gentoo auto-resync : 27:04:2024 - 23:59:42

11 files changed, 45 insertions, 154 deletions

diff --git a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild
deleted file mode 100644
index b4b7974e60d0..000000000000
--- a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_IN_SOURCE_BUILD=1
-PYTHON_COMPAT=( python3_{9..11} )
-
-inherit distutils-r1 flag-o-matic
-
-DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
-HOMEPAGE="https://htseq.readthedocs.io/"
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/htseq/htseq.git"
-else
-	SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-	S="${WORKDIR}"/htseq-release_${PV}
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="GPL-3+"
-SLOT="0"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-biology/pysam[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	test? (
-		dev-python/matplotlib[${PYTHON_USEDEP}]
-		dev-python/pandas[${PYTHON_USEDEP}]
-		dev-python/scipy[${PYTHON_USEDEP}]
-	)"
-BDEPEND="
-	>=dev-lang/swig-3.0.8
-	dev-python/cython[${PYTHON_USEDEP}]"
-
-distutils_enable_tests pytest
-
-src_configure() {
-	# mask broken asserts in src/step_vector.h:72
-	append-cppflags -DNDEBUG
-
-	distutils-r1_src_configure
-}
-
-python_test() {
-	distutils_install_for_testing
-
-	# Due to the build directories creating a competing
-	# hierarchy, we move to the test/ dir to avoid implicitly
-	# injecting the root HTSeq/ dir into the PYTHONPATH,
-	# which leads the python module lookup astray:
-	#   ${PWD}
-	#   ├── build
-	#   │   ├── lib
-	#   │   │   └── HTSeq
-	#   │   [...]
-	#   ├── HTSeq
-	#   └── test
-	cd test/ || die
-	ln -s ../example_data || die
-	epytest
-}
diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild
deleted file mode 100644
index b4b7974e60d0..000000000000
--- a/sci-biology/HTSeq/HTSeq-9999.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_IN_SOURCE_BUILD=1
-PYTHON_COMPAT=( python3_{9..11} )
-
-inherit distutils-r1 flag-o-matic
-
-DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
-HOMEPAGE="https://htseq.readthedocs.io/"
-
-if [[ ${PV} == *9999 ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/htseq/htseq.git"
-else
-	SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-	S="${WORKDIR}"/htseq-release_${PV}
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="GPL-3+"
-SLOT="0"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-biology/pysam[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	test? (
-		dev-python/matplotlib[${PYTHON_USEDEP}]
-		dev-python/pandas[${PYTHON_USEDEP}]
-		dev-python/scipy[${PYTHON_USEDEP}]
-	)"
-BDEPEND="
-	>=dev-lang/swig-3.0.8
-	dev-python/cython[${PYTHON_USEDEP}]"
-
-distutils_enable_tests pytest
-
-src_configure() {
-	# mask broken asserts in src/step_vector.h:72
-	append-cppflags -DNDEBUG
-
-	distutils-r1_src_configure
-}
-
-python_test() {
-	distutils_install_for_testing
-
-	# Due to the build directories creating a competing
-	# hierarchy, we move to the test/ dir to avoid implicitly
-	# injecting the root HTSeq/ dir into the PYTHONPATH,
-	# which leads the python module lookup astray:
-	#   ${PWD}
-	#   ├── build
-	#   │   ├── lib
-	#   │   │   └── HTSeq
-	#   │   [...]
-	#   ├── HTSeq
-	#   └── test
-	cd test/ || die
-	ln -s ../example_data || die
-	epytest
-}
diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest
deleted file mode 100644
index 052df8b8e9b4..000000000000
--- a/sci-biology/HTSeq/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST HTSeq-2.0.2.gh.tar.gz 48468261 BLAKE2B c68ec67906f3cf78954e94214b82fd51bc19e0c505f994a3df4bfc682d804fa26f4883e9a8fa1e8ddf1e4f8ba8690d605705ebdd2d1695470984c2f04b6a19ce SHA512 96c0b4de6c9cfa9e405f02e366ecfed63bb0dba0ab76fe872f6f48b52a4956b08fa75efa4b1e4c6e4560e34b4e2921bf1ec9671831226ad415ed421a88ec3f6d
-EBUILD HTSeq-2.0.2.ebuild 1530 BLAKE2B 1a6bcac47e4f7b92e627e8982664061f6eea9961ea4bb9f3610a5d10ab75bfa87292314fdc92e7bfbc81897aea5567af7e49d27be61c7a575995bdbb35b4ac04 SHA512 4ea3d3733f87952b0c46449f95d740ed5be7abdf92f951f6c2773173d319508552baf744c9619d6859eb84aa730f0e265f7a0c15be095063adec2e41ca685a37
-EBUILD HTSeq-9999.ebuild 1530 BLAKE2B 1a6bcac47e4f7b92e627e8982664061f6eea9961ea4bb9f3610a5d10ab75bfa87292314fdc92e7bfbc81897aea5567af7e49d27be61c7a575995bdbb35b4ac04 SHA512 4ea3d3733f87952b0c46449f95d740ed5be7abdf92f951f6c2773173d319508552baf744c9619d6859eb84aa730f0e265f7a0c15be095063adec2e41ca685a37
-MISC metadata.xml 381 BLAKE2B 3f734f3608731ea9d4e893965a96d3abceddbdff04309350ede193ef721eb8faec3e6050850fb4410557536058d9852ae5b02e0d99b9eb79f4b2091b58bcb6f2 SHA512 227191a1fd9fc0e5cbf9091a48eb51baa5bfe97637b5fc27c419b2b2225c03759ca98bc84b7974338bd2b52db5dbf848b084c2b2f1f300b70b94fb209528fe91
diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml
deleted file mode 100644
index 6ada1a530737..000000000000
--- a/sci-biology/HTSeq/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="pypi">HTSeq</remote-id>
-		<remote-id type="github">htseq/htseq</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index d667d62efa4b..93d82fa77140 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/maq/Manifest b/sci-biology/maq/Manifest
index 56728e9a4ce6..28258aa9b4e4 100644
--- a/sci-biology/maq/Manifest
+++ b/sci-biology/maq/Manifest
@@ -1,8 +1,9 @@
 AUX maq-0.7.1-bfr-overfl.patch 527 BLAKE2B 41a4b6bff80faa02158cb4a7884e47c9516394f93e46686483ab9209b2c889ca49c756d4e3516ba58fb2054fcf22828ff94affb877a54ca6cdf6806b5dd0ac8b SHA512 953587e9354f2d3a070aae67ee999105b96678b2b781b9fbe8416d040a594d1db2ed6e7de0516cd29c2020de5129bbc26b78b7bfa5a258ebb5cb9fd4715f8bcf
 AUX maq-0.7.1-flags.patch 799 BLAKE2B 2f65c9357d8fbbf5cf3450a63b0a6e322472bcc978829d9245e522e2a9d83aaebe52b87e34a231dd8cb319864a8e54761b4f0e98f14e2436eaf8669ccb52caf0 SHA512 f13d8af7884691f2d8c8e9bd9d370c5ca12e863aaf05e156a964ba88053d86dcb63f24169fbc3b2a9264423510061c26d88904b87ea8aeb8bf446b51e190aedb
 AUX maq-0.7.1-gcc-4.7.patch 1429 BLAKE2B af81651b07186eed305d70534e9f7c41375f60a8376878da80180503daea59a30de5ee726b0b9e87cd45ab6a3e033e5ba1d09a4e02a84c8b723dfec72e6dd068 SHA512 e2936757fff7f32d8dea3da3181839b7b4190a15f4bfb5c3b6cb6a723a10ba8f6e4f762eca32387345a4263c9bf525a425d5e58c78f387a1813508fdc5fb364c
+AUX maq-0.7.1-gcc14-build-fix.patch 603 BLAKE2B a1c2722f4bc53014b5281fc8532573d5c0ab3d064fe2e49efb349cd1dfa7e705f045cbe5b5c6125c3703c6699954019c03f9bf2c911ccb5642b47737e9d252b0 SHA512 a1e4c5b896a04fecd50430de14d1e967e78cbf6f499544bbf4259d417c91778a5453de474f8f343b1f63b87e1bad0b842eaeefd30d43bed2a543eac658d7cd23
 AUX maq-0.7.1-remove-64bit-flag.patch 787 BLAKE2B 2e94066962194133ccdae4095d3d6bf6f058f7a7d5d04f8737e03fc725508b3e291c76554418c6ff9a15969e332d340b86e11ae3cab90406ec60e9ea63361f5e SHA512 4864453afa79679c253b17a2b125bf0b44c1a05a6ae6341821382991217026b599437288a1c96625cdc2a1fad2cf73c79798a230bbfccef46e1c92012a6c3df1
 DIST calib-36.dat.gz 196371 BLAKE2B e4dab71e0830603a7c25bb4c8e15f92e4a5068eeeece451a3e0a2a9e2c4f65b87325e7ff4e4e5543b79f2c3d9dd43c9398cdb32241535bf44e66705bfdf683f7 SHA512 1033ad47b31882823f71f16054f366a6853b4b5e1fb286ab2c5f62c1409ed20e6dc0faec7e356350e91c71d25a198d8e0d7a521b3662b5e2fae22af44098e8b7
 DIST maq-0.7.1.tar.bz2 368645 BLAKE2B a7989ae2348a7332f17a75c6fccba55deb8bd9330863d0c5ab3bf997f2f07abd1ca89ebb41d034902f6571ee36365f63db9c8c84c1e5d3d788236279581b989e SHA512 acaba2d172f8f4ef7a2b1254bd220f134a5eb8e4936af16bf7fa6695d016e6b6fa9a5b00d073ec1ecc0ecc39dfb1c9700c38fd017edb5bd49a83de383cb0d30c
-EBUILD maq-0.7.1-r3.ebuild 784 BLAKE2B 092e9683af6c7a9248c7336da930947168e937df9bc80829a5a5d7a07046acd9f1d2c6667cfb4d0a62c8f616802c607db8f6926d26166abe8bca5345318bd855 SHA512 52d16dcffa83aba11f6d1a50a0520252ac410b697793dc6f42ca8459d4ae47b56f22fbafe8af8a75a7f522f1e0b94507d1ac6397f19837fc101f8fb866dc3746
+EBUILD maq-0.7.1-r4.ebuild 827 BLAKE2B 1c5389612a5c79df5ab8321c8835b7933abb17136e60c14b85254ea9320b1a9d4b0e433f0df99c5158b3662b8fcb260c283c208e02db4503f47da154fff1a454 SHA512 a7e3ab88ea0b4c51f1f223f3e7c15930345ff614f6e6c468b3195843ff8e6007981bda055949e9c319c417b9fa0b2df0bd08622ea5b93dc7eba63cd7b50e7625
 MISC metadata.xml 345 BLAKE2B 3f590b0bf8c9f9fa9470f6b8ed3b20643c84fc92839740e6aebe720edd0a6e0b8bb5d2b74d4dcd8cf80a89c2769308b89e21f2f386a62fc28686f883eff56bbf SHA512 244600e6c19400a837eb859a09582fa78a670d81a58e6a461689d2695273b450df999334ffc44eecdfbed9232784af84e7cdcabe7ee045ae51a24509f2aabdcc
diff --git a/sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch b/sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch
new file mode 100644
index 000000000000..b92b7711bfe0
--- /dev/null
+++ b/sci-biology/maq/files/maq-0.7.1-gcc14-build-fix.patch
@@ -0,0 +1,23 @@
+Bug: https://bugs.gentoo.org/921137
+--- a/fastq2bfq.c
++++ b/fastq2bfq.c
+@@ -15,7 +15,7 @@ int64_t fastq2bfq(FILE *fp_fq, const char *fn_bfq, int n_reads)
+ 	char name[256], str[1024];
+ 	int l, is_new = 0, l_prefix = 0;
+ 	bit64_t n;
+-	gzFile *fp = 0;
++	gzFile fp = 0;
+ 	INIT_SEQ(seq); INIT_SEQ(qual);
+ 	seq_set_block_size(256);
+ 	n = 0;
+--- a/simulate.c
++++ b/simulate.c
+@@ -74,7 +74,7 @@ int maq_simutrain(int argc, char *argv[])
+ {
+ 	fqc_t *fqc;
+ 	FILE *fp;
+-	gzFile *fpout;
++	gzFile fpout;
+ 	if (argc < 3) {
+ 		fprintf(stderr, "Usage: maq simutrain <simupars.dat> <known_reads.fastq>\n");
+ 		return 1;
diff --git a/sci-biology/maq/maq-0.7.1-r3.ebuild b/sci-biology/maq/maq-0.7.1-r4.ebuild
index a64b2b6f4e81..8930c780cfa5 100644
--- a/sci-biology/maq/maq-0.7.1-r3.ebuild
+++ b/sci-biology/maq/maq-0.7.1-r4.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
@@ -6,7 +6,7 @@ EAPI=8
 inherit autotools
 
 DESCRIPTION="Mapping and Assembly with Qualities, mapping NGS reads to reference genomes"
-HOMEPAGE="http://maq.sourceforge.net/"
+HOMEPAGE="https://maq.sourceforge.net/"
 SRC_URI="
 	mirror://sourceforge/${PN}/${P}.tar.bz2
 	mirror://sourceforge/${PN}/calib-36.dat.gz"
@@ -23,6 +23,7 @@ PATCHES=(
 	"${FILESDIR}"/${P}-bfr-overfl.patch
 	"${FILESDIR}"/${P}-gcc-4.7.patch
 	"${FILESDIR}"/${P}-remove-64bit-flag.patch
+	"${FILESDIR}"/${P}-gcc14-build-fix.patch
 )
 
 src_prepare() {
diff --git a/sci-biology/maqview/Manifest b/sci-biology/maqview/Manifest
index 250be2139824..304d8c466c41 100644
--- a/sci-biology/maqview/Manifest
+++ b/sci-biology/maqview/Manifest
@@ -1,6 +1,7 @@
 AUX 0.2.5-ldflags.patch 1335 BLAKE2B 537a13dc3248efae0573a527cb40565081114886478fd1138f6e8815ad8ff95019d18167bf8e4a8c19821b06d1c8b10c978edda35bc1118d21783450b083f360 SHA512 ae034ae1279e49c71f9daf658aece35063c56afc7ac3269d21d21a2f5b6f8e7974be48c82b52f4d250a9dcacfd5e8c9208b40c904ff73af8592c7f39395c6b6e
 AUX 0.2.5-zlib.patch 1437 BLAKE2B c8a8908ca6586f3fdff730c2eca39e54b3d08e8fe07fd6dc7ee6676f8a21c0943d939c937f47e3920286acec94b51daec64bf1e500661c661e054315de8d7e36 SHA512 7925f70d1f68bfa4fa87134d8ef20b05a6f022b1a9478a8e594e7b655852d858c0928b101f7eafd4e1ef44a17f8d353d49a6d1ede4072ac85ec452f75bd06c03
+AUX maqview-0.2.5-gcc14-build-fix.patch 337 BLAKE2B 8478ffbe452e25d663b452a2f562f2e7461fb211ebbe5c9401de3288534c6e3dfba599f42a833b156032b2a2ba299b229883f5fb7205fcfb727394b5c86deb56 SHA512 ac53e33dff1d9da5fd1b39e9e2c02e408809eb27059b08a42bf4568f8c4382d2e0e991ded1b33ff429617d881ca094aecd698821cda387cb0175415bb1c04695
 AUX maqview-0.2.5-gcc4.7.patch 575 BLAKE2B 8e461d07e0421e5dc1e209e83ed3fccfdcd541954481bbbb1f478cddb9ff045c3704a086a18d6e7a8b255d226a24eca7d791cde9e59673c842a4094d56f03ba0 SHA512 277086e1d6d536ae368083032421029d64d5173e643edaafbad2833d56e8ec283152a49d9874a7142333e0fee976d3600ed118b6beb0482ec7e0e95f4a36fba4
 DIST maqview-0.2.5.tar.gz 383410 BLAKE2B 7058f32e49267dfcc8b25da2ca2bbbd5134f66f0f9cbd10de7e876365d955d2e51cbab342af817f13018b7b1903872033c363fe077f10ce76e5fcc87da568dc1 SHA512 40bed0a1005ca96fdb12773cd9c22ddc926fe722c64652031609a17a50ff725a3dc117d51f4f27eda68b48861da78427469aaedff744f29921236b486396aed6
-EBUILD maqview-0.2.5-r4.ebuild 596 BLAKE2B 4d0efd2a53413b64f88e3831df0262503dc525be738ffbd498e988153524f0fed26ae810b9764dc3eaa83514cc627b6bf035c1baf478c76eb181c7bd781eb718 SHA512 398bc583d66e545dea4cb6194cb757acec65289c6e55099a24f3c51cf3cd3a5d9c1e505fd277612f50fe772c25d7e77ca99f11ecaf8de375db1dbe897be03c52
+EBUILD maqview-0.2.5-r5.ebuild 639 BLAKE2B 9260a2b388ff95f7ffe16b27d157373186efd497909d58fbf2aa9f459e9de7c69450679b225e0276666fd44ff4a522a38d2208c2d3605d922878668b47d5ceba SHA512 74da5046442b3bf9ec58c08a75ffdec93907739deb49647acf0ea49edb8a7998c3556a7b311c41f17d1302f59e474ffa9fc96375713002a0b5d95ce465bd0858
 MISC metadata.xml 345 BLAKE2B 3f590b0bf8c9f9fa9470f6b8ed3b20643c84fc92839740e6aebe720edd0a6e0b8bb5d2b74d4dcd8cf80a89c2769308b89e21f2f386a62fc28686f883eff56bbf SHA512 244600e6c19400a837eb859a09582fa78a670d81a58e6a461689d2695273b450df999334ffc44eecdfbed9232784af84e7cdcabe7ee045ae51a24509f2aabdcc
diff --git a/sci-biology/maqview/files/maqview-0.2.5-gcc14-build-fix.patch b/sci-biology/maqview/files/maqview-0.2.5-gcc14-build-fix.patch
new file mode 100644
index 000000000000..8f973f38a272
--- /dev/null
+++ b/sci-biology/maqview/files/maqview-0.2.5-gcc14-build-fix.patch
@@ -0,0 +1,12 @@
+Bug: https://bugs.gentoo.org/930767
+--- a/socket_view.c
++++ b/socket_view.c
+@@ -267,7 +267,7 @@ int service_core(ViewServer *server, int sock){
+ 
+ int runViewServer(ViewServer *server){
+ 	int i, sock, state;
+-	size_t size;
++	socklen_t size;
+ 	fd_set active_fd_set, read_fd_set;
+ 	struct timeval timeout;
+ 	struct sockaddr_in clientname;
diff --git a/sci-biology/maqview/maqview-0.2.5-r4.ebuild b/sci-biology/maqview/maqview-0.2.5-r5.ebuild
index 80cf5c0f9410..479d0c01af91 100644
--- a/sci-biology/maqview/maqview-0.2.5-r4.ebuild
+++ b/sci-biology/maqview/maqview-0.2.5-r5.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
@@ -6,7 +6,7 @@ EAPI=8
 inherit autotools
 
 DESCRIPTION="GUI for sci-biology/maq, a short read mapping assembler"
-HOMEPAGE="http://maq.sourceforge.net/"
+HOMEPAGE="https://maq.sourceforge.net/"
 SRC_URI="mirror://sourceforge/maq/${P}.tar.gz"
 S="${WORKDIR}/${PN}"
 
@@ -24,6 +24,7 @@ PATCHES=(
 	"${FILESDIR}"/${PV}-ldflags.patch
 	"${FILESDIR}"/${PV}-zlib.patch
 	"${FILESDIR}"/${P}-gcc4.7.patch
+	"${FILESDIR}"/${P}-gcc14-build-fix.patch
 )
 
 src_prepare() {