[med-svn] [sra-sdk] 01/06: Add libncbi-vdb-dev and do not use --with-debug option since it tries to access header files like compiler.h which is private to libncbi-vdb-dev

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

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

commit 1b7e23249e0129fa83ce9b2986790d55b5c3d6c2
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jul 21 13:57:34 2016 +0200

    Add libncbi-vdb-dev and do not use --with-debug option since it tries to access header files like compiler.h which is private to libncbi-vdb-dev
---
 debian/control                     |  3 ++-
 debian/patches/find_ncbi-vdb.patch | 27 +++++++++++++++++++++++++++
 debian/patches/series              |  1 +
 debian/rules                       |  6 +++++-
 4 files changed, 35 insertions(+), 2 deletions(-)

diff --git a/debian/control b/debian/control
index 636bb9b..b0471a0 100644
--- a/debian/control
+++ b/debian/control
@@ -11,7 +11,8 @@ Build-Depends: debhelper (>= 9),
                libhdf5-dev,
                libmagic-dev,
                libfuse-dev,
-               libngs-sdk-dev (>= 1.2.4)
+               libngs-sdk-dev (>= 1.2.4),
+               libncbi-vdb-dev
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/sra-sdk.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/sra-sdk.git
diff --git a/debian/patches/find_ncbi-vdb.patch b/debian/patches/find_ncbi-vdb.patch
new file mode 100644
index 0000000..04a1ffe
--- /dev/null
+++ b/debian/patches/find_ncbi-vdb.patch
@@ -0,0 +1,27 @@
+--- a/setup/package.prl
++++ b/setup/package.prl
+@@ -34,10 +34,10 @@ sub REQ { (
+               boption => 'with-ncbi-vdb-build',
+               origin  => 'I',
+               type    => 'SB',
+-              srcpath => '../ncbi-vdb',
+-              pkgpath => '/usr/local/ncbi/ncbi-vdb',
++              srcpath => '/usr/include',
++              pkgpath => '/usr',
+               usrpath =>      '$HOME/ncbi/ncbi-vdb',
+-              bldpath => '$HOME/ncbi-outdir/ncbi-vdb',
++              bldpath => '/usr',
+               locbldpath=>'$Bin/../../OUTDIR/ncbi-vdb',
+               include => 'klib/rc.h',
+               lib     => 'libncbi-vdb.a',
+--- a/setup/konfigure.perl
++++ b/setup/konfigure.perl
+@@ -1318,7 +1318,7 @@ sub find_in_dir {
+             my $buildarch = `dpkg-architecture -qDEB_BUILD_MULTIARCH`;
+             chomp $buildarch;
+             my $libdir  = File::Spec->catdir($dir, 'lib', $buildarch);
+-            my $ilibdir = File::Spec->catdir($builddir, 'ilib');
++            my $ilibdir = File::Spec->catdir($dir, 'lib', $buildarch);
+             my $f = File::Spec->catdir($libdir, $lib);
+             print "\n\t\tchecking $f\n\t" if ($OPT{'debug'});
+             my $found;
diff --git a/debian/patches/series b/debian/patches/series
index 3c29095..a036502 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ find_configure_libs.patch
 hardening.patch
 find_hdf5_serial.patch
 find_ngs-sdk.patch
+find_ncbi-vdb.patch
diff --git a/debian/rules b/debian/rules
index 26ead17..9d01e2d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -16,7 +16,11 @@ override_dh_update_autotools_config:
 
 override_dh_auto_configure:
         # that's no standard configure script lacking support of default options
-	./configure --build=$(BUILDTYPE) --prefix=/usr --build-prefix=$(CURDIR)/debian/tmp/usr --with-ngs-sdk-prefix=/usr --with-debug
+	#
+	# --with-debug sets some options that require header files like compiler.h which
+	# is internal to ncbi-vcb and not installed into the package - so this option
+	# should not be used.
+	./configure --build=$(BUILDTYPE) --prefix=/usr --build-prefix=$(CURDIR)/debian/tmp/usr --with-ngs-sdk-prefix=/usr
 
 override_dh_auto_build:
 	export LD_LIBRARY_PATH="$$LD_LIBRARY_PATH:$(OUTDIR)/lib"; export OUTDIR=$(OUTDIR) ; make DEB_CFLAGS="$(CFLAGS)" DEB_LDFLAGS="$(LDFLAGS)"

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git