[ncbi-blast+] Don't directly include internal GCC headers

[Petr Machata]

commit cf36d34fcf364dce7b830dbe6403fe9ddda4c32c
Author: Petr Machata <pmachata at redhat.com>
Date:   Thu May 22 21:09:53 2014 +0200

    Don't directly include internal GCC headers

 ncbi-blast+-2.2.29-ptr.patch |   15 +++++++++++++++
 ncbi-blast+.spec             |    5 +++++
 2 files changed, 20 insertions(+), 0 deletions(-)
---
diff --git a/ncbi-blast+-2.2.29-ptr.patch b/ncbi-blast+-2.2.29-ptr.patch
new file mode 100644
index 0000000..e9969c5
--- /dev/null
+++ b/ncbi-blast+-2.2.29-ptr.patch
@@ -0,0 +1,15 @@
+diff -up ncbi-blast-2.2.29\+-src/c\+\+/include/corelib/ncbistl.hpp\~ ncbi-blast-2.2.29\+-src/c\+\+/include/corelib/ncbistl.hpp
+--- ncbi-blast-2.2.29+-src/c++/include/corelib/ncbistl.hpp~	2013-09-06 20:29:54.000000000 +0200
++++ ncbi-blast-2.2.29+-src/c++/include/corelib/ncbistl.hpp	2014-05-22 20:43:03.583373611 +0200
+@@ -215,8 +215,7 @@ END_NCBI_SCOPE
+ #  elif defined(_GLIBCXX_DEPRECATED)
+ #    include <ext/concurrence.h>
+ #    ifdef _GLIBCXX_THROW_OR_ABORT /* using libstdc++ from GCC 4.8 or later */
+-#      include <bits/unique_ptr.h>
+-#      include <bits/shared_ptr.h>
++#      include <memory>
+ #    endif
+ #    undef _GLIBCXX_DEPRECATED
+ #    define _GLIBCXX_DEPRECATED /* temporarily empty */
+
+Diff finished.  Thu May 22 20:43:07 2014
diff --git a/ncbi-blast+.spec b/ncbi-blast+.spec
index 02f2289..0e055c2 100644
--- a/ncbi-blast+.spec
+++ b/ncbi-blast+.spec
@@ -77,6 +77,8 @@ Source0:     ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-bla
 Patch1:      ncbi-blast+-2.2.28-libdeps.patch
 # Ignore unknown ./configure options to be able to use configure rpm macro
 Patch2:      ncbi-blast+-2.2.28-configure.patch
+# Don't directly include internal GCC headers bits/{unique,shared}_ptr.h.
+Patch3:      ncbi-blast+-2.2.29-ptr.patch
 Summary:     NCBI BLAST+ finds regions of similarity between biological sequences
 
 BuildRequires: hostname
@@ -100,6 +102,7 @@ members of gene families.
 %setup -q -n ncbi-blast-%{version}+-src
 %patch1 -p1 -b .libdeps
 %patch2 -p1 -b .configure
+%patch3 -p1 -b .ptr
 
 # Remove executable mode from header files
 find c++ -type f -name *.h -exec chmod -x {} \;
@@ -156,6 +159,8 @@ popd
 %changelog
 * Thu May 22 2014 Petr Machata <pmachata at redhat.com> - 2.2.29-3
 - Rebuild for boost 1.55.0
+- Don't directly include internal GCC headers
+  (ncbi-blast+-2.2.29-ptr.patch)
 
 * Tue Jan 28 2014 Jan Kaluza <jkaluza at redhat.com> - 2.2.29-2
 - build with debugging symbols (#1058441)