gentoo resync : 29.06.2020

4 files changed, 92 insertions, 15 deletions

diff --git a/sci-biology/mcl/Manifest b/sci-biology/mcl/Manifest
index 8bef0282bc82..39003fd43076 100644
--- a/sci-biology/mcl/Manifest
+++ b/sci-biology/mcl/Manifest
@@ -1,4 +1,5 @@
-AUX mcl-14.137-qa-implicit-declarations.patch 786 BLAKE2B c7a5ed8f32dd3542766beaed19c9236a137444fdf69252becedfcc2d97136b0eba276355d2b24a38a06e0f78e6eaeb813bdc713cb01161167d4a2c65425e3c03 SHA512 e1388441e06075e951a1ff9994a8e9fe1083042c09e072c68e9abb20dc4a83498eb4cb71aa71d738268a50a0e03ee8e7976df9bbb304b8c90314d682bb8625d3
+AUX mcl-14.137-fix-autotools.patch 1524 BLAKE2B baad5d167379b8f38543159d88f66367bc625e53f457a59dfbbddadd998423d924afdff6d826c6c35004e1f4a83bbbb464d3bfe367f3257adcd6fad5cd2d5aad SHA512 bb7384d8f5a819fa1e0af7bdc5b7ef157f76c1ddb3bcc5d9bca06347b5bd86d977d9580e99161e173fef8aee288ec1075d19ab9878782fa1d97eca50bae099de
+AUX mcl-14.137-fix-declarations.patch 1266 BLAKE2B 2df8acbe98dfbf804b81950e1d60963fea49aeff0b8bce52c75bb757d72cb16adbf13b8567acb8b63ab76af63da3086fdedf25d363f2986881bb70e2b27630b9 SHA512 cce0825fe7d01a3f6c69bf1d1fcac1277b3beef6cca0f3ee729d2c4f60f57ef2a9223b7f3a8f63743011751790c625ec3601cc46fddde236eef37cbce982a9d6
 DIST mcl-14-137.tar.gz 3035491 BLAKE2B d6b975841a9094055306056ae0cd646cc92af69018893981d32b0604a583f61d3764bc67c1e21a0861b89a17013c01bcd4c1d7cbb4e0c5856403c2a767121423 SHA512 7e399e571de60da5e1ba9e643b7f0cd98fe484cc8cef517222a57322b5c7a04afa675c7cf0ab88b5801efa9565e5e67a14c4914987964308391d88dd4be1bea2
-EBUILD mcl-14.137.ebuild 651 BLAKE2B 73ba9d5ac8159a10ced22a9a39e0d5c1c4943fe5cc4ad1e823592e6362ef1f9bd3f850173a6e2c91d43bcfb825d3fd4de91dad469b27e58bd2a43c036889415f SHA512 042277297965d4796d0805dad2a951e8bd467630c7904fe1a5211616fc2a620c041ea6093bbaf10e6fed17037bccd7013afcfb0260e69c09bd1cdc3ca2f76f53
+EBUILD mcl-14.137.ebuild 569 BLAKE2B 0fae322e4911c52407d9b053dfcb1d08dc19624c1b32e68800135338b44e16d82eee4f77f1b11b88f002c5739b2f01c356d21154c48fe305800b88d802febaa0 SHA512 1be49c6038260326f6fe64bf0afba78258d355e8e74f3f3cfc30dd1f0de2971159ac3fb969b09710df8eeb28fa559135516189d9e56544287fd2089a572b68e3
 MISC metadata.xml 336 BLAKE2B 077cf6e56ca5ba6480b00411536b1814f73b8dc93faf9337e0e81f3c47f174172894487ef072637dd396f39a95cd3a6538c2fd3e62328c3659882629c9b96dff SHA512 41ed664e2fdc26c5984fb55d90365cb02fe0de893d74e74935d2a9f6eb17e2e56a33210ed7d03c28375fb27ebbae3dca472de79a2e387ecf769a604aea629da3
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 000000000000..0d2c052a91b0
--- /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/files/mcl-14.137-qa-implicit-declarations.patch b/sci-biology/mcl/files/mcl-14.137-fix-declarations.patch
index df4309874d48..4974d352bf7b 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 e48198deca29..e7924bccec30 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}-fix-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
 }