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authorV3n3RiX <venerix@koprulu.sector>2024-03-08 13:07:48 +0000
committerV3n3RiX <venerix@koprulu.sector>2024-03-08 13:07:48 +0000
commit7825305c5ddf11fffe24fa30453c4e8468f64305 (patch)
treef3c43caefa7210acc3d8fd79ac82f8ade47a8dc9 /sci-biology
parentdc22a05dc2db2827053483e8cab136b33b339307 (diff)
gentoo auto-resync : 08:03:2024 - 13:07:48
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/Manifest.gzbin19317 -> 19323 bytes
-rw-r--r--sci-biology/abyss/Manifest2
-rw-r--r--sci-biology/abyss/abyss-2.3.4.ebuild10
3 files changed, 8 insertions, 4 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 9dd890d7398e..e479838ad584 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
Binary files differ
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
index 2938800747b8..72af9963d941 100644
--- a/sci-biology/abyss/Manifest
+++ b/sci-biology/abyss/Manifest
@@ -1,3 +1,3 @@
DIST abyss-2.3.4.tar.gz 3511137 BLAKE2B 2b7449233055d22330f44951f9f6d5ff1a116fa3e19c09c17cd4fa517d2fc055c4f00ccb82c7e09b1b939ac6f7a1caf73cf73c33bd3c8aa9ff11879c227a2aaa SHA512 9d4e418399dd62883b53e831f51a0bd2ba228da73eda6c6459cd729c002eb0487f9613fca1c9bd0f4fbb076eed8a9b952505ee97143ab7dde537c23e4a246cd4
-EBUILD abyss-2.3.4.ebuild 1269 BLAKE2B bf4a1edb477650f3d6650c7ae1cfb0d37132215bf8bb4c395a702c506a0d648386168731ad329875380fd46f1a3ccbe673d3211d1ee854538bbe28dbeb49ecb5 SHA512 26a5fec0fbed0c0fdb0f328b993553ec1ceb7632d2d9ad18736f3099df542a88da0d1996c444d3fdbfe59d1dda55161e7de8ea121a22a1bb80c507656999d39c
+EBUILD abyss-2.3.4.ebuild 1351 BLAKE2B dec0e08aa8a05f0561ff84b6e0875b82bd59784631e2f4b6012e67f57ddc7c4f6891fb72707ff20d6908672a76b1eeb296d3185950f7f4fdf95295d97a04cff3 SHA512 9ac5c0829c67e674ac23a70514a5c51576dff5018d54a53e6056826aacd718095c7fd03dbc33c0ad96a22c785c2a4ebaa2b6eff3309c01691331ff0a05007de6
MISC metadata.xml 443 BLAKE2B 5507d404ef996facd3cc1a70253dc2e692bf371d5d47ab5abccb65d6cae5dd1e30432177e709ec370e13f90e760a5628816878c4317053f76b9084ad24a71094 SHA512 3b5b3e543775d0909e107483af930aeb82a255214f5bcfb791f29e6e6835658915be79496c5dffd2eda98219b4d00a2fe287affcf938078ff91f1c84908b0531
diff --git a/sci-biology/abyss/abyss-2.3.4.ebuild b/sci-biology/abyss/abyss-2.3.4.ebuild
index c2e1ffd29b32..2c2c14d35bd5 100644
--- a/sci-biology/abyss/abyss-2.3.4.ebuild
+++ b/sci-biology/abyss/abyss-2.3.4.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-inherit autotools toolchain-funcs
+inherit autotools flag-o-matic toolchain-funcs
DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
HOMEPAGE="https://www.bcgsc.ca/resources/software/abyss/"
@@ -44,11 +44,15 @@ pkg_setup() {
src_prepare() {
default
sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
eautoreconf
}
src_configure() {
+ # -Werror=lto-type-mismatch
+ # https://bugs.gentoo.org/862252
+ # https://github.com/bcgsc/abyss/issues/474
+ filter-lto
+
# disable building haskell tool Misc/samtobreak
# unless request by user: bug #534412
use misc-haskell || export ac_cv_prog_ac_ct_GHC=