From e1002a3320f481ba538a926c5b80dd8626d97b63 Mon Sep 17 00:00:00 2001
From: Olivier Sallou <osallou@debian.org>
Date: Tue, 25 Nov 2014 17:44:08 +0000
Subject: [PATCH] adapt patches to new release, add status to changelog

---
 debian/changelog               |  2 ++
 debian/patches/fix_compilation | 11 +++++++++++
 debian/patches/fix_lib_deps    |  2 +-
 debian/patches/series          |  1 +
 debian/rules                   |  3 ++-
 5 files changed, 17 insertions(+), 2 deletions(-)
 create mode 100644 debian/patches/fix_compilation

diff --git a/debian/changelog b/debian/changelog
index 9ebad7c6..8a5f9352 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,8 @@ ncbi-blast+ (2.2.30-1) UNRELEASED; urgency=medium
   * New upstream release
   * d/control: switch to Standards 3.9.6 
     [TODO] fix missing Makefile.flat
+    [ISSUE] problem at compilation:
+      /usr/bin/ld: blastp_app.o: undefined symbol «kBlastMinorVersion»
     [DONE] updates patches to new release
 
  -- Olivier Sallou <osallou@debian.org>  Fri, 21 Nov 2014 18:21:26 +0100
diff --git a/debian/patches/fix_compilation b/debian/patches/fix_compilation
new file mode 100644
index 00000000..92129086
--- /dev/null
+++ b/debian/patches/fix_compilation
@@ -0,0 +1,11 @@
+--- a/c++/src/util/regexp/pcretest.c
++++ b/c++/src/util/regexp/pcretest.c
+@@ -250,7 +250,7 @@
+     /* Read the next line by normal means, prompting if the file is stdin. */
+ 
+       {
+-      if (f == stdin) printf(prompt);
++      if (f == stdin) printf("%s",prompt);
+       if (fgets((char *)here, rlen,  f) == NULL)
+         return (here == start)? NULL : start;
+       }
diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index 4e1a626e..4ebe1257 100644
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -336,7 +336,7 @@ Last-Update: 2011-08-28
  # Dependencies for shared library
  DLL_LIB = ncbi_xreader$(DLL)
  
-+DLL_DLIB = ncbi_xreader_id2 ncbi_xreader_id1 ncbi_xreader_cache ncbi_xreader \
++DLL_DLIB = id2 id1 ncbi_xreader \
 +           xobjmgr seq xutil xncbi
 +
  WATCHERS = vasilche
diff --git a/debian/patches/series b/debian/patches/series
index b74b155f..8d79322c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,3 +6,4 @@ no_multiarch_rpath
 use_pie_for_apps
 skip_services_unit_test
 fix_configure
+fix_compilation
diff --git a/debian/rules b/debian/rules
index d5cb058f..d85e1689 100755
--- a/debian/rules
+++ b/debian/rules
@@ -42,7 +42,8 @@ override_dh_auto_configure:
 
 override_dh_auto_build:
 	cd c++/BUILD/build  && \
-	    make -f Makefile.flat all_projects="$(proj)"
+	     make all_r
+#	    make -f Makefile.flat all_projects="$(proj)"
 
 override_dh_auto_test:
 	-dh_auto_test
-- 
2.30.2