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: Thu, 18 May 2023 18:17:32 +0000

Module Name:    pkgsrc
Committed By:   bacon
Date:           Thu May 18 18:17:32 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
Added Files:
        pkgsrc/biology/canu/patches:
            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
Removed Files:
        pkgsrc/biology/canu/patches: patch-fastq-utilities_fastqSimulate_C
            patch-utility_objectStore.C

Log Message:
biology/canu: Update to 2.2

Numerous new features, enhancements, and bug fixes since 1.8
Enabled support for aarch64
May work on other 64-bit platforms, but untested

Changes: https://github.com/marbl/canu/releases


To generate a diff of this commit:
cvs rdiff -u -r1.18 -r1.19 pkgsrc/biology/canu/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/canu/PLIST
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/canu/distinfo
cvs rdiff -u -r1.1 -r1.2 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 -r0 \
    pkgsrc/biology/canu/patches/patch-fastq-utilities_fastqSimulate_C \
    pkgsrc/biology/canu/patches/patch-utility_objectStore.C
cvs rdiff -u -r0 -r1.1 \
    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:1.18 pkgsrc/biology/canu/Makefile:1.19
--- pkgsrc/biology/canu/Makefile:1.18   Sun Apr 23 14:26:11 2023
+++ pkgsrc/biology/canu/Makefile        Thu May 18 18:17:32 2023
@@ -1,10 +1,10 @@
-# $NetBSD: Makefile,v 1.18 2023/04/23 14:26:11 adam Exp $
+# $NetBSD: Makefile,v 1.19 2023/05/18 18:17:32 bacon Exp $
 
-DISTNAME=      canu-1.8
-PKGREVISION=   15
+DISTNAME=      canu-2.2
 CATEGORIES=    biology java
-MASTER_SITES=  ${MASTER_SITE_GITHUB:=marbl/}
-GITHUB_TAG=    v${PKGVERSION_NOREV}
+# Github-generaged files are incomplete
+MASTER_SITES=  https://github.com/marbl/canu/releases/download/v${PKGVERSION_NOREV}/
+EXTRACT_SUFX=  .tar.xz
 
 MAINTAINER=    bacon%NetBSD.org@localhost
 HOMEPAGE=      https://canu.readthedocs.io/
@@ -24,42 +24,46 @@ SUBST_SED.optimize+=        -e 's|-fexpensive-o
 SUBST_SED.optimize+=   -e 's|-finline-functions||g'
 SUBST_FILES.optimize+= Makefile
 
-SUBST_CLASSES+=                jar
-SUBST_STAGE.jar=       pre-configure
-SUBST_SED.jar+=                -e 's|\\$$bin/\.\./share/java/classes/mhap-|${PREFIX}/${JAVAJARDIR}/mhap-|g'
-SUBST_FILES.jar+=      pipelines/canu/OverlapMhap.pm
-
 SUBST_CLASSES+=                perl
 SUBST_STAGE.perl=      pre-configure
 SUBST_SED.perl+=       -e 's|$$FindBin::RealBin/../lib/site_perl|${PREFIX}/${SITE_PERL_REL}|g'
 SUBST_FILES.perl+=     pipelines/canu.pl
 
-REPLACE_PERL+=         *.pl */*.pl
+REPLACE_PERL+= bogart/*.pl
+REPLACE_PERL+= pipelines/*.pl
+REPLACE_PERL+= bogus/*.pl
+REPLACE_PERL+= bogart-analysis/*.pl
+REPLACE_PERL+= overlapBasedTrimming/*.pl
+REPLACE_PERL+= overlapInCore-analysis/*.pl
+REPLACE_PERL+= merTrim/*.pl
+REPLACE_PERL+= erateEstimate/*.pl
+REPLACE_PERL+= meryl/.pl
+REPLACE_PERL+= fastq-utilities/*.pl
+REPLACE_PERL+= *.pl
 
 # May work on other 64-bit processors, but untested
-ONLY_FOR_PLATFORM=     *-*-x86_64
+ONLY_FOR_PLATFORM=     *-*-x86_64 *-*-aarch64
 
 USE_LANGUAGES= c c++
 USE_JAVA=      run
 USE_JAVA2=     8
 USE_TOOLS+=    gmake pax perl
-GCC_REQD+=     4.8
 
 WRKSRC=                ${WRKDIR}/canu-${PKGVERSION_NOREV}/src
 MAKE_ENV+=     DESTDIR=${WRKSRC}
 
-TMP_INST=              ${WRKSRC}${PREFIX}/${OPSYS}-${MACHINE_ARCH:S/x86_64/amd64/}
+TMP_INST=              ${WRKSRC}/build
 SITE_PERL_REL=         lib/perl5/site_perl
 JAVAJARDIR=            share/java/classes
 INSTALLATION_DIRS=     bin ${JAVAJARDIR}
 
 post-extract:
-       ${CHMOD} -R g-w ${WRKDIR}/${DISTNAME}
+       ${CHMOD} -R g-w ${WRKDIR}
 
+# Upstream does not want to use lib/perl5/site_perl
 post-build:
        ${MKDIR} ${TMP_INST}/lib/perl5
        ${MV} ${TMP_INST}/lib/site_perl ${TMP_INST}/lib/perl5
-       ${RM} -f ${TMP_INST}/bin/canu.defaults
 
 do-install:
        cd ${TMP_INST}/bin && ${PAX} -wr * ${DESTDIR}${PREFIX}/bin
@@ -67,5 +71,6 @@ do-install:
        cd ${TMP_INST}/share && ${PAX} -wr * ${DESTDIR}${PREFIX}/share
 
 .include "../../devel/boost-libs/buildlink3.mk"
+.include "../../devel/simde/buildlink3.mk"
 .include "../../lang/perl5/module.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/biology/canu/PLIST
diff -u pkgsrc/biology/canu/PLIST:1.1 pkgsrc/biology/canu/PLIST:1.2
--- pkgsrc/biology/canu/PLIST:1.1       Mon Jan  7 02:33:17 2019
+++ pkgsrc/biology/canu/PLIST   Thu May 18 18:17:32 2023
@@ -1,25 +1,26 @@
-@comment $NetBSD: PLIST,v 1.1 2019/01/07 02:33:17 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2023/05/18 18:17:32 bacon Exp $
 bin/alignGFA
 bin/bogart
-bin/bogus
 bin/canu
+bin/canu-time
+bin/canu.defaults
 bin/correctOverlaps
+bin/draw-tig
 bin/dumpBlob
 bin/edalign
 bin/errorEstimate
 bin/falconsense
-bin/fastqAnalyze
-bin/fastqSample
-bin/fastqSimulate
-bin/fastqSimulate-sort
 bin/filterCorrectionLayouts
 bin/filterCorrectionOverlaps
 bin/findErrors
 bin/findErrors-Dump
+bin/fixErrors
 bin/generateCorrectionLayouts
+bin/layoutReads
 bin/loadCorrectedReads
 bin/loadErates
 bin/loadTrimmedReads
+bin/mergeRanges
 bin/meryl
 bin/mhapConvert
 bin/mmapConvert
@@ -30,29 +31,25 @@ bin/ovStoreDump
 bin/ovStoreIndexer
 bin/ovStoreSorter
 bin/ovStoreStats
+bin/overlapAlign
+bin/overlapCheck
 bin/overlapConvert
 bin/overlapImport
 bin/overlapInCore
 bin/overlapInCorePartition
 bin/overlapPair
 bin/prefixEditDistance-matchLimitGenerate
-bin/readConsensus
-bin/sequence
 bin/splitHaplotype
 bin/splitReads
 bin/sqStoreCreate
-bin/sqStoreCreatePartition
 bin/sqStoreDumpFASTQ
 bin/sqStoreDumpMetaData
 bin/tgStoreCompress
-bin/tgStoreCoverageStat
 bin/tgStoreDump
-bin/tgStoreFilter
 bin/tgStoreLoad
 bin/tgTigDisplay
 bin/trimReads
 bin/utgcns
-bin/wtdbgConvert
 lib/perl5/site_perl/canu/Configure.pm
 lib/perl5/site_perl/canu/Consensus.pm
 lib/perl5/site_perl/canu/CorrectReads.pm
@@ -62,6 +59,7 @@ lib/perl5/site_perl/canu/Grid.pm
 lib/perl5/site_perl/canu/Grid_Cloud.pm
 lib/perl5/site_perl/canu/Grid_DNANexus.pm
 lib/perl5/site_perl/canu/Grid_LSF.pm
+lib/perl5/site_perl/canu/Grid_Local.pm
 lib/perl5/site_perl/canu/Grid_PBSTorque.pm
 lib/perl5/site_perl/canu/Grid_SGE.pm
 lib/perl5/site_perl/canu/Grid_Slurm.pm

Index: pkgsrc/biology/canu/distinfo
diff -u pkgsrc/biology/canu/distinfo:1.4 pkgsrc/biology/canu/distinfo:1.5
--- pkgsrc/biology/canu/distinfo:1.4    Tue Oct 26 10:03:37 2021
+++ pkgsrc/biology/canu/distinfo        Thu May 18 18:17:32 2023
@@ -1,10 +1,15 @@
-$NetBSD: distinfo,v 1.4 2021/10/26 10:03:37 nia Exp $
+$NetBSD: distinfo,v 1.5 2023/05/18 18:17:32 bacon Exp $
 
-BLAKE2s (canu-1.8.tar.gz) = 7eb8fabdb5355c7f6ba27c2ceb5d33ddaa9b977c8445fcbda4eabe95d9930c19
-SHA512 (canu-1.8.tar.gz) = 650bc96675f371596f8e7748d4ab2d229f0262bf84cee8fed59af43d534d76095a72e4ba0b4a5ce9f561992268c317964cda2f6c89ee514f4920e2ba47fbc86c
-Size (canu-1.8.tar.gz) = 2465314 bytes
+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-fastq-utilities_fastqSimulate_C) = 959beef6e42c8158050958964924813b814b5a11
-SHA1 (patch-pipelines_canu_Defaults.pm) = 55a4631d86abb1881b0cc997514d44c536209ea6
-SHA1 (patch-pipelines_canu_Execution.pm) = fbb080c06ea5d2393d1835a61771715d2aef0274
-SHA1 (patch-utility_objectStore.C) = c8407de79abbaf296f027f704080cc7e878b85f4
+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
+SHA1 (patch-utility_src_parasail_internal__sse.h) = 3eca097b64273ada2df6f9be895823980ea79902
+SHA1 (patch-utility_src_utility_align-ssw.H) = 146e1959207dfe1deaae7f8f9809ed72be116841
+SHA1 (patch-utility_src_utility_files.H) = bc28dfd6957a2e2928b5df6a0e1d08c8ba5b2c27
+SHA1 (patch-utility_src_utility_logging.H) = 13e9ced966710cef4a2d38fd2b752f8a726ba07b
+SHA1 (patch-utility_src_utility_system.H) = e0bab7ed20431948845fac907584215c0b891406
+SHA1 (patch-utility_src_utility_types.H) = 2d7f94b774c0d557b5f4ea89294fd82b1341f9d3

Index: pkgsrc/biology/canu/patches/patch-Makefile
diff -u pkgsrc/biology/canu/patches/patch-Makefile:1.1 pkgsrc/biology/canu/patches/patch-Makefile:1.2
--- pkgsrc/biology/canu/patches/patch-Makefile:1.1      Mon Jan  7 02:33:17 2019
+++ pkgsrc/biology/canu/patches/patch-Makefile  Thu May 18 18:17:32 2023
@@ -1,4 +1,4 @@
-$NetBSD: patch-Makefile,v 1.1 2019/01/07 02:33:17 bacon Exp $
+$NetBSD: patch-Makefile,v 1.2 2023/05/18 18:17:32 bacon Exp $
 
 # Template Makefile requires platform-specific defaults for each OS
 # To be sent upstream following commit
Index: pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm
diff -u pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.1 pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.2
--- pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.1    Mon Jan  7 02:33:17 2019
+++ pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm        Thu May 18 18:17:32 2023
@@ -1,11 +1,10 @@
-$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.1 2019/01/07 02:33:17 bacon Exp $
+$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.2 2023/05/18 18:17:32 bacon Exp $
 
-# Add resource limits for SLURM
-# Upstream is considering a scheduler-independent approach to this feature
+# Better task limit control under slurm
 
---- pipelines/canu/Defaults.pm.orig    2018-06-22 08:20:52.000000000 +0000
+--- pipelines/canu/Defaults.pm.orig    2018-10-22 16:47:31 UTC
 +++ pipelines/canu/Defaults.pm
-@@ -812,6 +812,16 @@ sub setDefaults () {
+@@ -917,6 +917,16 @@ sub setDefaults () {
      setDefault("gridEngineArraySubmitID",             undef, "Grid engine configuration, not documented");
      setDefault("gridEngineJobID",                     undef, "Grid engine configuration, not documented");
  
Index: pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm
diff -u pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.1 pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.2
--- pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.1   Mon Jan  7 02:33:17 2019
+++ pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm       Thu May 18 18:17:32 2023
@@ -1,22 +1,10 @@
-$NetBSD: patch-pipelines_canu_Execution.pm,v 1.1 2019/01/07 02:33:17 bacon Exp $
+$NetBSD: patch-pipelines_canu_Execution.pm,v 1.2 2023/05/18 18:17:32 bacon Exp $
 
-# Add resource limits for SLURM
-# Upstream is considering a scheduler-independent approach to this feature
+# Better task limit control under slurm
 
---- pipelines/canu/Execution.pm.orig   2018-06-22 08:20:52.000000000 +0000
+--- pipelines/canu/Execution.pm.orig   2020-09-07 19:08:24 UTC
 +++ pipelines/canu/Execution.pm
-@@ -303,10 +303,6 @@ sub skipStage ($$@) {
- sub getInstallDirectory () {
-     my $installDir = $FindBin::RealBin;
- 
--    if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) {
--        $installDir = $1;
--    }
--
-     return($installDir);
- }
- 
-@@ -694,8 +690,8 @@ sub submitScript ($$) {
+@@ -762,8 +762,8 @@ sub submitScript ($$) {
  
  
  
@@ -27,7 +15,7 @@ $NetBSD: patch-pipelines_canu_Execution.
      my  $off = 0;
  
      #  In some grids (SGE)   this is the maximum size of an array job.
-@@ -725,8 +721,42 @@ sub buildGridArray ($$$$) {
+@@ -803,9 +803,43 @@ sub buildGridArray ($$$$) {
          $off = "-F \"$off\"";
      }
  
@@ -40,7 +28,7 @@ $NetBSD: patch-pipelines_canu_Execution.
 +    elsif( $opt =~ m/(ARRAY_JOBS)/ )
 +    {
 +      $opt =~ s/$1/$bgn-$end/; # Replace ARRAY_JOBS with 'bgn-end'
-+
+ 
 +      if( lc( getGlobal( 'gridEngine' ) ) eq 'slurm' && $end > 1 )
 +      {
 +          if( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) )
@@ -69,10 +57,11 @@ $NetBSD: patch-pipelines_canu_Execution.
 +          }
 +      }
 +    }
- 
++
      return($opt, $off);
  }
-@@ -870,7 +900,7 @@ sub buildGridJob ($$$$$$$$$) {
+ 
+@@ -951,7 +985,7 @@ sub buildGridJob ($$$$$$$$$) {
      my $jobNameT               = makeUniqueJobName($jobType, $asm);
  
      my ($jobName,  $jobOff)    = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayName"));

Added files:

Index: pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp
diff -u /dev/null pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.1
--- /dev/null   Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp Thu May 18 18:17:32 2023
@@ -0,0 +1,14 @@
+$NetBSD: patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp,v 1.1 2023/05/18 18:17:32 bacon Exp $
+
+# Portability
+
+--- utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp.orig       2021-12-18 13:01:24 UTC
++++ utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp
+@@ -25,6 +25,7 @@
+ #include <boost/config.hpp>
+ #include <boost/checked_delete.hpp>
+ #include <boost/throw_exception.hpp>
++#include <boost/detail/sp_typeinfo.hpp>
+ #include <boost/smart_ptr/bad_weak_ptr.hpp>
+ #include <boost/smart_ptr/detail/sp_counted_base.hpp>
+ #include <boost/smart_ptr/detail/sp_counted_impl.hpp>
Index: pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h
diff -u /dev/null pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h:1.1
--- /dev/null   Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_parasail_internal__sse.h      Thu May 18 18:17:32 2023
@@ -0,0 +1,16 @@
+$NetBSD: patch-utility_src_parasail_internal__sse.h,v 1.1 2023/05/18 18:17:32 bacon Exp $
+
+# Portability
+
+--- utility/src/parasail/internal_sse.h.orig   2021-12-17 22:10:09 UTC
++++ utility/src/parasail/internal_sse.h
+@@ -10,7 +10,8 @@
+ 
+ #include <stdint.h>
+ 
+-#include <emmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde.h>
+ 
+ #include "parasail.h"
+ 
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H
diff -u /dev/null pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H:1.1
--- /dev/null   Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_align-ssw.H   Thu May 18 18:17:32 2023
@@ -0,0 +1,16 @@
+$NetBSD: patch-utility_src_utility_align-ssw.H,v 1.1 2023/05/18 18:17:32 bacon Exp $
+
+# Portability
+
+--- utility/src/utility/align-ssw.H.orig       2021-12-17 22:12:23 UTC
++++ utility/src/utility/align-ssw.H
+@@ -33,7 +33,8 @@
+ #include <stdio.h>
+ #include <stdint.h>
+ #include <string.h>
+-#include <emmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde.h.h>
+ 
+ 
+ #define MAPSTR "MIDNSHP=X"
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H
diff -u /dev/null pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.1
--- /dev/null   Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H       Thu May 18 18:17:32 2023
@@ -0,0 +1,15 @@
+$NetBSD: patch-utility_src_utility_files.H,v 1.1 2023/05/18 18:17:32 bacon Exp $
+
+# Portability
+
+--- utility/src/utility/files.H.orig   2021-12-17 20:57:15 UTC
++++ utility/src/utility/files.H
+@@ -22,7 +22,7 @@
+ 
+ #include "types.H"
+ #include <vector>
+-
++#include <cmath>
+ 
+ //  Provides a safe and reliable mechanism for reading / writing
+ //  binary data.
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H
diff -u /dev/null pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.1
--- /dev/null   Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H     Thu May 18 18:17:32 2023
@@ -0,0 +1,15 @@
+$NetBSD: patch-utility_src_utility_logging.H,v 1.1 2023/05/18 18:17:32 bacon Exp $
+
+# Portability
+
+--- utility/src/utility/logging.H.orig 2023-05-18 15:39:08.832210910 +0000
++++ utility/src/utility/logging.H
+@@ -20,6 +20,8 @@
+ #ifndef LOGGING_H
+ #define LOGGING_H
+ 
++#include <stdarg.h>
++
+ #include "types.H"
+ #include "files.H"
+ 
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H
diff -u /dev/null pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.1
--- /dev/null   Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H      Thu May 18 18:17:32 2023
@@ -0,0 +1,15 @@
+$NetBSD: patch-utility_src_utility_system.H,v 1.1 2023/05/18 18:17:32 bacon Exp $
+
+# Portability
+
+--- utility/src/utility/system.H.orig  2021-12-17 20:57:47 UTC
++++ utility/src/utility/system.H
+@@ -23,7 +23,7 @@
+ #include "types.H"
+ 
+ #include <signal.h>
+-
++#include <cmath>
+ 
+ 
+ double   getTime(void);
Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H
diff -u /dev/null pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.1
--- /dev/null   Thu May 18 18:17:32 2023
+++ pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H       Thu May 18 18:17:32 2023
@@ -0,0 +1,15 @@
+$NetBSD: patch-utility_src_utility_types.H,v 1.1 2023/05/18 18:17:32 bacon Exp $
+
+# Portability
+
+--- utility/src/utility/types.H.orig   2021-12-17 20:58:13 UTC
++++ utility/src/utility/types.H
+@@ -55,7 +55,7 @@
+ #include <ctype.h>
+ 
+ #include <float.h>
+-#include <math.h>
++#include <cmath>
+ 
+ #include <assert.h>
+ #include <errno.h>

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