[med-svn] [sra-sdk] 06/07: Refresh patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository sra-sdk.

commit 27b7b0896cb72ef5333728307f055963530e2c7d
Author: Andreas Tille <tille at debian.org>
Date:   Fri Oct 20 00:02:44 2017 +0200

    Refresh patches
---
 debian/patches/find_configure_libs.patch                 | 2 +-
 debian/patches/find_hdf5_serial.patch                    | 2 +-
 debian/patches/find_ncbi-vdb.patch                       | 4 ++--
 debian/patches/find_ngs-sdk.patch                        | 4 ++--
 debian/patches/ignore_failing_tests_for_the_moment.patch | 4 ++--
 5 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/debian/patches/find_configure_libs.patch b/debian/patches/find_configure_libs.patch
index 4a53036..3d3d469 100644
--- a/debian/patches/find_configure_libs.patch
+++ b/debian/patches/find_configure_libs.patch
@@ -4,7 +4,7 @@ Description: Help configure finding Debian packaged libraries
 
 --- a/setup/konfigure.perl
 +++ b/setup/konfigure.perl
-@@ -1487,7 +1487,7 @@ sub check_compiler {
+@@ -1506,7 +1506,7 @@ sub check_compiler {
              $flags = $n;
              $log = '                      int main() {                     }\n'
          } elsif ($n eq 'hdf5') {
diff --git a/debian/patches/find_hdf5_serial.patch b/debian/patches/find_hdf5_serial.patch
index 43a78df..ddaabd0 100644
--- a/debian/patches/find_hdf5_serial.patch
+++ b/debian/patches/find_hdf5_serial.patch
@@ -4,7 +4,7 @@ Description: Debian has several flavours of hdf5 - use serial here
 
 --- a/setup/konfigure.perl
 +++ b/setup/konfigure.perl
-@@ -1488,7 +1488,7 @@ sub check_compiler {
+@@ -1507,7 +1507,7 @@ sub check_compiler {
              $log = '                      int main() {                     }\n'
          } elsif ($n eq 'hdf5') {
              $library = '-lhdf5_serial';
diff --git a/debian/patches/find_ncbi-vdb.patch b/debian/patches/find_ncbi-vdb.patch
index c487938..87d7854 100644
--- a/debian/patches/find_ncbi-vdb.patch
+++ b/debian/patches/find_ncbi-vdb.patch
@@ -29,7 +29,7 @@ Description: Make sure libncbi-vdb will be found
                locbldpath=>'$Bin/../../OUTDIR/ncbi-vdb',
 --- a/setup/konfigure.perl
 +++ b/setup/konfigure.perl
-@@ -1304,6 +1304,9 @@ sub find_in_dir {
+@@ -1307,6 +1307,9 @@ sub find_in_dir {
          } elsif (-e "$dir/interfaces/$include") {
              println $dir unless ($AUTORUN);
              $found_inc = "$dir/interfaces";
@@ -39,7 +39,7 @@ Description: Make sure libncbi-vdb will be found
          } else {
              print "$dir: " if ($OPT{'debug'});
              println 'no' unless ($AUTORUN);
-@@ -1316,7 +1319,7 @@ sub find_in_dir {
+@@ -1319,7 +1322,7 @@ sub find_in_dir {
              my $buildarch = `dpkg-architecture -qDEB_BUILD_MULTIARCH`;
              chomp $buildarch;
              my $libdir  = File::Spec->catdir($dir, 'lib', $buildarch);
diff --git a/debian/patches/find_ngs-sdk.patch b/debian/patches/find_ngs-sdk.patch
index 8e6cf76..8e5c387 100644
--- a/debian/patches/find_ngs-sdk.patch
+++ b/debian/patches/find_ngs-sdk.patch
@@ -12,7 +12,7 @@ Description: ngs-sdk header files are in /usr/include
  my %DEPEND_OPTIONS;
  foreach my $href (DEPENDS()) {
      $_ = $href->{name};
-@@ -934,7 +935,7 @@ EndText
+@@ -937,7 +938,7 @@ EndText
  
      if ($PKG{LNG} eq 'JAVA') {
          L($F,
@@ -21,7 +21,7 @@ Description: ngs-sdk header files are in /usr/include
      }
  
      print $F <<EndText;
-@@ -1312,7 +1313,9 @@ sub find_in_dir {
+@@ -1315,7 +1316,9 @@ sub find_in_dir {
          print "\tlibraries... " unless ($AUTORUN);
          if ($lib) {
              my $builddir = File::Spec->catdir($dir, $OS, $TOOLS, $ARCH, $BUILD);
diff --git a/debian/patches/ignore_failing_tests_for_the_moment.patch b/debian/patches/ignore_failing_tests_for_the_moment.patch
index 7a565ca..2414b8e 100644
--- a/debian/patches/ignore_failing_tests_for_the_moment.patch
+++ b/debian/patches/ignore_failing_tests_for_the_moment.patch
@@ -61,9 +61,9 @@ Description: Exclude failing tests
  #   accepting ascii quality values up to 126
 --- a/test/Makefile
 +++ b/test/Makefile
-@@ -36,7 +36,7 @@ include $(TOP)/build/Makefile.config
- #
+@@ -37,7 +37,7 @@ include $(TOP)/build/Makefile.config
  SUBDIRS =    \
+ 	vdb-config      \
  	fastq-loader    \
 -	vcf-loader      \
 +	# vcf-loader      \

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