Date: Wed, 18 Aug 2021 17:17:48 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: e231650c4aeb - main - biology/ngs-sdk: Update 2.11.0-> 2.11.1 Message-ID: <202108181717.17IHHmHX077659@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=e231650c4aeb1c62fbd6e95ba7354dd07af64a33 commit e231650c4aeb1c62fbd6e95ba7354dd07af64a33 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2021-08-18 16:34:56 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2021-08-18 17:17:44 +0000 biology/ngs-sdk: Update 2.11.0-> 2.11.1 Reported by: portscout --- biology/ngs-sdk/Makefile | 5 ++--- biology/ngs-sdk/distinfo | 6 +++--- .../files/patch-ngs-sdk_setup_konfigure.perl | 22 ++-------------------- biology/ngs-sdk/pkg-plist | 6 +++--- 4 files changed, 10 insertions(+), 29 deletions(-) diff --git a/biology/ngs-sdk/Makefile b/biology/ngs-sdk/Makefile index 21517e76a934..8ac3c93758ab 100644 --- a/biology/ngs-sdk/Makefile +++ b/biology/ngs-sdk/Makefile @@ -1,6 +1,5 @@ PORTNAME= ngs -DISTVERSION= 2.11.0 -PORTREVISION= 2 +DISTVERSION= 2.11.1 CATEGORIES= biology PKGNAMESUFFIX= -sdk @@ -39,6 +38,6 @@ do-install: # install target from the project breaks: https://github.com/ncbi/ng # The above command installs broken-looking static libs with symlinks. # This is intentional, see comments https://github.com/ncbi/ncbi-vdb/issues/36#issuecomment-817990790 This may change in future versions. # strip - ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libngs-sdk.so.2.11.0 + ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libngs-sdk.so.${DISTVERSION} .include <bsd.port.mk> diff --git a/biology/ngs-sdk/distinfo b/biology/ngs-sdk/distinfo index 5d95554582cb..2ce5d901ca91 100644 --- a/biology/ngs-sdk/distinfo +++ b/biology/ngs-sdk/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1616222114 -SHA256 (ncbi-ngs-2.11.0_GH0.tar.gz) = 5fde50784760c00b403c2cc42ead15a4e9477697ee439f0a16edb4de3f52dfcc -SIZE (ncbi-ngs-2.11.0_GH0.tar.gz) = 1100365 +TIMESTAMP = 1629303705 +SHA256 (ncbi-ngs-2.11.1_GH0.tar.gz) = f39c56bbfdb0bdacdd5e86b5d3b65c448df17e419f3f533b1a0168e99f532553 +SIZE (ncbi-ngs-2.11.1_GH0.tar.gz) = 1101141 diff --git a/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl b/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl index ef1f8a936a62..5fc8fb532a2c 100644 --- a/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl +++ b/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl @@ -1,14 +1,5 @@ ---- ngs-sdk/setup/konfigure.perl.orig 2021-03-15 18:08:20 UTC +--- ngs-sdk/setup/konfigure.perl.orig 2021-08-18 16:26:23 UTC +++ ngs-sdk/setup/konfigure.perl -@@ -204,7 +204,7 @@ print "checking system type... " unless ($AUTORUN); - my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch(); - println $OSTYPE unless ($AUTORUN); - --unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') { -+unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /freebsd/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') { - println "configure: error: unsupported system '$OSTYPE'"; - exit 1; - } @@ -225,7 +225,7 @@ if ($OS eq 'linux') { print "checking machine architecture... " unless ($AUTORUN); @@ -27,7 +18,7 @@ } elsif ($MARCH eq 'fat86') { $BITS = '32_64'; } elsif ($MARCH =~ /i?86/i) { -@@ -337,6 +339,25 @@ if ($OSTYPE =~ /linux/i) { +@@ -337,6 +339,16 @@ if ($OSTYPE =~ /linux/i) { $OSINC = 'unix'; $TOOLS = 'gcc' unless ($TOOLS); $PYTHON = 'python'; @@ -41,15 +32,6 @@ + $OSINC = 'unix'; + $TOOLS = 'clang' unless ($TOOLS); + $PYTHON = $ENV{FREEBSD_PYTHON_CMD}; -+} elsif ($OSTYPE =~ /darwin/i) { -+ $LPFX = 'lib'; -+ $OBJX = 'o'; -+ $LOBX = 'pic.o'; -+ $LIBX = 'a'; -+ $SHLX = 'dylib'; -+ $EXEX = ''; -+ $OSINC = 'unix'; -+ $TOOLS = 'clang' unless ($TOOLS); } elsif ($OSTYPE =~ /darwin/i) { $LPFX = 'lib'; $OBJX = 'o'; diff --git a/biology/ngs-sdk/pkg-plist b/biology/ngs-sdk/pkg-plist index 93a82bd6b5e9..4b46d04f486c 100644 --- a/biology/ngs-sdk/pkg-plist +++ b/biology/ngs-sdk/pkg-plist @@ -90,11 +90,11 @@ include/ngs/unix/x86_64/atomic32.h lib/libngs-adapt-c++-static.a lib/libngs-adapt-c++.a lib/libngs-adapt-c++.a.2 -lib/libngs-adapt-c++.a.2.11.0 +lib/libngs-adapt-c++.a.2.11.1 lib/libngs-c++-static.a lib/libngs-c++.a lib/libngs-c++.a.2 -lib/libngs-c++.a.2.11.0 +lib/libngs-c++.a.2.11.1 lib/libngs-sdk.so lib/libngs-sdk.so.2 -lib/libngs-sdk.so.2.11.0 +lib/libngs-sdk.so.2.11.1
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