Received: by mail.netbsd.org (Postfix, from userid 605) id 1536984EED; Thu, 18 May 2023 18:17:35 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id 44D6284EA7 for ; Thu, 18 May 2023 18:17:34 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([IPv6:::1]) by localhost (mail.netbsd.org [IPv6:::1]) (amavisd-new, port 10025) with ESMTP id IZ5GDV_bxSvh for ; Thu, 18 May 2023 18:17:32 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.NetBSD.org [IPv6:2001:470:a085:999:28c:faff:fe03:5984]) by mail.netbsd.org (Postfix) with ESMTP id A541184D0C for ; Thu, 18 May 2023 18:17:32 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 98D4DFA87; Thu, 18 May 2023 18:17:32 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1684433852135880" MIME-Version: 1.0 Date: Thu, 18 May 2023 18:17:32 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/canu To: pkgsrc-changes@NetBSD.org Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20230518181732.98D4DFA87@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1684433852135880 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" 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. --_----------=_1684433852135880 Content-Disposition: inline Content-Length: 16009 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii 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 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 + #include + #include ++#include + #include + #include + #include 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 + +-#include ++#define SIMDE_ENABLE_NATIVE_ALIASES ++#include + + #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 + #include + #include +-#include ++#define SIMDE_ENABLE_NATIVE_ALIASES ++#include + + + #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 +- ++#include + + // 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 ++ + #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 +- ++#include + + + 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 + + #include +-#include ++#include + + #include + #include --_----------=_1684433852135880--