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authorV3n3RiX <venerix@redcorelinux.org>2021-06-15 14:57:03 +0100
committerV3n3RiX <venerix@redcorelinux.org>2021-06-15 14:57:03 +0100
commitd18bf1e01b65ee4bf0c804e2843b282d3d4e5d7c (patch)
tree4a95cbc6ffdf13bad6ecbc7f8d5af99631984123 /sci-biology
parente748ba9741f6540f4675c23e3e37b73e822c13a4 (diff)
gentoo resync : 15.06.2021
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/GBrowse/GBrowse-2.48-r1.ebuild4
-rw-r--r--sci-biology/GBrowse/Manifest2
-rw-r--r--sci-biology/Manifest.gzbin22133 -> 22137 bytes
-rw-r--r--sci-biology/amap/Manifest2
-rw-r--r--sci-biology/amap/amap-2.2-r4.ebuild (renamed from sci-biology/amap/amap-2.2-r3.ebuild)8
-rw-r--r--sci-biology/bioperl-run/Manifest2
-rw-r--r--sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild4
-rw-r--r--sci-biology/uchime/Manifest2
-rw-r--r--sci-biology/uchime/uchime-4.2.40.ebuild11
-rw-r--r--sci-biology/ucsc-genome-browser/Manifest2
-rw-r--r--sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild10
11 files changed, 28 insertions, 19 deletions
diff --git a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild
index 739950568156..2fcef3b41aff 100644
--- a/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild
+++ b/sci-biology/GBrowse/GBrowse-2.48-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -9,7 +9,7 @@ inherit perl-module webapp
DESCRIPTION="Generic Model Organism Database Project - The Generic Genome Browser"
HOMEPAGE="http://gmod.org/wiki/GBrowse"
KEYWORDS="~amd64 ~x86"
-IUSE="-minimal mysql postgres +sqlite"
+IUSE="minimal mysql postgres +sqlite"
SLOT="0"
WEBAPP_MANUAL_SLOT="yes"
diff --git a/sci-biology/GBrowse/Manifest b/sci-biology/GBrowse/Manifest
index d37bda834922..e92d62a928d6 100644
--- a/sci-biology/GBrowse/Manifest
+++ b/sci-biology/GBrowse/Manifest
@@ -1,4 +1,4 @@
AUX GBrowseInstall.pm-2.39.patch 2878 BLAKE2B 99ca47ef69aad80322bcc2f0a856a2e0e8d2185189172c842f3bfdc9efbda383f8d00ca5e6a829dbb48f1f668047ec4e66ac83cef433347453a91ee557820c1a SHA512 637dea799290213def1368cdb153463c96964ada99fd6c09d0b95e0d1e42a16942d66ef36282d39b92284ae6eb26c8346d5ad1289b5ec7b2196a1ba5090db85e
DIST GBrowse-2.48.tar.gz 11958127 BLAKE2B e9527eb47302775d62e37990c42154b677284fff0f0f9624e9173e30e46c5aebbc8a02ee8dec0a1e98761812ef2363e0183008087bce4d283528b7935b4d5f91 SHA512 d5a07caf1517fb15741e8e6056669763eb04678a42637a9e90788c91e74fb34515b5f86aac10a00f29d8848aceb19d6f5f7258d2dda0e281feee550e9e2fb3db
-EBUILD GBrowse-2.48-r1.ebuild 1863 BLAKE2B fdeef1bc80dba3fd92568d59886341d1ce768b7a794cf0018388c5cf547f1f78818317f4e18f54fda3d0778d7e334d2b36bce516d4342dbe7cd74c447d0db39a SHA512 5ca80f79071c4312c0f79ef05855d5928b47973a068bcf573296c97367f79091fc686dfa474795c2ec7b89573333de91b63b0d51d316cbcfc24a618f16dc5cd8
+EBUILD GBrowse-2.48-r1.ebuild 1859 BLAKE2B c738aeb5114fc688fea7b2277332530452489c02309926a1acd7a5cde1225577a6c07e432f8aac8515c4d16c97962fbc0833807134292edfc0e3e4b4a768798e SHA512 e763f68e6c3d0d76284a68f918e39c00dfff5be6110852d6f9dde74072d8c1e686157a517c0a15a948bce679a77792d175acf1be1a93326c0e541f544e30086a
MISC metadata.xml 327 BLAKE2B e8a0d72f6cbb085df2578e6bf4a5cafd9306643487adac84a1e60f135977df472ec0fcc5816a2002f2fe2764b919f7e4a838463ae16460e0e0b5710ca9ce5c73 SHA512 12bed277a17513c5e45f782c500c6aa4cbaad988ffb902220dbacde7e908246a62663b976a822c63a5446306ad705ad27c504713dd61e7cf90dd23ce37d98e48
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index c80b291004a6..5f89a213cf0b 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
Binary files differ
diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest
index d76312d85849..eb89d028a7b0 100644
--- a/sci-biology/amap/Manifest
+++ b/sci-biology/amap/Manifest
@@ -1,5 +1,5 @@
AUX amap-2.2-includes.patch 1088 BLAKE2B 3b870c229f3efb9819d9f176b59b014ad4bae3034ed4fe9f8c8474ebf8ce7c8373efef66c3c61c8f6fe04a645243f09639aa4a4c95ee75f692e504f4478fcf77 SHA512 e9c2ae7ea75f059b816a8562c9ac79e343d73b9a3d63ac1182fe41b3634bf0b949738a4bdd90c09f61bb4505a721e2faa98334b81ad17c0d7360a2e3f37f9044
AUX amap-2.2-makefile.patch 1201 BLAKE2B e404de0909f501dbf5005d6c995fbb6ecf588fe06798483703c25d29c070faa6ce5eb06e98e35b8deeeddbeb309eb6560d13af6a0fa64ec9435d00e41f2bfad2 SHA512 8cd43b70299e12f32dd6b46a73e6ef10c7e85b5ec6d152aef69f54954a1083c92570c40bf35ea363084a3626161c3e28d214bb2c5fb76bb396d9be2edaa869a3
DIST amap.2.2.tar.gz 102861 BLAKE2B 7f9b1cb747946232db0b5b469896cc4f83ef78d190e929e28f37df790dfac342e6e7f913797bc9ff00191253318db2d42f79577dc72128d62a21d0e241bfb0e1 SHA512 a297b6eb1b52d5deab65db5bb1344b06a85c7ef6fa4b550798501041091357e605543eaadd85c053a74e857ebdd7b846dca4b226c5c61bedc329bf93c886c18f
-EBUILD amap-2.2-r3.ebuild 1135 BLAKE2B bc214283c42ef027c605c678ef08b5b385cbcc9763580c6dc54f3c2a9ad44bb8005681b28b6a4036400ced23bb61b9766a467b8892df457590bee45f652e51bd SHA512 d5bbb29ad83fd210b3ba7f84884f4bb517d132fbdaa58b658c679cccd96f1219f9fe3d6f8f58a029a10c782e916f441a9e8de969390c168c0202fb230fdb21a1
+EBUILD amap-2.2-r4.ebuild 1142 BLAKE2B c4bf57de7f838559bb4fc5c1b6358802fb54dd2a1d5ef401218ce4c2efaf829f8a0c05a45333b81747539d286bb2e5d0233ea19177aa7ef59b691581c27f3ad9 SHA512 22230076080ef49996c9cc8adea62b488a877f95832d88f53094b71ba868b33c5bc5bee170a444f4a4a928e152b1fa8f348fecfbc37600f02db4a79bc4722e8f
MISC metadata.xml 257 BLAKE2B c0d9bf845137c20d86333bbe5f6f7d27e5ae2edbdd6997f870a6678825b5494b8160a4dc5fba6221f252e1146c57d3237f3d7feb098a9beed9c272f57f30d708 SHA512 5be44a06c71b100dfe66effc1d12a9801f6daf2e252f74b6499528644db9b3dd00d51827a984817b78755e8d544f9c674c27c6a370c4c4414ce26a09b478b69b
diff --git a/sci-biology/amap/amap-2.2-r3.ebuild b/sci-biology/amap/amap-2.2-r4.ebuild
index 7776e25bc56e..df3b16efba30 100644
--- a/sci-biology/amap/amap-2.2-r3.ebuild
+++ b/sci-biology/amap/amap-2.2-r4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -8,7 +8,7 @@ inherit java-pkg-opt-2 java-ant-2 toolchain-funcs
MY_P=${PN}.${PV}
DESCRIPTION="Protein multiple-alignment-based sequence annealing"
-HOMEPAGE="http://bio.math.berkeley.edu/amap/"
+HOMEPAGE="https://wiki.gentoo.org/wiki/No_homepage"
SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz"
LICENSE="GPL-2"
@@ -16,8 +16,8 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="java"
-RDEPEND="java? ( >=virtual/jre-1.5 )"
-DEPEND="java? ( >=virtual/jdk-1.5 )"
+RDEPEND="java? ( >=virtual/jre-1.8:* )"
+DEPEND="java? ( >=virtual/jdk-1.8:* )"
S=${WORKDIR}/${PN}-align
diff --git a/sci-biology/bioperl-run/Manifest b/sci-biology/bioperl-run/Manifest
index 3807c07be987..2e4b7b17ab01 100644
--- a/sci-biology/bioperl-run/Manifest
+++ b/sci-biology/bioperl-run/Manifest
@@ -1,3 +1,3 @@
DIST BioPerl-Run-1.006900.tar.gz 14546677 BLAKE2B 9faf58796b9874b19b66e74abc51ed1d1b6e2928bcf9904506b2af6b2b7c1772a90eab24bf0e7c050fd4a2b120ba506ad5edb8a693496b7468fe7c8d05d11f0a SHA512 47f2b853885c604291ac0aba3269b897de59cf7da6f7d54a50ff950cca836338091309df550f32695159c620be23391306d0421d2bbc22eebbb61a9e280ad83c
-EBUILD bioperl-run-1.6.9.ebuild 931 BLAKE2B e956a7d12719560e9b4cc33800f8a53d8c590d739ecf694f8fd334ced2b01a6fc81fcbcaad61cf5c69f9ede5a02afd2dcfe1051cc99f7fbf93466bf427bf00a0 SHA512 b512b3fc62208ab6ef1c6f160d43c5e9b8a3f03131398144ec4e4e1ddb1973f45b121220e71724a0c621ff58ea33b5f639cd23dedd62e033f3e78118dde2e94e
+EBUILD bioperl-run-1.6.9.ebuild 927 BLAKE2B 035f172e5ee9d617bb5eb0b522d17f07624be54773c58b21b5435835ebc3cde67028ef7cc3254cec5f257b67256d10bd19c2f1d390b26e73cc877971320b3116 SHA512 798dfb678a67013499b317281bbe8b0f6012fa2daabb5f77223e1839f1dc2b926c866e39164de745855577adea46f972a25726b8fcc8bcfe969c44634c38455b
MISC metadata.xml 345 BLAKE2B 91a15324464d913875ad2c449052e2f26d7c48cac90e9e36a66d91ff43d02e424841b8758121ec06625402dbadbfd4455e7e39a17009832fc4b2655d381379ae SHA512 23370e5fb887d48f37f6ef1d3fa45092fb3b45e111f82488153ce5235bdd7671bed559093927ad92e3c7876f390e385d032fbf9e76a55cb00a0da7fa80bea2ad
diff --git a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
index e5dc816bc78a..461c4f51b071 100644
--- a/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
+++ b/sci-biology/bioperl-run/bioperl-run-1.6.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI="5"
@@ -15,7 +15,7 @@ HOMEPAGE="http://www.bioperl.org/"
SLOT="0"
KEYWORDS="amd64 x86"
-IUSE="-minimal test"
+IUSE="minimal test"
#SRC_TEST="do"
RESTRICT="test"
diff --git a/sci-biology/uchime/Manifest b/sci-biology/uchime/Manifest
index b64b2369ba21..b9dfe31e446b 100644
--- a/sci-biology/uchime/Manifest
+++ b/sci-biology/uchime/Manifest
@@ -1,4 +1,4 @@
AUX CMakeLists.txt 589 BLAKE2B 183caf5f107482c410296eee8136271e261696a3c11255960b840bd4db16cf461c386fa7374b3a2afb3fd38e97593ad98f9efc621104106cfe4463939c6d0d31 SHA512 06e9f9c8806c27b268968b28fb6059fc6d52295a5d38635612728ac577656fcfae5eb6b15c63e3e9de57e1c8cac832cd4dff70d8a6f3182358a5eb06eb354642
DIST uchime4.2.40_src.tar.gz 66772 BLAKE2B 9133853d616ab6e1e6a397da78fc846ba00fc70c2c375eb16a98fbdec25ba6034bd1c876b7ec4a99305e76e47cf7984c1aa30b64bdc96e125f661a0150bae060 SHA512 c3afecb23d164d9c3db6229f54faa13120ac4d88132d9aef707f8d043091099db4205ac80f60242920af6efc23813b3e7e4966d562bdb75ff53244fd525e656b
-EBUILD uchime-4.2.40.ebuild 513 BLAKE2B 85980c9a60fbfd3d155e371b9638606bc4a0e54ca670a12e5f0f8bfa647c6d27b27879aaa1d5c7f724c2f0135d384b54fa61ab334c9a6382140004261334b7e1 SHA512 0c1a1f0f78d1b8da99153a601f5012ae7b74d05a672dc649cdcdfe62b4231474801165bdb70b4be17182ff8da0c77395638e465997715d94fbdd7b745a942210
+EBUILD uchime-4.2.40.ebuild 654 BLAKE2B d9ddacb096c43c43858f4b4f572304543c7f5ae059fe9c4a8696d1debcd3304af88f360f312fd470ee9f3c733460840537835dfa67a446a18e4bdab6b460a278 SHA512 a7274df383897140b4db99610a2f0fea6b5364799f32b660b78c2e8ef6d9f59b8e629e331629b3b5877380f0e9700967180216e7ad9235f308389c754bc083e9
MISC metadata.xml 896 BLAKE2B 1041ed416b2ba4670f85856ed2bfe1508d3bea0a310a29a9265b04372df51ee39090d76fa6a282c908e26541986bd10dd47ea73260d5180fe382fc97de556509 SHA512 641d91bff3651a49a3b7e15260cf2a758199ae49ece16643d3104f0f4e202938935edeb3bef18f7afc40a4eb1b1b3e469b07fec95d30a5e686e4b66535ff3e7e
diff --git a/sci-biology/uchime/uchime-4.2.40.ebuild b/sci-biology/uchime/uchime-4.2.40.ebuild
index 75827ab3a304..9b346f4fbc8d 100644
--- a/sci-biology/uchime/uchime-4.2.40.ebuild
+++ b/sci-biology/uchime/uchime-4.2.40.ebuild
@@ -4,7 +4,7 @@
EAPI=7
MY_P="${PN}${PV}_src"
-inherit cmake
+inherit cmake flag-o-matic
DESCRIPTION="Fast, accurate chimera detection"
HOMEPAGE="https://www.drive5.com/usearch/manual/uchime_algo.html"
@@ -13,7 +13,6 @@ SRC_URI="https://www.drive5.com/${PN}/${MY_P}.tar.gz"
LICENSE="public-domain"
SLOT="0"
KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="debug"
S="${WORKDIR}"/${MY_P}
@@ -21,3 +20,11 @@ src_prepare() {
cp "${FILESDIR}"/CMakeLists.txt . || die
cmake_src_prepare
}
+
+src_configure() {
+ # "myutils.h: error: reference to byte is ambiguous""
+ # bug #786297
+ append-cppflags -std=c++14
+
+ cmake_src_configure
+}
diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest
index eb0164497a1f..a70b216f346f 100644
--- a/sci-biology/ucsc-genome-browser/Manifest
+++ b/sci-biology/ucsc-genome-browser/Manifest
@@ -1,3 +1,3 @@
DIST jksrc.v260.zip 59090224 BLAKE2B 755bb97f50cde97e7634f38aa81f0843de52710cac78f5b0a2ee6129cffc99f730b8e1ab41d24e2faebb3c0a3e1d1309c84307e2dc4af1efe9a30fb0b9ae1670 SHA512 48aa964ab3ae456ab7e7ddc5d73b91774bd4892f21f1498578a5de38d3a07e4684778ddb1ac1ae389d5bbb3586f9b8506ca3697acca1f6777b85d343cf5d9485
-EBUILD ucsc-genome-browser-260-r1.ebuild 3024 BLAKE2B 76db4fac4462ccd1cfb3163f57ea05635e8e230f408397085c22d21697351b286b4136bf54c0d8187fd5380d4d44b08ddde31bc93eb8252dac8fddecb6f003f5 SHA512 89408eb1ee03c94f3f862f28db45c195d83a15ad40e84070e12473e1018188f3fe6f4212d4d2eb180b9a048740cec50b06ef8d0ed6c0adef301aadb6964e3b58
+EBUILD ucsc-genome-browser-260-r1.ebuild 3134 BLAKE2B f9b628c78939377f66c9aca6b68ca3cbebf7c41dde18a8d03dbc4533593069dff0381d0fe206b0287569739a96010661d275c2d43a8ffc9e1ad8f73b4d73be5e SHA512 6f33bd29ac24661d8a495913b6746d60ca4eb95e91e5ca7325420a9b430f9ca8fe990d9167ab2ffd500f151f8cce045601e1dde24efde05b185511c1b06593a7
MISC metadata.xml 435 BLAKE2B fb242aaf17920e320c65bbd8bf83c79ffc0a9e97c112e2e19f89ed9c0a3fd2e48e7444c81dd82bc30b38c1e9251737d93bea310f77ddff5a183301276588b1a3 SHA512 1acffee210c77abc41a93b5b78e52b27ed18df50a2eff3c6463e34bc031a4b2c97d1472a0dcf14bbf513c77d930a67434194c2e5ac435a5f7fd1e79294335a81
diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
index 0423f509cec9..f0bb0676ae85 100644
--- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
+++ b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild
@@ -64,14 +64,16 @@ src_compile() {
export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none"
- use mysql && export MYSQLLIBS="-L${EROOT}usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
- MYSQLINC="${ROOT}usr/include/mysql"
+ # TODO: Change ${EPREFIX} to ${ESYSROOT} in EAPI 7
+ # (and ideally use pkg-config here)
+ use mysql && export MYSQLLIBS="-L${EPREFIX%/}/usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \
+ MYSQLINC="${EPREFIX%/}/usr/include/mysql"
use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \
CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin"
- mkdir -p "$BINDIR" "$SCRIPTS" "$ENCODE_PIPELINE_BIN" || die
- use server && mkdir -p "$CGI_BIN" "$DOCUMENTROOT"
+ mkdir -p "${BINDIR}" "${SCRIPTS}" "${ENCODE_PIPELINE_BIN}" || die
+ use server && mkdir -p "${CGI_BIN}" "${DOCUMENTROOT}"
emake -C src clean
emake -C src/lib
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-29 07:26:38 +0000