Received: by mail.netbsd.org (Postfix, from userid 605) id 36A2E84D83; Sat, 16 May 2020 19:41:00 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id B2EBB84D51 for ; Sat, 16 May 2020 19:40:59 +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 QVvbFibbsYB2 for ; Sat, 16 May 2020 19:40:59 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.netbsd.org [199.233.217.197]) by mail.netbsd.org (Postfix) with ESMTP id 3B1F184D33 for ; Sat, 16 May 2020 19:40:59 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 337E9FB27; Sat, 16 May 2020 19:40:59 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1589658059219710" MIME-Version: 1.0 Date: Sat, 16 May 2020 19:40:59 +0000 From: "Roland Illig" Subject: CVS commit: pkgsrc/biology/canu To: pkgsrc-changes@NetBSD.org Reply-To: rillig@netbsd.org X-Mailer: log_accum Message-Id: <20200516194059.337E9FB27@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: pkgsrc-changes.NetBSD.org Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1589658059219710 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: rillig Date: Sat May 16 19:40:59 UTC 2020 Modified Files: pkgsrc/biology/canu: Makefile Log Message: biology/canu: fix SUBST blocks to actually find the Java code To generate a diff of this commit: cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/canu/Makefile Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1589658059219710 Content-Disposition: inline Content-Length: 1868 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:1.8 pkgsrc/biology/canu/Makefile:1.9 --- pkgsrc/biology/canu/Makefile:1.8 Thu May 14 18:30:05 2020 +++ pkgsrc/biology/canu/Makefile Sat May 16 19:40:59 2020 @@ -1,7 +1,7 @@ -# $NetBSD: Makefile,v 1.8 2020/05/14 18:30:05 rillig Exp $ +# $NetBSD: Makefile,v 1.9 2020/05/16 19:40:59 rillig Exp $ DISTNAME= canu-1.8 -PKGREVISION= 5 +PKGREVISION= 6 CATEGORIES= biology java MASTER_SITES= ${MASTER_SITE_GITHUB:=marbl/} GITHUB_TAG= v${PKGVERSION_NOREV} @@ -22,29 +22,19 @@ 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+= ${WRKSRC}/Makefile +SUBST_FILES.optimize+= Makefile SUBST_CLASSES+= jar SUBST_STAGE.jar= pre-configure -SUBST_SED.jar+= -e 's|\\$$bin/mhap-|${PREFIX}/${JAVAJARDIR}/mhap-|g' -SUBST_FILES.jar+= ${WRKSRC}/pipelines/canu/OverlapMhap.pm +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+= ${WRKSRC}/pipelines/canu.pl +SUBST_FILES.perl+= pipelines/canu.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 +REPLACE_PERL+= *.pl */*.pl # May work on other 64-bit processors, but untested ONLY_FOR_PLATFORM= *-*-x86_64 --_----------=_1589658059219710--