git: e231650c4aeb - main - biology/ngs-sdk: Update 2.11.0-> 2.11.1

[Yuri Victorovich]

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=e231650c4aeb1c62fbd6e95ba7354dd07af64a33

commit e231650c4aeb1c62fbd6e95ba7354dd07af64a33
Author:     Yuri Victorovich <yuri at FreeBSD.org>
AuthorDate: 2021-08-18 16:34:56 +0000
Commit:     Yuri Victorovich <yuri at 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