[med-svn] r6993 - in trunk/packages/ncbi-blast+/trunk/debian: . patches

[Aaron M. Ucko]

Author: ucko
Date: 2011-06-11 00:31:52 +0000 (Sat, 11 Jun 2011)
New Revision: 6993

Added:
   trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes
Modified:
   trunk/packages/ncbi-blast+/trunk/debian/changelog
   trunk/packages/ncbi-blast+/trunk/debian/patches/series
Log:
debian/patches/hurd_fixes: new; fix hurd-specific issues.
(Closes: #629656, this time for sure. ;-)


Modified: trunk/packages/ncbi-blast+/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog	2011-06-11 00:30:24 UTC (rev 6992)
+++ trunk/packages/ncbi-blast+/trunk/debian/changelog	2011-06-11 00:31:52 UTC (rev 6993)
@@ -3,8 +3,10 @@
   * NOT YET RELEASED.
   * Team upload.
   * debian/patches/support_other_cpus: belatedly add a descriptive header.
+  * debian/patches/hurd_fixes: new; fix hurd-specific issues.
+    (Closes: #629656, this time for sure. ;-)
 
- -- Aaron M. Ucko <ucko at debian.org>  Fri, 10 Jun 2011 20:30:19 -0400
+ -- Aaron M. Ucko <ucko at debian.org>  Fri, 10 Jun 2011 20:31:47 -0400
 
 ncbi-blast+ (2.2.25-3) unstable; urgency=low
 

Added: trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes	                        (rev 0)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/hurd_fixes	2011-06-11 00:31:52 UTC (rev 6993)
@@ -0,0 +1,48 @@
+Subject: fix portability issues that led to Hurd build failures
+
+* src/build-system/configure(.ac): when checking how select works, reset
+  the alarm from the signal handler to avoid spinning forever.
+* src/connect/ncbi_socket_cxx.cpp: cope with missing PATH_MAX everywhere,
+  not just under Windows.
+
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Update: 2011-06-10
+Index: b/c++/src/build-system/configure
+===================================================================
+--- a/c++/src/build-system/configure	2011-06-10 20:18:43.000000000 -0400
++++ b/c++/src/build-system/configure	2011-06-10 20:19:52.000000000 -0400
+@@ -11416,7 +11416,7 @@
+          #ifdef HAVE_UNISTD_H
+          #  include <unistd.h>
+          #endif
+-         RETSIGTYPE handler(int sig) { }
++         RETSIGTYPE handler(int sig) { alarm(0); }
+ int
+ main ()
+ {
+Index: b/c++/src/build-system/configure.ac
+===================================================================
+--- a/c++/src/build-system/configure.ac	2011-06-10 20:18:43.000000000 -0400
++++ b/c++/src/build-system/configure.ac	2011-06-10 20:19:39.000000000 -0400
+@@ -2811,7 +2811,7 @@
+          #ifdef HAVE_UNISTD_H
+          #  include <unistd.h>
+          #endif
+-         RETSIGTYPE handler(int sig) { }]],
++         RETSIGTYPE handler(int sig) { alarm(0); }]],
+        [[struct timeval timeout = { 5, 0 };
+          signal(SIGALRM, &handler);
+          alarm(1);
+Index: b/c++/src/connect/ncbi_socket_cxx.cpp
+===================================================================
+--- a/c++/src/connect/ncbi_socket_cxx.cpp	2011-06-10 20:19:06.000000000 -0400
++++ b/c++/src/connect/ncbi_socket_cxx.cpp	2011-06-10 20:20:12.000000000 -0400
+@@ -34,7 +34,7 @@
+ #include <ncbi_pch.hpp>
+ #include <connect/ncbi_socket_unix.hpp>
+ #include <limits.h>                     // for PATH_MAX
+-#if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX)
++#ifndef PATH_MAX
+ #  define PATH_MAX 512                  // will actually use less than 32 chars
+ #endif
+ 

Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/series
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/series	2011-06-11 00:30:24 UTC (rev 6992)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/series	2011-06-11 00:31:52 UTC (rev 6993)
@@ -1,3 +1,4 @@
+hurd_fixes
 legacy_rename_rpsblast
 fix_checks
 fix_gcc46_errors