Package: r-bioc-biocparallel Version: 1.12.0-1 Severity: important Tags: patch User: ubuntu-de...@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/ slanga...@ubuntu.com vor...@debian.org
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.langa...@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