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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-11-16 16:25:57 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-11-16 16:25:57 +0100 |
| commit | 269f8ec2296020516eed5b613c332d752349ef8f (patch) | |
| tree | 9578022e5248e37c6963c0df222ef0d61b21dc5b /sci-biology/lastz | |
| parent | sci-biology/gbench: add missing SLOT (diff) | |
| download | sci-269f8ec2296020516eed5b613c332d752349ef8f.tar.gz sci-269f8ec2296020516eed5b613c332d752349ef8f.tar.bz2 sci-269f8ec2296020516eed5b613c332d752349ef8f.zip | |
sci-biology/lastz: fix long-lasting ebuild errors and version bump
Seems Gentoo newer compiled/installed the lastz_32 binary, which allows
indexing larger genomes. This ebuild fixes that for current version
and contains practically same Makefile-related patch as before.
Package-Manager: Portage-2.3.13, Repoman-2.3.3
Diffstat (limited to 'sci-biology/lastz')
| -rw-r--r-- | sci-biology/lastz/Manifest | 2 | ||||
| -rw-r--r-- | sci-biology/lastz/files/lastz-1.04.00-build.patch (renamed from sci-biology/lastz/files/lastz-1.03.66-build.patch) | 22 | ||||
| -rw-r--r-- | sci-biology/lastz/lastz-1.04.00.ebuild (renamed from sci-biology/lastz/lastz-1.03.66.ebuild) | 11 |
3 files changed, 27 insertions, 8 deletions
diff --git a/sci-biology/lastz/Manifest b/sci-biology/lastz/Manifest index b8f2a76b1..1b4cc1eff 100644 --- a/sci-biology/lastz/Manifest +++ b/sci-biology/lastz/Manifest @@ -1 +1 @@ -DIST lastz-1.03.66.tar.gz 727104 SHA256 8eb2db3fcf235065a099536f3a41323df25c6643d30b0db3a79f4b2f7430a5d0 SHA512 904c91b4f36ff94805096bd52fe3790801199739a43e5b14d06ceda06b4d38cde8f202b3492245ff5f1efc4d9070f6807fe1e19db802759fe1f23f45133e314d WHIRLPOOL 0440fd08a0a7620e094e68cff746bcbd95f0a6cf31526728f9ad2dd2697cc22ba2fda99865d83504b206d1ca986b2003b614408c0a9275889119804c702885c6 +DIST lastz-1.04.00.tar.gz 734145 SHA256 dd2e417c088a794532125d4c3e83a2c4ce39e6d287ed69312fb8c665f885ed52 SHA512 fa027141d8c797e9c425755b928bd40616ea193bfbd99ebbabc7bc44042edb894eafc493e9953a48cda94702109a9ec295d12c334f3db225e9880d51488e7972 WHIRLPOOL 8b4ef3bd3c9cdd4d3fdffc294d232a93b33399bd46b62f58136319e40c65220329f891b975fa317c56932b779737e4e4ea4eb317d52be8b9ef438db74db754c4 diff --git a/sci-biology/lastz/files/lastz-1.03.66-build.patch b/sci-biology/lastz/files/lastz-1.04.00-build.patch index 0b9a948d3..d3705c514 100644 --- a/sci-biology/lastz/files/lastz-1.03.66-build.patch +++ b/sci-biology/lastz/files/lastz-1.04.00-build.patch @@ -1,5 +1,5 @@ ---- src/Makefile.old 2015-05-02 15:07:56.169136255 +0200 -+++ src/Makefile 2015-05-02 15:10:02.249137955 +0200 +--- lastz-distrib-1.04.00/src/Makefile.ori 2017-11-16 16:09:47.232140878 +0100 ++++ lastz-distrib-1.04.00/src/Makefile 2017-11-16 16:14:12.589271305 +0100 @@ -1,7 +1,7 @@ include ../make-include.mak include version.mak @@ -9,16 +9,28 @@ # default targets -@@ -71,7 +71,7 @@ - -DSUBVERSION_REV="\"${SUBVERSION_REV}"\" +@@ -54,7 +54,8 @@ + # + #--------- + +-definedForAll = -Wall -Wextra -Werror -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE ++mycflags = -O3 -Wall -Wextra -Werror ++definedForAll = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE + flagsFor32 = -Dmax_sequence_index=32 -Dmax_malloc_index=40 -Ddiag_hash_size=4194304 + allowBackToBackGaps ?= 0 # by default allowBackToBackGaps +@@ -70,8 +71,8 @@ + -DREVISION_DATE="\"${REVISION_DATE}"\" \ + -DSUBVERSION_REV="\"${SUBVERSION_REV}"\" +- -CFLAGS = -O3 ${definedForAll} ${VERSION_FLAGS} ++CFLAGS ?= ${mycflags} +CFLAGS += ${definedForAll} ${VERSION_FLAGS} srcFiles = lastz infer_scores \ -@@ -101,13 +101,13 @@ +@@ -101,13 +102,13 @@ lastz: $(foreach part,${srcFiles},${part}.o) diff --git a/sci-biology/lastz/lastz-1.03.66.ebuild b/sci-biology/lastz/lastz-1.04.00.ebuild index bc6925199..6acd3d39c 100644 --- a/sci-biology/lastz/lastz-1.03.66.ebuild +++ b/sci-biology/lastz/lastz-1.04.00.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -25,8 +25,15 @@ src_prepare() { tc-export CC } +src_compile(){ + emake + emake lastz_32 +} + src_install(){ - dobin src/lastz src/lastz_D + emake install + emake install_32 + dobin src/lastz src/lastz_D src/lastz_32 dodoc README.lastz.html dohtml lav_format.html } |