From owner-svn-ports-head@freebsd.org Sat Apr 4 20:09:10 2020 Return-Path: Delivered-To: svn-ports-head@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 7DF8D2A15D1; Sat, 4 Apr 2020 20:09:10 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 48vnv918Qgz3C31; Sat, 4 Apr 2020 20:09:08 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 1DBE4271F3; Sat, 4 Apr 2020 20:09:01 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 034K90GJ018703; Sat, 4 Apr 2020 20:09:00 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 034K90pJ018699; Sat, 4 Apr 2020 20:09:00 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <202004042009.034K90pJ018699@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Sat, 4 Apr 2020 20:09:00 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r530713 - in head/biology/ngs-sdk: . files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology/ngs-sdk: . files X-SVN-Commit-Revision: 530713 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 04 Apr 2020 20:09:11 -0000 Author: yuri Date: Sat Apr 4 20:09:00 2020 New Revision: 530713 URL: https://svnweb.freebsd.org/changeset/ports/530713 Log: biology/ngs-sdk: Update 2.10.4 -> 2.10.5 Reported by: portscout Modified: head/biology/ngs-sdk/Makefile head/biology/ngs-sdk/distinfo head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl head/biology/ngs-sdk/pkg-plist Modified: head/biology/ngs-sdk/Makefile ============================================================================== --- head/biology/ngs-sdk/Makefile Sat Apr 4 19:48:01 2020 (r530712) +++ head/biology/ngs-sdk/Makefile Sat Apr 4 20:09:00 2020 (r530713) @@ -1,7 +1,7 @@ # $FreeBSD$ PORTNAME= ngs -DISTVERSION= 2.10.4 +DISTVERSION= 2.10.5 CATEGORIES= biology PKGNAMESUFFIX= -sdk Modified: head/biology/ngs-sdk/distinfo ============================================================================== --- head/biology/ngs-sdk/distinfo Sat Apr 4 19:48:01 2020 (r530712) +++ head/biology/ngs-sdk/distinfo Sat Apr 4 20:09:00 2020 (r530713) @@ -1,3 +1,3 @@ -TIMESTAMP = 1583611036 -SHA256 (ncbi-ngs-2.10.4_GH0.tar.gz) = 6f5db2269c6afc8e51a50fbcab9c63f4b1d6b69e483c6acb40d8f9e52f8282b1 -SIZE (ncbi-ngs-2.10.4_GH0.tar.gz) = 1093978 +TIMESTAMP = 1586029714 +SHA256 (ncbi-ngs-2.10.5_GH0.tar.gz) = c39ee65a625e3646e0212c5d8be846e45d368c644a053d3b54cf63f53853f02f +SIZE (ncbi-ngs-2.10.5_GH0.tar.gz) = 1099528 Modified: head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl ============================================================================== --- head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl Sat Apr 4 19:48:01 2020 (r530712) +++ head/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl Sat Apr 4 20:09:00 2020 (r530713) @@ -1,4 +1,4 @@ ---- ngs-sdk/setup/konfigure.perl.orig 2019-08-20 18:05:02 UTC +--- ngs-sdk/setup/konfigure.perl.orig 2020-04-01 16:34:36 UTC +++ ngs-sdk/setup/konfigure.perl @@ -202,7 +202,7 @@ print "checking system type... " unless ($AUTORUN); my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch(); @@ -20,12 +20,11 @@ print "checking machine architecture... " unless ($AUTORUN); println $MARCH unless ($AUTORUN); unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) { -@@ -332,6 +336,16 @@ if ($OSTYPE =~ /linux/i) { - $EXEX = ''; +@@ -333,6 +337,16 @@ if ($OSTYPE =~ /linux/i) { $OSINC = 'unix'; $TOOLS = 'gcc' unless ($TOOLS); + $PYTHON = 'python'; +} elsif ($OSTYPE =~ /freebsd/i) { -+ $BITS = ''; + $LPFX = 'lib'; + $OBJX = 'o'; + $LOBX = 'pic.o'; @@ -34,10 +33,11 @@ + $EXEX = ''; + $OSINC = 'unix'; + $TOOLS = 'clang' unless ($TOOLS); ++ $PYTHON = 'python'; } elsif ($OSTYPE =~ /darwin/i) { $LPFX = 'lib'; $OBJX = 'o'; -@@ -377,11 +391,11 @@ if ($TOOLS =~ /gcc$/) { +@@ -379,11 +393,11 @@ if ($TOOLS =~ /gcc$/) { } elsif ($TOOLS eq 'clang') { $CPP = 'clang++' unless ($CPP); $CC = 'clang -c'; @@ -51,7 +51,7 @@ $AR = 'ar rc'; $LD = "clang $ARCH_FL"; $LP = "$CPP $versionMin $ARCH_FL"; -@@ -478,7 +492,7 @@ foreach my $href (DEPENDS()) { +@@ -508,7 +522,7 @@ foreach my $href (DEPENDS()) { $I = $t if (-e $t); } push ( @L, File::Spec->catdir($OPT{$o}, 'lib') ); @@ -60,7 +60,7 @@ } my ($i, $l) = find_lib($_, $I, @L); if (defined $i || $l) { -@@ -898,8 +912,7 @@ EndText +@@ -929,8 +943,7 @@ EndText L($F, "PIC = $PIC") if ($PIC); if ($PKG{LNG} eq 'C') { if ($TOOLS =~ /clang/i) { Modified: head/biology/ngs-sdk/pkg-plist ============================================================================== --- head/biology/ngs-sdk/pkg-plist Sat Apr 4 19:48:01 2020 (r530712) +++ head/biology/ngs-sdk/pkg-plist Sat Apr 4 20:09:00 2020 (r530713) @@ -92,4 +92,4 @@ lib/libngs-adapt-c++.a lib/libngs-c++.a lib/libngs-sdk.so lib/libngs-sdk.so.2 -lib/libngs-sdk.so.2.10.4 +lib/libngs-sdk.so.2.10.5