[gentoo-commits] repo/gentoo:master commit in: sci-biology/mcl/, sci-biology/mcl/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/mcl/, sci-biology/mcl/files/

[David Seifert]

commit:     4129eb414e8ac4027b2e7c4b9445aa8075fd8dea
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 21 13:49:32 2020 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 21 13:49:32 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4129eb41

sci-biology/mcl: Fix building against GCC 10

Closes: https://bugs.gentoo.org/706530
Package-Manager: Portage-2.3.101, Repoman-2.3.22
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 ...ons.patch => mcl-14.137-fix-declarations.patch} | 34 +++++++++++++++++++---
 sci-biology/mcl/mcl-14.137.ebuild                  |  2 +-
 2 files changed, 31 insertions(+), 5 deletions(-)

diff --git a/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch b/sci-biology/mcl/files/mcl-14.137-fix-declarations.patch
similarity index 51%
rename from sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch
rename to sci-biology/mcl/files/mcl-14.137-fix-declarations.patch
index df4309874d4..4974d352bf7 100644
--- a/sci-biology/mcl/files/mcl-14.137-qa-implicit-declarations.patch
+++ b/sci-biology/mcl/files/mcl-14.137-fix-declarations.patch
@@ -5,8 +5,34 @@ Fix QA issues related to implicit declarations.
 * clmadjust.c:184:10: warning: implicit declaration of function ‘mcxFree’ [-Wimplicit-function-declaration]
 * mcxi.c:42:16: warning: implicit declaration of function ‘isatty’ [-Wimplicit-function-declaration]
 
---- mcl-14-137/src/shcl/clmadjust.c
-+++ mcl-14-137/src/shcl/clmadjust.c
+--- a/src/impala/iface.h
++++ b/src/impala/iface.h
+@@ -16,15 +16,15 @@
+ 
+ /* This file currently provides nothing */
+ 
+-dim nu_meet_can  ;
+-dim nu_meet_sl   ;
+-dim nu_meet_zip  ;
+-dim nu_diff_can  ;
+-dim nu_diff_sl   ;
+-dim nu_diff_zip  ;
+-double nu_magic  ;
++extern dim nu_meet_can  ;
++extern dim nu_meet_sl   ;
++extern dim nu_meet_zip  ;
++extern dim nu_diff_can  ;
++extern dim nu_diff_sl   ;
++extern dim nu_diff_zip  ;
++extern double nu_magic  ;
+ 
+-dim mclx_n_thread_g  ;
++extern dim mclx_n_thread_g  ;
+ 
+ #endif
+ 
+--- a/src/shcl/clmadjust.c
++++ b/src/shcl/clmadjust.c
 @@ -14,6 +14,7 @@
  #include "report.h"
  #include "clmadjust.h"
@@ -15,8 +41,8 @@ Fix QA issues related to implicit declarations.
  #include "util/io.h"
  #include "util/types.h"
  #include "util/err.h"
---- mcl-14-137/src/shmcx/mcxi.c
-+++ mcl-14-137/src/shmcx/mcxi.c
+--- a/src/shmcx/mcxi.c
++++ b/src/shmcx/mcxi.c
 @@ -8,6 +8,7 @@
  */
  

diff --git a/sci-biology/mcl/mcl-14.137.ebuild b/sci-biology/mcl/mcl-14.137.ebuild
index 40c96e8a4b1..e7924bccec3 100644
--- a/sci-biology/mcl/mcl-14.137.ebuild
+++ b/sci-biology/mcl/mcl-14.137.ebuild
@@ -19,7 +19,7 @@ IUSE="+blast"
 S="${WORKDIR}/${MY_P}"
 
 PATCHES=(
-	"${FILESDIR}"/${P}-qa-implicit-declarations.patch
+	"${FILESDIR}"/${P}-fix-declarations.patch
 	"${FILESDIR}"/${P}-fix-autotools.patch
 )
 

[gentoo-commits] repo/gentoo:master commit in: sci-biology/mcl/, sci-biology/mcl/files/

[David Seifert]

commit:     e551399e2f1a78e5037eb8930c0a53e11d97618c
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 21 13:49:29 2020 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 21 13:49:29 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e551399e

sci-biology/mcl: [QA] Call AM_PROG_AR

Closes: https://bugs.gentoo.org/725326
Package-Manager: Portage-2.3.101, Repoman-2.3.22
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 .../mcl/files/mcl-14.137-fix-autotools.patch       | 52 ++++++++++++++++++++++
 sci-biology/mcl/mcl-14.137.ebuild                  | 16 +++----
 2 files changed, 59 insertions(+), 9 deletions(-)

diff --git a/sci-biology/mcl/files/mcl-14.137-fix-autotools.patch b/sci-biology/mcl/files/mcl-14.137-fix-autotools.patch
new file mode 100644
index 00000000000..0d2c052a91b
--- /dev/null
+++ b/sci-biology/mcl/files/mcl-14.137-fix-autotools.patch
@@ -0,0 +1,52 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -144,6 +144,7 @@
+ AC_PROG_INSTALL
+ AC_PROG_LN_S
+ AC_PROG_RANLIB
++AM_PROG_AR
+ 
+ # Checks for libraries.
+ # FIXME: Replace `main' with a function in `-lm':
+--- a/doc/Makefile.am
++++ b/doc/Makefile.am
+@@ -9,7 +9,6 @@
+ ## http://www.w3.org/People/Raggett/tidy/ , by Dave Raggett <dsr@w3.org>
+ TIDY = tidy
+ 
+-docdir = $(datadir)/doc/$(PACKAGE)
+ 
+ # mclfamily.html mclfamily.ps
+ 
+--- a/graphs/Makefile.am
++++ b/graphs/Makefile.am
+@@ -1,7 +1,7 @@
+ ## Process this file with automake to produce Makefile.in
+ ## $Id: Makefile.am,v 1.7 2007-01-29 11:35:37 flux Exp $
+ 
+-exampledir = $(datadir)/doc/$(PACKAGE)/examples
++exampledir = $(docdir)/examples
+ 
+ example_DATA = falkner.mci falkner2.mci falkner.coords make-falkner.pl \
+    proteins.mci matula.mci lattice.mci honey.mci seven.mci infinity.mci \
+--- a/img/Makefile.am
++++ b/img/Makefile.am
+@@ -1,7 +1,7 @@
+ ## Process this file with automake to produce Makefile.in
+ ## $Id: Makefile.am,v 1.7 2007-01-29 11:35:37 flux Exp $
+ 
+-exampledir = $(datadir)/doc/$(PACKAGE)/examples
++exampledir = $(docdir)/examples
+ 
+ example_DATA = fa_1024.png fa_400.png fa_600.png fa_large.png fa.ps falkner-bidi.ps falkner.ps small.ps small.png
+ 
+--- a/src/alien/oxygen/doc/Makefile.am
++++ b/src/alien/oxygen/doc/Makefile.am
+@@ -17,7 +17,6 @@
+ ## http://www.w3.org/People/Raggett/tidy/ , by Dave Raggett <dsr@w3.org>
+ TIDY = tidy
+ 
+-docdir = $(datadir)/doc/$(PACKAGE)
+ 
+ ## zoemtut.html is "on hold": do not install; zoem is not yet ready
+ ## for prime time

diff --git a/sci-biology/mcl/mcl-14.137.ebuild b/sci-biology/mcl/mcl-14.137.ebuild
index e48198deca2..40c96e8a4b1 100644
--- a/sci-biology/mcl/mcl-14.137.ebuild
+++ b/sci-biology/mcl/mcl-14.137.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit autotools
 
@@ -16,16 +16,14 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="+blast"
 
-PATCHES=("${FILESDIR}/${P}-qa-implicit-declarations.patch")
 S="${WORKDIR}/${MY_P}"
 
+PATCHES=(
+	"${FILESDIR}"/${P}-qa-implicit-declarations.patch
+	"${FILESDIR}"/${P}-fix-autotools.patch
+)
+
 src_prepare() {
-	find \
-		-name Makefile.am \
-		-exec sed \
-			-e '/docdir/d' \
-			-e '/exampledir/s:doc::g' \
-			-i '{}' + || die
 	default
 	eautoreconf
 }