[Debian-med-packaging] Bug#889524: r-bioc-biocparallel: Fixes needed for compatibility with boost 1.65

[Steve Langasek]

Package: r-bioc-biocparallel
Version: 1.12.0-1
Severity: important
Tags: patch
User: ubuntu-devel at lists.ubuntu.com
Usertags: origin-ubuntu bionic ubuntu-patch

Dear Andreas,

The latest r-bioc-biocparallel has failed to build on arm64 and ppc64el in
Ubuntu, because Ubuntu has moved to boost 1.65, and as of this version,
librt is needed because boost::interprocess::shared_memory_object is
implemented on top of shm_open().

I have uploaded the attached patch to Ubuntu to fix this build failure.  You
may wish to consider including it in Debian as well, since this will
eventually become a build failure there once Debian also updates boost.

Cheers,
-- 
Steve Langasek                   Give me a lever long enough and a Free OS
Debian Developer                   to set it on, and I can move the world.
Ubuntu Developer                                    http://www.debian.org/
slangasek at ubuntu.com                                     vorlon at debian.org
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diff -Nru r-bioc-biocparallel-1.12.0/debian/patches/librt-linkage.patch r-bioc-biocparallel-1.12.0/debian/patches/librt-linkage.patch
--- r-bioc-biocparallel-1.12.0/debian/patches/librt-linkage.patch	1969-12-31 16:00:00.000000000 -0800
+++ r-bioc-biocparallel-1.12.0/debian/patches/librt-linkage.patch	2018-02-03 23:25:35.000000000 -0800
@@ -0,0 +1,13 @@
+Description: link librt for shm_open()
+ In boost 1.65, boost::interprocess::shared_memory_object is implemented
+ in terms of shm_open(), which according to shm_open(3), requires linking
+ against librt.  Pass this option explicitly in src/Makevars, since boost
+ can't do this for us.
+Author: Steve Langasek <steve.langasek at ubuntu.com>
+
+Index: r-bioc-biocparallel-1.12.0/src/Makevars
+===================================================================
+--- /dev/null
++++ r-bioc-biocparallel-1.12.0/src/Makevars
+@@ -0,0 +1 @@
++PKG_LIBS = -lrt
diff -Nru r-bioc-biocparallel-1.12.0/debian/patches/series r-bioc-biocparallel-1.12.0/debian/patches/series
--- r-bioc-biocparallel-1.12.0/debian/patches/series	2017-11-07 08:30:12.000000000 -0800
+++ r-bioc-biocparallel-1.12.0/debian/patches/series	2018-02-03 23:20:21.000000000 -0800
@@ -1,2 +1,3 @@
 ignore_test_requiring_rmpi.patch
 use_debian_packages_boost.patch
+librt-linkage.patch