CVS commit: pkgsrc/biology/canu

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/canu
From: "Jason Bacon" <bacon%netbsd.org@localhost>
Date: Sat, 20 May 2023 11:27:27 +0000

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat May 20 11:27:27 UTC 2023

Modified Files:
        pkgsrc/biology/canu: Makefile PLIST distinfo
        pkgsrc/biology/canu/patches: patch-Makefile
            patch-pipelines_canu_Defaults.pm patch-pipelines_canu_Execution.pm
            patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp
            patch-utility_src_parasail_internal__sse.h
            patch-utility_src_utility_align-ssw.H
            patch-utility_src_utility_files.H
            patch-utility_src_utility_logging.H
            patch-utility_src_utility_system.H
            patch-utility_src_utility_types.H

Log Message:
biology/canu: Hacks to support Darwin x86

OpenMP support needs improvement
Darwin aarch64 still blocked by glib2 build issues
No changes to binaries on other platforms


To generate a diff of this commit:
cvs rdiff -u -r1.19 -r1.20 pkgsrc/biology/canu/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/canu/PLIST
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/canu/distinfo
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/canu/patches/patch-Makefile \
    pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm \
    pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm
cvs rdiff -u -r1.1 -r1.2 \
    pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp \
    pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h \
    pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H \
    pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H \
    pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H \
    pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H \
    pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H

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

Modified files:

Index: pkgsrc/biology/canu/Makefile
diff -u pkgsrc/biology/canu/Makefile:1.19 pkgsrc/biology/canu/Makefile:1.20
--- pkgsrc/biology/canu/Makefile:1.19   Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/Makefile        Sat May 20 11:27:27 2023
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.19 2023/05/18 18:17:32 bacon Exp $
+# $NetBSD: Makefile,v 1.20 2023/05/20 11:27:27 bacon Exp $
 
 DISTNAME=      canu-2.2
 CATEGORIES=    biology java
@@ -13,17 +13,6 @@ LICENSE=     gnu-gpl-v2
 
 DEPENDS+=      gnuplot>0:../../graphics/gnuplot
 
-# Makefile compiles directly into ${DESTDIR}${PREFIX}
-SUBST_CLASSES+=                optimize
-SUBST_STAGE.optimize=  pre-configure
-SUBST_SED.optimize+=   -e 's|-g3||g'
-SUBST_SED.optimize+=   -e 's|-O3||g'
-SUBST_SED.optimize+=   -e 's|-O4||g'
-SUBST_SED.optimize+=   -e 's|-funroll-loops||g'
-SUBST_SED.optimize+=   -e 's|-fexpensive-optimizations||g'
-SUBST_SED.optimize+=   -e 's|-finline-functions||g'
-SUBST_FILES.optimize+= Makefile
-
 SUBST_CLASSES+=                perl
 SUBST_STAGE.perl=      pre-configure
 SUBST_SED.perl+=       -e 's|$$FindBin::RealBin/../lib/site_perl|${PREFIX}/${SITE_PERL_REL}|g'
@@ -55,7 +44,7 @@ MAKE_ENV+=    DESTDIR=${WRKSRC}
 TMP_INST=              ${WRKSRC}/build
 SITE_PERL_REL=         lib/perl5/site_perl
 JAVAJARDIR=            share/java/classes
-INSTALLATION_DIRS=     bin ${JAVAJARDIR}
+INSTALLATION_DIRS=     bin lib/perl5 ${JAVAJARDIR}
 
 post-extract:
        ${CHMOD} -R g-w ${WRKDIR}
@@ -70,6 +59,15 @@ do-install:
        cd ${TMP_INST}/lib/perl5 && ${PAX} -wr * ${DESTDIR}${PREFIX}/lib/perl5
        cd ${TMP_INST}/share && ${PAX} -wr * ${DESTDIR}${PREFIX}/share
 
+.include "../../mk/bsd.prefs.mk"
+
+# Xcode supports -Xpreprocessor -fopenmp, but does not supply OpenMP libs
+# parallel/openmp installs an entire llvm
+# Maybe a libomp package would suffice?
+.if ${OPSYS} == Darwin
+.include "../../parallel/openmp/buildlink3.mk"
+.endif
+
 .include "../../devel/boost-libs/buildlink3.mk"
 .include "../../devel/simde/buildlink3.mk"
 .include "../../lang/perl5/module.mk"

Index: pkgsrc/biology/canu/PLIST
diff -u pkgsrc/biology/canu/PLIST:1.2 pkgsrc/biology/canu/PLIST:1.3
--- pkgsrc/biology/canu/PLIST:1.2       Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/PLIST   Sat May 20 11:27:27 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2023/05/18 18:17:32 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2023/05/20 11:27:27 bacon Exp $
 bin/alignGFA
 bin/bogart
 bin/canu

Index: pkgsrc/biology/canu/distinfo
diff -u pkgsrc/biology/canu/distinfo:1.5 pkgsrc/biology/canu/distinfo:1.6
--- pkgsrc/biology/canu/distinfo:1.5    Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/distinfo        Sat May 20 11:27:27 2023
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.5 2023/05/18 18:17:32 bacon Exp $
+$NetBSD: distinfo,v 1.6 2023/05/20 11:27:27 bacon Exp $
 
 BLAKE2s (canu-2.2.tar.xz) = 5b585a2e0a31c2181817798b5f267dd4cf43c3ffeba4b0a04ffc8021a4603aed
 SHA512 (canu-2.2.tar.xz) = af08874a319dd5fd6bbe666c8a5d0a43b7c0caaaca3a3cbf4d3fe022d6d6b8c14cd967c2e26f4fbf571129be240dcb65e92fe61fad1e51d554f15254d0b6ce8f
 Size (canu-2.2.tar.xz) = 2400192 bytes
-SHA1 (patch-Makefile) = aa83003677cbb12558e438c776402ec48df0598d
+SHA1 (patch-Makefile) = 54a3a216948fea81cfeb6ce91458126adc2ad8da
 SHA1 (patch-pipelines_canu_Defaults.pm) = 5ecea8ebac667499916b0243f34dc25838992444
 SHA1 (patch-pipelines_canu_Execution.pm) = 75c019a93f5b6a4491191b4f32931ac0b8435421
 SHA1 (patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp) = fd219645141ebe9d6f23153a2a2b0f56abc103af

Index: pkgsrc/biology/canu/patches/patch-Makefile
diff -u pkgsrc/biology/canu/patches/patch-Makefile:1.2 pkgsrc/biology/canu/patches/patch-Makefile:1.3
--- pkgsrc/biology/canu/patches/patch-Makefile:1.2      Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-Makefile  Sat May 20 11:27:27 2023
@@ -1,11 +1,61 @@
-$NetBSD: patch-Makefile,v 1.2 2023/05/18 18:17:32 bacon Exp $
+$NetBSD: patch-Makefile,v 1.3 2023/05/20 11:27:27 bacon Exp $
 
-# Template Makefile requires platform-specific defaults for each OS
-# To be sent upstream following commit
+# Portability
 
---- Makefile.orig      2018-10-22 16:47:31.000000000 +0000
+--- Makefile.orig      2021-08-04 00:21:51.000000000 +0000
 +++ Makefile
-@@ -545,6 +545,40 @@ endif
+@@ -418,12 +418,12 @@ endif
+ ifeq ($(origin CXXFLAGS), undefined)
+   ifeq ($(BUILDOPTIMIZED), 1)
+   else
+-    CXXFLAGS += -g3
++    CXXFLAGS += 
+   endif
+ 
+   ifeq ($(BUILDDEBUG), 1)
+   else
+-    CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer
++    CXXFLAGS +=     -fomit-frame-pointer
+   endif
+ 
+   ifeq ($(BUILDJEMALLOC), 1)
+@@ -497,27 +497,8 @@ endef
+ ifeq (${OSTYPE}, Darwin)
+   $(foreach suffix,mp-9 9  mp-8 8  mp-7 7,$(eval $(call TEST_COMPILER,${suffix})))
+ 
+-  ifneq ($(shell echo `$(CXX) --version 2>&1 | grep -c clang`), 0)
+-     CPATH := $(shell echo `which $(CXX)`)
+-     CLANG := $(shell echo `$(CXX) --version 2>&1 | grep clang`)
+-     space := 
+-
+-     $(warning )
+-     ifeq ($(CXX), $(CPATH))
+-       $(warning Compiler '$(CXX)' reports version '$(CLANG)'.)
+-     else
+-       $(warning Compiler '$(CXX)' at '$(CPATH)' reports version '$(CLANG)'.)
+-     endif
+-     $(warning )
+-     $(warning Canu cannot be compiled with this compiler.  Please install GCC and/or)
+-     $(warning specify a non-Clang compiler on the command line, e.g.,)   #  Quite the evil trick to get
+-     $(warning $(space)    make CC=/path/to/gcc CXX=/path/to/g++);        #  this line indented!
+-     $(warning )
+-     $(error unsupported compiler)
+-  endif
+-
+-  CXXFLAGS += -fopenmp -pthread -fPIC -m64 -Wno-format
+-  LDFLAGS  += -fopenmp -pthread -lm
++  CXXFLAGS += -std=c++11 -Xpreprocessor -fopenmp -pthread -fPIC -m64 -Wno-format
++  LDFLAGS  += -L${PREFIX}/lib -lomp -pthread -lm
+ endif
+ 
+ 
+@@ -559,11 +540,45 @@ else
+   #LDFLAGS   += -lprofiler
+ 
+   #  callgrind
+-  #CXXFLAGS  += -g3 -Wa,--gstabs -save-temps
++  #CXXFLAGS  +=  -Wa,--gstabs -save-temps
+ endif
  endif
  
  
@@ -29,16 +79,16 @@ $NetBSD: patch-Makefile,v 1.2 2023/05/18
 +  #LDFLAGS   += -lprofiler
 +
 +  #  callgrind
-+  #CXXFLAGS  += -g3 -Wa,--gstabs -save-temps
++  #CXXFLAGS  +=  -Wa,--gstabs -save-temps
 +
 +  ifeq ($(BUILDOPTIMIZED), 1)
 +  else
-+    CXXFLAGS += -g3
++    CXXFLAGS += 
 +  endif
 +
 +  ifeq ($(BUILDDEBUG), 1)
 +  else
-+    CXXFLAGS += -O3   -finline-functions -fomit-frame-pointer
++    CXXFLAGS +=     -fomit-frame-pointer
 +  endif
 +endif
 +
Index: pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm
diff -u pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.2 pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.3
--- pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.2    Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm        Sat May 20 11:27:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.2 2023/05/18 18:17:32 bacon Exp $
+$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.3 2023/05/20 11:27:27 bacon Exp $
 
 # Better task limit control under slurm
 
Index: pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm
diff -u pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.2 pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.3
--- pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.2   Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm       Sat May 20 11:27:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-pipelines_canu_Execution.pm,v 1.2 2023/05/18 18:17:32 bacon Exp $
+$NetBSD: patch-pipelines_canu_Execution.pm,v 1.3 2023/05/20 11:27:27 bacon Exp $
 
 # Better task limit control under slurm
 

Index: pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp
diff -u pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.1 pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.2
--- pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.1     Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp Sat May 20 11:27:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp,v 1.1 2023/05/18 18:17:32 bacon Exp $
+$NetBSD: patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp,v 1.2 2023/05/20 11:27:27 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h
diff -u pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h:1.1 pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h:1.2
--- pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h:1.1  Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h      Sat May 20 11:27:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-utility_src_parasail_internal__sse.h,v 1.1 2023/05/18 18:17:32 bacon Exp $
+$NetBSD: patch-utility_src_parasail_internal__sse.h,v 1.2 2023/05/20 11:27:27 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H
diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H:1.1 pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H:1.2
--- pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H:1.1       Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H   Sat May 20 11:27:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-utility_src_utility_align-ssw.H,v 1.1 2023/05/18 18:17:32 bacon Exp $
+$NetBSD: patch-utility_src_utility_align-ssw.H,v 1.2 2023/05/20 11:27:27 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H
diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.1 pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.2
--- pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.1   Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H       Sat May 20 11:27:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-utility_src_utility_files.H,v 1.1 2023/05/18 18:17:32 bacon Exp $
+$NetBSD: patch-utility_src_utility_files.H,v 1.2 2023/05/20 11:27:27 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H
diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.1 pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.2
--- pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.1 Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H     Sat May 20 11:27:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-utility_src_utility_logging.H,v 1.1 2023/05/18 18:17:32 bacon Exp $
+$NetBSD: patch-utility_src_utility_logging.H,v 1.2 2023/05/20 11:27:27 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H
diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.1 pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.2
--- pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.1  Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H      Sat May 20 11:27:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-utility_src_utility_system.H,v 1.1 2023/05/18 18:17:32 bacon Exp $
+$NetBSD: patch-utility_src_utility_system.H,v 1.2 2023/05/20 11:27:27 bacon Exp $
 
 # Portability
 
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H
diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.1 pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.2
--- pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.1   Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H       Sat May 20 11:27:27 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-utility_src_utility_types.H,v 1.1 2023/05/18 18:17:32 bacon Exp $
+$NetBSD: patch-utility_src_utility_types.H,v 1.2 2023/05/20 11:27:27 bacon Exp $
 
 # Portability

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