[Debian-med-packaging] Bug#920240: abyss fails to build on hurd due to missing header file

[Samuel Thibault]

Hello,

Andreas Tille, le mer. 23 janv. 2019 08:23:16 +0100, a ecrit:
> On Wed, Jan 23, 2019 at 06:03:10AM +0100, Boud Roukema wrote:
> > Source: abyss
> > Version: 2.1.5-3
> > Severity: important
> 
> Could you please adjust the severity?  Regarding the description[1]
> important means:
> 
>       a bug which has a major effect on the usability of a package, without rendering it completely unusable to everyone.
> 
> I do not think that non-released architectures have a major effect on
> the usability of a package.

No, but it does have a major effect on the usability of the package on
that architecture, that's why we are usually using that priority.

> That said I would also fix packages with any severity, but for the
> moment I'm very busy with RC stuff and if you want this be fixed soon I
> would need a patch I would apply as soon as possible.

Here is one for the task_info issue. When g++ provides a full prototype
for the missing function, it means the header was included outside
extern "C" { }, and thus the symbol is mangled (see nm's output on the
.o file).

Now, there is another build issue, with tests:

Common/SAM.cc: In member function 'virtual void parseCigarDeath_invalid_cigar_Test::TestBody()':
Common/SAM.cc:62:2: error: 'EXPECT_DEATH' was not declared in this scope
  EXPECT_DEATH(SAMAlignment::parseCigar("20SS", false), "error: invalid CIGAR: `20SS'");
  ^~~~~~~~~~~~

Samuel
-------------- next part --------------
Index: abyss-2.1.5/Common/MemoryUtil.h
===================================================================
--- abyss-2.1.5.orig/Common/MemoryUtil.h
+++ abyss-2.1.5/Common/MemoryUtil.h
@@ -7,8 +7,14 @@
 #include <unistd.h> // for sbrk
 
 #if __MACH__
-# include <mach/mach.h> // for mach_task_self
-# include <mach/task.h> // for task_info
+# ifdef __APPLE__
+#  include <mach/mach.h> // for mach_task_self
+#  include <mach/task.h> // for task_info
+# else
+extern "C" {
+#  include <mach/mach.h> // for mach_task_self and task_info
+}
+# endif
 #endif
 
 /** Return the number of bytes used by the data and stack segments.