40cd97849d7682fe44121a33e284c0beccad1ba3 SHA512 5c5ef4be1b62ea57f41abaacc08300652d3d982ec1e55c2e3e10d1b9e5446b0e2132d9ab5e0fb213877af102b53d6446e354df0dbca37bdba1d96d7215ed1ab5
-MISC metadata.xml 988 BLAKE2B 4ea83948391c49d6987869d1546745d4ba7313e051ea42be067d1220a070e8cab72c65508637a80fd0820f3bd7ed1d337f552f4c05d8f2c05b383d6b3c19b065 SHA512 03d5b6411827b46610731d20363b0fa8943f9eb94bf55c458dc7d8b7be9944fe5111e441cd684996e52d3f44fe8c494bdb1bf54430eafa66dbf8cd61144fe7a5
+EBUILD m4rie-20200115-r1.ebuild 928 BLAKE2B 5f5e8498c0a413f9be7170970fcb18b00ebcfcbf38874421478f0ae58cd9425e97f8980bb8acafed52c5368a2a56215df7261c75781223e961ea6c4cd343dbc0 SHA512 ee3d9feef5db72962418b92af8078b1ad5e71a1ed27055b31e01ef528204a0618f33e8e91b01d7e983a9d10ccba9eb6204656fa97aa597c2447b32641d849c76
+MISC metadata.xml 985 BLAKE2B 0b5601161f57de941bf8cff616bc4c92260587517200e0f44a1501d56a938eb2e0727d61659bc2eda2dc42bf376fc8a40db4c7edde32c65c5d2d2d3c7ca82828 SHA512 6e9b2e0467d85aa9a1d18b185ccb7798e4a0cd75c86d70ff6facb644d7bb8657d9e195b38577fd874fe08accd576f231bcdc4b988a9478ab27cd5893d6fb3c51
diff --git a/sci-libs/m4rie/m4rie-20200115-r1.ebuild b/sci-libs/m4rie/m4rie-20200115-r1.ebuild
index f89f9de0c3d0..60d518b539d8 100644
--- a/sci-libs/m4rie/m4rie-20200115-r1.ebuild
+++ b/sci-libs/m4rie/m4rie-20200115-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -6,7 +6,7 @@ EAPI=7
 inherit autotools
 
 DESCRIPTION="Fast dense matrix arithmetic over GF(2^e) for 2 <= e <= 16"
-HOMEPAGE="https://bitbucket.org/malb/m4rie/"
+HOMEPAGE="https://github.com/malb/m4rie"
 SRC_URI="https://bitbucket.org/malb/${PN}/downloads/${P}.tar.gz"
 
 LICENSE="GPL-2+"
diff --git a/sci-libs/m4rie/metadata.xml b/sci-libs/m4rie/metadata.xml
index 0c2d7316d127..37eece3977cd 100644
--- a/sci-libs/m4rie/metadata.xml
+++ b/sci-libs/m4rie/metadata.xml
@@ -25,6 +25,6 @@
   </longdescription>
 
   <upstream>
-    <remote-id type="bitbucket">malb/m4rie</remote-id>
+    <remote-id type="github">malb/m4rie</remote-id>
   </upstream>
 </pkgmetadata>