CVS commit: pkgsrc/biology/rna-star

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Tue Aug 29 21:49:57 UTC 2023

Modified Files:
        pkgsrc/biology/rna-star: Makefile PLIST distinfo
        pkgsrc/biology/rna-star/patches: patch-Makefile patch-SharedMemory.cpp
            patch-SoloBarcode.cpp patch-SuffixArrayFuns.cpp
            patch-bamSortByCoordinate.cpp
Added Files:
        pkgsrc/biology/rna-star/patches: patch-opal_opal.cpp

Log Message:
biology/rna-star: Fix build on Darwin 21.6.0 x86

Remove extern "C" in file build with c++


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/rna-star/Makefile \
    pkgsrc/biology/rna-star/PLIST pkgsrc/biology/rna-star/distinfo
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/rna-star/patches/patch-Makefile \
    pkgsrc/biology/rna-star/patches/patch-SharedMemory.cpp \
    pkgsrc/biology/rna-star/patches/patch-SoloBarcode.cpp \
    pkgsrc/biology/rna-star/patches/patch-SuffixArrayFuns.cpp \
    pkgsrc/biology/rna-star/patches/patch-bamSortByCoordinate.cpp
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/rna-star/patches/patch-opal_opal.cpp

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/rna-star/Makefile
diff -u pkgsrc/biology/rna-star/Makefile:1.1 pkgsrc/biology/rna-star/Makefile:1.2
--- pkgsrc/biology/rna-star/Makefile:1.1        Mon Jul 31 14:34:18 2023
+++ pkgsrc/biology/rna-star/Makefile    Tue Aug 29 21:49:56 2023
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.1 2023/07/31 14:34:18 bacon Exp $
+# $NetBSD: Makefile,v 1.2 2023/08/29 21:49:56 bacon Exp $
 
 DISTNAME=      STAR-2.7.10b
 PKGNAME=       rna-star-2.7.10b
Index: pkgsrc/biology/rna-star/PLIST
diff -u pkgsrc/biology/rna-star/PLIST:1.1 pkgsrc/biology/rna-star/PLIST:1.2
--- pkgsrc/biology/rna-star/PLIST:1.1   Mon Jul 31 14:34:18 2023
+++ pkgsrc/biology/rna-star/PLIST       Tue Aug 29 21:49:56 2023
@@ -1,2 +1,2 @@
-@comment $NetBSD: PLIST,v 1.1 2023/07/31 14:34:18 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2023/08/29 21:49:56 bacon Exp $
 bin/STAR
Index: pkgsrc/biology/rna-star/distinfo
diff -u pkgsrc/biology/rna-star/distinfo:1.1 pkgsrc/biology/rna-star/distinfo:1.2
--- pkgsrc/biology/rna-star/distinfo:1.1        Mon Jul 31 14:34:18 2023
+++ pkgsrc/biology/rna-star/distinfo    Tue Aug 29 21:49:56 2023
@@ -1,4 +1,4 @@
-$NetBSD: distinfo,v 1.1 2023/07/31 14:34:18 bacon Exp $
+$NetBSD: distinfo,v 1.2 2023/08/29 21:49:56 bacon Exp $
 
 BLAKE2s (STAR-2.7.10b.tar.gz) = ae5b1c236c1b5975d60277dbd5634661a4598e6f3f906f3d6b582b403edb58d3
 SHA512 (STAR-2.7.10b.tar.gz) = c4e94fd19f2a8145c38d59b39d91af16b53af63da2d77275445b9aeadfd287e3d2749829352a034e45e4352c64884275fa5b7b2ed28b95bf47cac3183b0d74aa
@@ -8,3 +8,4 @@ SHA1 (patch-SharedMemory.cpp) = e4b97d68
 SHA1 (patch-SoloBarcode.cpp) = a939a97cadd05b1ec6b6dfcddb469acd5072b0e8
 SHA1 (patch-SuffixArrayFuns.cpp) = b7c623c02277fdfc2bd9d6fa8068afafeb46b1cf
 SHA1 (patch-bamSortByCoordinate.cpp) = e91a4ac9f04beb29c95c7bfbb5d89c5bf41aca41
+SHA1 (patch-opal_opal.cpp) = e41a9981fbaf43d18264fc4ac13163501aac93bb

Index: pkgsrc/biology/rna-star/patches/patch-Makefile
diff -u pkgsrc/biology/rna-star/patches/patch-Makefile:1.1 pkgsrc/biology/rna-star/patches/patch-Makefile:1.2
--- pkgsrc/biology/rna-star/patches/patch-Makefile:1.1  Mon Jul 31 14:34:18 2023
+++ pkgsrc/biology/rna-star/patches/patch-Makefile      Tue Aug 29 21:49:57 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile,v 1.1 2023/07/31 14:34:18 bacon Exp $
+$NetBSD: patch-Makefile,v 1.2 2023/08/29 21:49:57 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/rna-star/patches/patch-SharedMemory.cpp
diff -u pkgsrc/biology/rna-star/patches/patch-SharedMemory.cpp:1.1 pkgsrc/biology/rna-star/patches/patch-SharedMemory.cpp:1.2
--- pkgsrc/biology/rna-star/patches/patch-SharedMemory.cpp:1.1  Mon Jul 31 14:34:18 2023
+++ pkgsrc/biology/rna-star/patches/patch-SharedMemory.cpp      Tue Aug 29 21:49:57 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-SharedMemory.cpp,v 1.1 2023/07/31 14:34:18 bacon Exp $
+$NetBSD: patch-SharedMemory.cpp,v 1.2 2023/08/29 21:49:57 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/rna-star/patches/patch-SoloBarcode.cpp
diff -u pkgsrc/biology/rna-star/patches/patch-SoloBarcode.cpp:1.1 pkgsrc/biology/rna-star/patches/patch-SoloBarcode.cpp:1.2
--- pkgsrc/biology/rna-star/patches/patch-SoloBarcode.cpp:1.1   Mon Jul 31 14:34:18 2023
+++ pkgsrc/biology/rna-star/patches/patch-SoloBarcode.cpp       Tue Aug 29 21:49:57 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-SoloBarcode.cpp,v 1.1 2023/07/31 14:34:18 bacon Exp $
+$NetBSD: patch-SoloBarcode.cpp,v 1.2 2023/08/29 21:49:57 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/rna-star/patches/patch-SuffixArrayFuns.cpp
diff -u pkgsrc/biology/rna-star/patches/patch-SuffixArrayFuns.cpp:1.1 pkgsrc/biology/rna-star/patches/patch-SuffixArrayFuns.cpp:1.2
--- pkgsrc/biology/rna-star/patches/patch-SuffixArrayFuns.cpp:1.1       Mon Jul 31 14:34:18 2023
+++ pkgsrc/biology/rna-star/patches/patch-SuffixArrayFuns.cpp   Tue Aug 29 21:49:57 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-SuffixArrayFuns.cpp,v 1.1 2023/07/31 14:34:18 bacon Exp $
+$NetBSD: patch-SuffixArrayFuns.cpp,v 1.2 2023/08/29 21:49:57 bacon Exp $
 
 # Drop obsolete modifier for c++17 compat
 
Index: pkgsrc/biology/rna-star/patches/patch-bamSortByCoordinate.cpp
diff -u pkgsrc/biology/rna-star/patches/patch-bamSortByCoordinate.cpp:1.1 pkgsrc/biology/rna-star/patches/patch-bamSortByCoordinate.cpp:1.2
--- pkgsrc/biology/rna-star/patches/patch-bamSortByCoordinate.cpp:1.1   Mon Jul 31 14:34:18 2023
+++ pkgsrc/biology/rna-star/patches/patch-bamSortByCoordinate.cpp       Tue Aug 29 21:49:57 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-bamSortByCoordinate.cpp,v 1.1 2023/07/31 14:34:18 bacon Exp $
+$NetBSD: patch-bamSortByCoordinate.cpp,v 1.2 2023/08/29 21:49:57 bacon Exp $
 
 # Portability
 

Added files:

Index: pkgsrc/biology/rna-star/patches/patch-opal_opal.cpp
diff -u /dev/null pkgsrc/biology/rna-star/patches/patch-opal_opal.cpp:1.1
--- /dev/null   Tue Aug 29 21:49:57 2023
+++ pkgsrc/biology/rna-star/patches/patch-opal_opal.cpp Tue Aug 29 21:49:57 2023
@@ -0,0 +1,17 @@
+$NetBSD: patch-opal_opal.cpp,v 1.1 2023/08/29 21:49:57 bacon Exp $
+
+# Fix compile error on Darwin 21.6.0
+
+--- opal/opal.cpp.orig 2023-08-29 21:20:11.000000000 +0000
++++ opal/opal.cpp
+@@ -5,10 +5,8 @@
+ #include <limits>
+ #include <vector>
+ 
+-extern "C" {
+ #define SIMDE_ENABLE_NATIVE_ALIASES
+ #include <simde_avx2.h> // AVX2 and lower
+-}
+ 
+ #include "opal.h"
+