debian/changelog

+fastlink (4.1P-fix100+dfsg-2) unstable; urgency=medium
+
+  * Secure URI in Homepage
+  * debian/get-orig-source: use https instead of ftp
+  * d/rules: Be more cross-building friendly
+  * hardening=+all
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+
+ -- Andreas Tille <tille@debian.org>  Thu, 05 Jul 2018 11:35:01 +0200
+
 fastlink (4.1P-fix100+dfsg-1) unstable; urgency=low
 
   * New upstream patch level

debian/compat

-9
+11

debian/control

@@ -4,11 +4,11 @@ Uploaders: Andreas Tille <tille@debian.org>,
            Charles Plessy <plessy@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.6
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fastlink.git
-Vcs-Git: git://anonscm.debian.org/debian-med/fastlink.git
-Homepage: http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
+Build-Depends: debhelper (>= 11~)
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/fastlink
+Vcs-Git: https://salsa.debian.org/med-team/fastlink.git
+Homepage: https://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html
 
 Package: fastlink
 Architecture: any

debian/fastlink-doc.doc-base.alleles

@@ -7,4 +7,4 @@ Abstract: This document describes the implementation in FASTLINK of some
 Section: Science/Biology
 
 Format: postscript
-Files: /usr/share/doc/fastlink-doc/paper5.ps.gz
+Files: /usr/share/doc/fastlink/paper5.ps.gz

debian/fastlink-doc.doc-base.autoselect

@@ -7,4 +7,4 @@ Abstract: This document describes how the LINKAGE program was enhanced
 Section: Science/Biology
 
 Format: postscript
-Files: /usr/share/doc/fastlink-doc/paper6.ps.gz
+Files: /usr/share/doc/fastlink/paper6.ps.gz

debian/fastlink-doc.doc-base.avoid-recomp

@@ -6,4 +6,4 @@ Abstract: This document describes improvements over the original LINKAGE
 Section: Science/Biology
 
 Format: postscript
-Files: /usr/share/doc/fastlink-doc/paper2.ps.gz
+Files: /usr/share/doc/fastlink/paper2.ps.gz

debian/fastlink-doc.doc-base.fastlink

@@ -7,4 +7,4 @@ Abstract: This document describes the basics of the fastlink allgorithm
 Section: Science/Biology
 
 Format: postscript
-Files: /usr/share/doc/fastlink-doc/paper1.ps.gz
+Files: /usr/share/doc/fastlink/paper1.ps.gz

debian/fastlink-doc.doc-base.loops

@@ -5,4 +5,4 @@ Abstract: This document describes some aspects of pedigree loops in fastlink.
 Section: Science/Biology
 
 Format: postscript
-Files: /usr/share/doc/fastlink-doc/loops.ps.gz
+Files: /usr/share/doc/fastlink/loops.ps.gz

debian/fastlink-doc.doc-base.parallelization

@@ -6,4 +6,4 @@ Abstract: This document describes a parallel implementation of a
 Section: Science/Biology
 
 Format: postscript
-Files: /usr/share/doc/fastlink-doc/paper3.ps.gz
+Files: /usr/share/doc/fastlink/paper3.ps.gz

debian/fastlink-doc.doc-base.parallelization2

@@ -7,4 +7,4 @@ Abstract: This document describes a second parallel implementation of the
 Section: Science/Biology
 
 Format: postscript
-Files: /usr/share/doc/fastlink-doc/paper4.ps.gz
+Files: /usr/share/doc/fastlink/paper4.ps.gz

debian/fastlink-doc.doc-base.random

@@ -6,4 +6,4 @@ Abstract: This document describes how to find a minimum loop cutset in a
 Section: Science/Biology
 
 Format: postscript
-Files: /usr/share/doc/fastlink-doc/paper7.ps.gz
+Files: /usr/share/doc/fastlink/paper7.ps.gz

debian/fastlink-doc.doc-base.traverse

@@ -6,4 +6,4 @@ Abstract: This document describes some aspects of pedigree traversal in
 Section: Science/Biology
 
 Format: postscript
-Files: /usr/share/doc/fastlink-doc/traverse.ps.gz
+Files: /usr/share/doc/fastlink/traverse.ps.gz

debian/fastlink-doc.doc-base.unknown

@@ -6,4 +6,4 @@ Abstract: This document describes some aspects of the UNKNOWN auxiliary
 Section: Science/Biology
 
 Format: postscript
-Files: /usr/share/doc/fastlink-doc/unknown.ps.gz
+Files: /usr/share/doc/fastlink/unknown.ps.gz

debian/get-orig-source

@@ -12,7 +12,7 @@ mkdir -p ../tarballs
 cd ../tarballs
 
 rm -f "$UPSTREAMTAR"
-wget ftp://ftp.ncbi.nih.gov/pub/fastlink/$UPSTREAMTAR
+wget https://ftp.ncbi.nih.gov/pub/fastlink/$UPSTREAMTAR
 tar -xzf "$UPSTREAMTAR"
 
 PATCHVERSION=`grep -v "^ " fastlink/README.updates | tail -n 1 | sed 's/^\([0-9a-z]\+\)\..*/\1/'`

debian/rules

 #!/usr/bin/make -f
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 %:
-	dh $@
+	dh $@ --sourcedirectory=4.1P/src
 
 override_dh_clean:
-	cd 4.1P/src; make allclean
+	dh_clean -- allclean
 
 override_dh_auto_build:
-	cd 4.1P/src && make CFLAGS="$(CFLAGS)" DEBIANLDFLAGS="$(LDFLAGS)"
+	dh_auto_build -- CFLAGS="$(CFLAGS)" DEBIANLDFLAGS="$(LDFLAGS)"
+
+override_dh_auto_test:
+	echo "There is no test suite provided but automatism is grabbing check.c for the check which fails."
 
 get-orig-source:
 	sh debian/get-orig-source