rna-star: Successful build on NetBSD

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Jul 23 12:41:47 2023 -0500
Changeset:	a0837731202ba083d1510697695a8d054a6b3b3d

Modified Files:
	rna-star/Makefile
	rna-star/PLIST
	rna-star/distinfo
	rna-star/patches/patch-Makefile
Added Files:
	rna-star/patches/patch-SharedMemory.cpp
	rna-star/patches/patch-SoloBarcode.cpp

Log Message:
rna-star: Successful build on NetBSD

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=a0837731202ba083d1510697695a8d054a6b3b3d

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

diffstat:
 rna-star/Makefile                       |  1 -
 rna-star/PLIST                          |  1 +
 rna-star/distinfo                       |  4 +++-
 rna-star/patches/patch-Makefile         | 10 ++++++----
 rna-star/patches/patch-SharedMemory.cpp | 15 +++++++++++++++
 rna-star/patches/patch-SoloBarcode.cpp  | 21 +++++++++++++++++++++
 6 files changed, 46 insertions(+), 6 deletions(-)

diffs:
diff --git a/rna-star/Makefile b/rna-star/Makefile
index ce268ba9d1..90b3de6523 100644
--- a/rna-star/Makefile
+++ b/rna-star/Makefile
@@ -51,7 +51,6 @@ USE_TOOLS+=	gmake
 
 WRKSRC=		${WRKDIR}/${DISTNAME}/source
 MAKE_FLAGS=	HTSLIB=''
-CXXFLAGS+=	-std=c++11
 
 INSTALLATION_DIRS=	bin
 
diff --git a/rna-star/PLIST b/rna-star/PLIST
index 48d96a5493..cc6c0208e2 100644
--- a/rna-star/PLIST
+++ b/rna-star/PLIST
@@ -1 +1,2 @@
 @comment $NetBSD$
+bin/STAR
diff --git a/rna-star/distinfo b/rna-star/distinfo
index de60f4a45a..44bbb3f8b0 100644
--- a/rna-star/distinfo
+++ b/rna-star/distinfo
@@ -3,7 +3,9 @@ $NetBSD$
 BLAKE2s (STAR-2.7.10b.tar.gz) = ae5b1c236c1b5975d60277dbd5634661a4598e6f3f906f3d6b582b403edb58d3
 SHA512 (STAR-2.7.10b.tar.gz) = c4e94fd19f2a8145c38d59b39d91af16b53af63da2d77275445b9aeadfd287e3d2749829352a034e45e4352c64884275fa5b7b2ed28b95bf47cac3183b0d74aa
 Size (STAR-2.7.10b.tar.gz) = 12443703 bytes
-SHA1 (patch-Makefile) = 6bf4600d222a89a95e1cc9e038226a8e419fc0e8
+SHA1 (patch-Makefile) = 7dd8ef0ba12182a4cb2722aacfc6691b4f0a0cfe
+SHA1 (patch-SharedMemory.cpp) = 42cd862f58f45ea09e63487ef4bd6baa00bbb25f
+SHA1 (patch-SoloBarcode.cpp) = a939a97cadd05b1ec6b6dfcddb469acd5072b0e8
 SHA1 (patch-SpliceGraph.cpp) = 17f5b819985914d075cc15ef67f9b1625a1a6ca3
 SHA1 (patch-SuffixArrayFuns.cpp) = 219abac0885e2e710e634335228baadf16138429
 SHA1 (patch-bamSortByCoordinate.cpp) = 8c3db8dff990c3ff69be02fc86a4b7a8bed17bd6
diff --git a/rna-star/patches/patch-Makefile b/rna-star/patches/patch-Makefile
index a3a42d9c63..e17aceece0 100644
--- a/rna-star/patches/patch-Makefile
+++ b/rna-star/patches/patch-Makefile
@@ -1,6 +1,8 @@
 $NetBSD$
 
---- Makefile.orig	2022-11-01 14:50:35 UTC
+# Portability
+
+--- Makefile.orig	2022-11-01 14:50:35.000000000 +0000
 +++ Makefile
 @@ -11,6 +11,10 @@ CXXFLAGSextra ?=
  # user may define the compiler
@@ -13,17 +15,17 @@ $NetBSD$
  # pre-defined flags
  LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
  LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
-@@ -18,7 +22,8 @@ LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
+@@ -18,7 +22,8 @@ LDFLAGS_Mac :=-pthread -lz htslib/libhts
  LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
  LDFLAGS_gdb := $(LDFLAGS_shared)
  
 -DATE_FMT = --iso-8601=seconds
 +# --iso-8601 is not portable
-+DATE_FMT = -Iseconds
++DATE_FMT = +%Y-%m-%dT%H:%M:%S%z
  ifdef SOURCE_DATE_EPOCH
      BUILD_DATE ?= $(shell date -u -d "@$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u -r "$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u "$(DATE_FMT)")
  else
-@@ -41,12 +46,12 @@ GIT_BRANCH_COMMIT_DIFF := -D'GIT_BRANCH_COMMIT_DIFF="$
+@@ -41,12 +46,12 @@ GIT_BRANCH_COMMIT_DIFF := -D'GIT_BRANCH_
  
  # Defaults, can be overridden by make arguments or environment
  CXXFLAGS ?= -pipe -Wall -Wextra
diff --git a/rna-star/patches/patch-SharedMemory.cpp b/rna-star/patches/patch-SharedMemory.cpp
new file mode 100644
index 0000000000..6a202520e9
--- /dev/null
+++ b/rna-star/patches/patch-SharedMemory.cpp
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Portability
+
+--- SharedMemory.cpp.orig	2023-07-23 17:37:47.154665669 +0000
++++ SharedMemory.cpp
+@@ -12,7 +12,7 @@
+ #include <errno.h>
+ #include <sys/types.h>
+ 
+-#if defined(COMPILE_FOR_MAC) || defined(__FreeBSD__)
++#if defined(COMPILE_FOR_MAC) || defined(__FreeBSD__) || defined(__NetBSD__)
+   //some Mac's idiosyncrasies: standard SHM libraries are very old and missing some definitions
+   #define SHM_NORESERVE 0
+ #endif
diff --git a/rna-star/patches/patch-SoloBarcode.cpp b/rna-star/patches/patch-SoloBarcode.cpp
new file mode 100644
index 0000000000..ac3ee62722
--- /dev/null
+++ b/rna-star/patches/patch-SoloBarcode.cpp
@@ -0,0 +1,21 @@
+$NetBSD$
+
+# Portability
+
+--- SoloBarcode.cpp.orig	2023-07-23 17:22:42.613062682 +0000
++++ SoloBarcode.cpp
+@@ -3,6 +3,7 @@
+ #include "SoloCommon.h"
+ #include "SequenceFuns.h"
+ #include "ParametersSolo.h"
++#include <cmath>
+ 
+ void wlAddMismatches(uint32 nMM, uint32 cbLen, vector<uintCB> &wl, vector<uintCB> &wlEd1, vector<uint32> &wlInd1);
+ 
+@@ -149,4 +150,4 @@ void wlAddMismatches(uint32 nMM, uint32 
+             ++icb;
+         };
+     };
+-};
+\ No newline at end of file
++};