debian/changelog

 seqan2 (2.4.0+dfsg-9) UNRELEASED; urgency=medium
 
-  * Generate the CWL descritions automatically, now that CTDConverter is
+  [ Michael R. Crusoe ]
+  * Generate the CWL descriptions automatically, now that CTDConverter is
     packaged.
 
- -- Michael R. Crusoe <michael.crusoe@gmail.com>  Thu, 22 Feb 2018 08:19:39 -0800
+  [ Steve Langasek ]
+  * use alignment-safe buffer handling
+    Closes: #892223
+
+  [ Andreas Tille ]
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+  * Remove trailing whitespace in debian/changelog
+  * Build-Depends: fakeroot (Something is broken since this is not
+    automatically installed.  This should not be necessary and should
+    be removed in next revision.)
+  * debian/rules: Fix PATH in attempt to create CWL descriptions
+  TODO: Fix generation of CWL descriptions
+
+ -- Andreas Tille <tille@debian.org>  Tue, 04 Dec 2018 11:19:05 +0100
 
 seqan2 (2.4.0+dfsg-8) unstable; urgency=medium
 

debian/compat

-10
+11

debian/control

@@ -5,25 +5,19 @@ Uploaders: Andreas Tille <tille@debian.org>,
            Kevin Murray <spam@kdmurray.id.au>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                python,
-               cmake
+               cmake,
+               fakeroot
 Build-Depends-Arch: zlib1g-dev,
                     libbz2-dev,
                     libbam-dev,
                     libboost-dev,
                     help2man,
                     ctdconverter
-#Build-Depends-Indep: dh-exec
-#dh-linktree,
-#python-nose,
-#python-jinja2,
-#default-jdk,
-#python-sphinx,
-#python-sphinx-rtd-theme,
-Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/seqan2.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/seqan2.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/seqan2
+Vcs-Git: https://salsa.debian.org/med-team/seqan2.git
 Homepage: http://www.seqan.de/
 Rules-Requires-Root: no
 
@@ -44,10 +38,10 @@ Description: C++ library for the analysis of biological sequences
 
 Package: libseqan2-dev
 Architecture: all
+Multi-Arch: foreign
 Section: libdevel
 Depends: ${misc:Depends}
 Conflicts: seqan-dev
-Multi-Arch: foreign
 Description: C++ library for the analysis of biological sequences (development)
  SeqAn is a C++ template library of efficient algorithms and data
  structures for the analysis of sequences with the focus on

debian/patches/no-unaligned-access.patch

+Description: use alignment-safe buffer handling.
+ Currently we are using assignment to copy the contents of a variable of
+ arbitrary type into a buffer, but this is not portable because the buffer
+ address may not be aligned.  Use memcpy() instead, which should be
+ comparable performance ut alignment-safe.
+Author: Steve Langasek <steve.langasek@ubuntu.com>
+Bug-Debian: https://bugs.debian.org/892223
+
+Index: seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h
+===================================================================
+--- seqan2-2.4.0+dfsg.orig/include/seqan/basic/basic_stream.h
++++ seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h
+@@ -1200,7 +1200,8 @@
+ inline void
+ appendRawPodImpl(TTargetValue * &ptr, TValue const & val)
+ {
+-    *reinterpret_cast<TValue* &>(ptr)++ = val;
++    std::memcpy(ptr, &val, sizeof(TValue));
++    ptr += sizeof(TValue);
+ }
+ 
+ template <typename TTarget, typename TValue>

debian/patches/series

@@ -6,3 +6,4 @@ tweak_readmes
 install_fiona_illumina
 ctdVersion.patch
 fix_manpage_formatting.patch
+no-unaligned-access.patch

debian/rules

@@ -79,7 +79,7 @@ override_dh_install-arch:
 	find $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/bin -type f \
 		-name "*.sh" | xargs chmod a+x
 	for app in $$(ls $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/bin); \
-		do $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/$${app} \
+		do $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/bin/$${app} \
 		--write-ctd $${app}.ctd && CTDConverter cwl -i $${app}.ctd \
 		-o $(CURDIR)/debian/$(pkgapps)/usr/share/commonwl/${app}.cwl; \
 	        done;