[med-svn] [Git][med-team/fastlink][master] 11 commits: Secure URI in Homepage

Andreas Tille gitlab at salsa.debian.org
Thu Jul 5 10:42:27 BST 2018 

Andreas Tille pushed to branch master at Debian Med / fastlink


Commits:
acbf75fa by Andreas Tille at 2018-07-05T11:07:46+02:00
Secure URI in Homepage

- - - - -
ac0bef03 by Andreas Tille at 2018-07-05T11:13:03+02:00
debian/get-orig-source: use https instead of ftp

- - - - -
f954ec5e by Andreas Tille at 2018-07-05T11:23:38+02:00
Be more cross-building friendly

- - - - -
6e1a7333 by Andreas Tille at 2018-07-05T11:27:15+02:00
hardening=+all

- - - - -
2fd30d25 by Andreas Tille at 2018-07-05T11:27:43+02:00
Enable debug symbols

- - - - -
6e9befec by Andreas Tille at 2018-07-05T11:28:19+02:00
debhelper 11

- - - - -
6693548f by Andreas Tille at 2018-07-05T11:28:27+02:00
Point Vcs fields to salsa.debian.org

- - - - -
5d19ba82 by Andreas Tille at 2018-07-05T11:28:27+02:00
Standards-Version: 4.1.4

- - - - -
aa5879be by Andreas Tille at 2018-07-05T11:31:31+02:00
Adapt doc-base files to new location of docs (caused by debhelper 11)

- - - - -
8efd91c5 by Andreas Tille at 2018-07-05T11:32:59+02:00
Revert adding -g since it does not help to create debug symbols

- - - - -
aa13d344 by Andreas Tille at 2018-07-05T11:36:02+02:00
Upload to unstable

- - - - -


15 changed files:

- debian/changelog
- debian/compat
- debian/control
- debian/fastlink-doc.doc-base.alleles
- debian/fastlink-doc.doc-base.autoselect
- debian/fastlink-doc.doc-base.avoid-recomp
- debian/fastlink-doc.doc-base.fastlink
- debian/fastlink-doc.doc-base.loops
- debian/fastlink-doc.doc-base.parallelization
- debian/fastlink-doc.doc-base.parallelization2
- debian/fastlink-doc.doc-base.random
- debian/fastlink-doc.doc-base.traverse
- debian/fastlink-doc.doc-base.unknown
- debian/get-orig-source
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,15 @@
+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 at 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
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -4,11 +4,11 @@ Uploaders: Andreas Tille <tille at debian.org>,
            Charles Plessy <plessy at 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
=====================================
--- a/debian/fastlink-doc.doc-base.alleles
+++ b/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
=====================================
--- a/debian/fastlink-doc.doc-base.autoselect
+++ b/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
=====================================
--- a/debian/fastlink-doc.doc-base.avoid-recomp
+++ b/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
=====================================
--- a/debian/fastlink-doc.doc-base.fastlink
+++ b/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
=====================================
--- a/debian/fastlink-doc.doc-base.loops
+++ b/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
=====================================
--- a/debian/fastlink-doc.doc-base.parallelization
+++ b/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
=====================================
--- a/debian/fastlink-doc.doc-base.parallelization2
+++ b/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
=====================================
--- a/debian/fastlink-doc.doc-base.random
+++ b/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
=====================================
--- a/debian/fastlink-doc.doc-base.traverse
+++ b/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
=====================================
--- a/debian/fastlink-doc.doc-base.unknown
+++ b/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
=====================================
--- a/debian/get-orig-source
+++ b/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
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -1,13 +1,18 @@
 #!/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



View it on GitLab: https://salsa.debian.org/med-team/fastlink/compare/1a96ca2070c7031c15386de3b73657f671b4e5de...aa13d344c3e7f7c648ee2dc123a7ceff6c0955b9

-- 
View it on GitLab: https://salsa.debian.org/med-team/fastlink/compare/1a96ca2070c7031c15386de3b73657f671b4e5de...aa13d344c3e7f7c648ee2dc123a7ceff6c0955b9
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