[gentoo-commits] proj/sci:master commit in: sci-biology/lastz/files/, sci-biology/lastz/

[Martin Mokrejs]

commit:     269f8ec2296020516eed5b613c332d752349ef8f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 16 15:25:57 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 16 15:25:57 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=269f8ec2

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

 ...03.66-build.patch => lastz-1.04.00-build.patch} | 22 +++++++++++++++++-----
 .../{lastz-1.03.66.ebuild => lastz-1.04.00.ebuild} | 11 +++++++++--
 2 files changed, 26 insertions(+), 7 deletions(-)

diff --git a/sci-biology/lastz/files/lastz-1.03.66-build.patch b/sci-biology/lastz/files/lastz-1.04.00-build.patch
similarity index 56%
rename from sci-biology/lastz/files/lastz-1.03.66-build.patch
rename to 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
similarity index 79%
rename from sci-biology/lastz/lastz-1.03.66.ebuild
rename to 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
 }