Package: pbbam Version: 0.5.0-2 Severity: normal Tags: patch User: ubuntu-de...@lists.ubuntu.com Usertags: origin-ubuntu zesty ubuntu-patch
Hi Afif, In Ubuntu, pbbam was failing to build because when linking libpbbam.so, the library arguments were listed on the commandline before the objects being linked. Ubuntu uses -Wl,--as-needed in its linker arguments, which causes libraries that aren't used to be ignored; and so libraries listed before the objects that use them are not linked against. You can read more about this behavior here: https://wiki.ubuntu.com/ToolChain/CompilerFlags#Flags_passed_to_the_linker I've applied a small patch in Ubuntu to fix this, with the following changelog explanation: * debian/rules: fix cmake arguments so that library arguments are in the right order for -Wl,--as-needed. While Debian does not currently use -Wl,--as-needed by default and this is not a build issue in Debian, applying this patch will make your package more portable in general. Please consider applying it. Thanks, -- 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 pbbam-0.5.0/debian/rules pbbam-0.5.0/debian/rules --- pbbam-0.5.0/debian/rules 2016-07-05 02:49:29.000000000 -0700 +++ pbbam-0.5.0/debian/rules 2016-10-21 16:16:40.000000000 -0700 @@ -16,8 +16,8 @@ -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH) \ -DCMAKE_SKIP_RPATH=ON \ -DHTSLIB_INCLUDE_DIRS=/usr/include \ - -DHTSLIB_LIBRARIES=/usr/lib \ - -DCMAKE_SHARED_LINKER_FLAGS="-lssl -lhts $(LDFLAGS)" + -DHTSLIB_LIBRARIES="-lssl -lcrypto -lhts" \ + -DCMAKE_SHARED_LINKER_FLAGS="$(LDFLAGS)" # -DPacBioBAM_wrap_python=ON \ # -DPacBioBAM_wrap_r=ON
