debian/changelog

-velvet (1.2.10+dfsg1-5) UNRELEASED; urgency=medium
+velvet (1.2.10+dfsg1-5) unstable; urgency=medium
 
+  [ Steffen Moeller ]
   * debian/upstream/metadata: Added references to registries.
 
- -- Steffen Moeller <moeller@debian.org>  Sun, 10 Sep 2017 12:38:50 +0200
+  [ Andreas Tille ]
+  * drop unneeded get-orig-source target
+  * debhelper 11 (--no-parallel needed)
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.1.4
+  * d/control: Drop unnecessary Testsuite field
+  * Provide manpages for versions with MAXKMERLENGTH = 127
+  * Try better hardening but failed (hints are welcome)
+  * Fix spelling
+  * Secure URI in watch file
+  * Remove unused lintian override
+
+ -- Andreas Tille <tille@debian.org>  Thu, 05 Jul 2018 10:17:41 +0200
 
 velvet (1.2.10+dfsg1-4) experimental; urgency=medium
 

debian/compat

-9
+11

debian/control

@@ -3,15 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Charles Plessy <plessy@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
-Testsuite: autopkgtest
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                zlib1g-dev,
                texlive-latex-base,
                texlive-latex-recommended
-Standards-Version: 3.9.6
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/velvet.git
-Vcs-Git: git://anonscm.debian.org/debian-med/velvet.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/velvet
+Vcs-Git: https://salsa.debian.org/med-team/velvet.git
 Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
 
 Package: velvet

debian/createmanpages

@@ -27,6 +27,17 @@ help2man --no-info --version-string="$VERSION" \
 help2man --no-info --version-string="$VERSION" \
 	--name="simple hashing program (LONGSEQUENCES)"									velveth_long	> ${MANDIR}/velveth_long.1
 
+# for MAXKMERLENGTH = 127
+help2man --no-info --version-option=" " --version-string="$VERSION" \
+	--name="de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 127)"		velvetg_127		> ${MANDIR}/velvetg_127.1
+help2man --no-info --version-option=" " --version-string="$VERSION" \
+	--name="de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 127, LONGSEQUENCES)"	velvetg_127_long	> ${MANDIR}/velvetg_127_long.1
+help2man --no-info --version-string="$VERSION" \
+	--name="simple hashing program (MAXKMERLENGTH = 127)"								velveth_127		> ${MANDIR}/velveth_127.1
+help2man --no-info --version-string="$VERSION" \
+	--name="simple hashing program (MAXKMERLENGTH = 127, LONGSEQUENCES)"						velveth_127_long	> ${MANDIR}/velveth_127_long.1
+
+
 cat <<EOT
 Please enhance the help2man output.
 The following web page might be helpful in doing so:

debian/manpages/velvetg.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETG "1" "July 2014" "velvetg 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETG "1" "July 2018" "velvetg 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velvetg \- de Bruijn graph construction, error removal and repeat resolution
 .SH DESCRIPTION

debian/manpages/velvetg_127.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETG_127 "1" "July 2014" "velvetg_127 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETG_127 "1" "July 2018" "velvetg_127 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velvetg_127 \- de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 127)
 .SH DESCRIPTION

debian/manpages/velvetg_127_long.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETG_127_LONG "1" "July 2014" "velvetg_127_long 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETG_127_LONG "1" "July 2018" "velvetg_127_long 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velvetg_127_long \- de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 127, LONGSEQUENCES)
 .SH DESCRIPTION

debian/manpages/velvetg_63.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETG_63 "1" "July 2014" "velvetg_63 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETG_63 "1" "July 2018" "velvetg_63 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velvetg_63 \- de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 63)
 .SH DESCRIPTION

debian/manpages/velvetg_63_long.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETG_63_LONG "1" "July 2014" "velvetg_63_long 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETG_63_LONG "1" "July 2018" "velvetg_63_long 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velvetg_63_long \- de Bruijn graph construction, error removal and repeat resolution (MAXKMERLENGTH = 63, LONGSEQUENCES)
 .SH DESCRIPTION

debian/manpages/velvetg_de.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETG_DE "1" "July 2014" "velvetg_de 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETG_DE "1" "July 2018" "velvetg_de 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velvetg_de \- de Bruijn graph construction, error removal and repeat resolution (colorspace version)
 .SH DESCRIPTION

debian/manpages/velvetg_long.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETG_LONG "1" "July 2014" "velvetg_long 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETG_LONG "1" "July 2018" "velvetg_long 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velvetg_long \- de Bruijn graph construction, error removal and repeat resolution (LONGSEQUENCES)
 .SH DESCRIPTION

debian/manpages/velveth.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETH "1" "July 2014" "velveth 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETH "1" "July 2018" "velveth 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velveth \- simple hashing program
 .SH DESCRIPTION

debian/manpages/velveth_127.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETH_127 "1" "July 2014" "velveth_127 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETH_127 "1" "July 2018" "velveth_127 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velveth_127 \- simple hashing program (MAXKMERLENGTH = 127)
 .SH DESCRIPTION

debian/manpages/velveth_127_long.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETH_127_LONG "1" "July 2014" "velveth_127_long 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETH_127_LONG "1" "July 2018" "velveth_127_long 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velveth_127_long \- simple hashing program (MAXKMERLENGTH = 127, LONGSEQUENCES)
 .SH DESCRIPTION

debian/manpages/velveth_63.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETH_63 "1" "July 2014" "velveth_63 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETH_63 "1" "July 2018" "velveth_63 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velveth_63 \- simple hashing program (MAXKMERLENGTH = 63)
 .SH DESCRIPTION

debian/manpages/velveth_63_long.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETH_63_LONG "1" "July 2014" "velveth_63_long 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETH_63_LONG "1" "July 2018" "velveth_63_long 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velveth_63_long \- simple hashing program (MAXKMERLENGTH = 63, LONGSEQUENCES)
 .SH DESCRIPTION

debian/manpages/velveth_de.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETH_DE "1" "July 2014" "velveth_de 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETH_DE "1" "July 2018" "velveth_de 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velveth_de \- simple hashing program (colorspace version)
 .SH DESCRIPTION

debian/manpages/velveth_long.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.45.1.
-.TH VELVETH_LONG "1" "July 2014" "velveth_long 1.2.10+dfsg1" "User Commands"
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH VELVETH_LONG "1" "July 2018" "velveth_long 1.2.10+dfsg1" "User Commands"
 .SH NAME
 velveth_long \- simple hashing program (LONGSEQUENCES)
 .SH DESCRIPTION

debian/patches/hardening.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Thu, 05 Jul 2018 09:22:07 +0200
+Description: Propagate hardening options
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,5 @@
+ CC = gcc
+-CFLAGS = -Wall
++CFLAGS += -Wall
+ DEBUG = -g
+ LIBS = -lm
+ OPT = -O3

debian/patches/series

@@ -2,3 +2,5 @@ include_debians_zlib.patch
 shuffleSequences_fasta.patch
 fix-perl-path.patch
 0001-isCreateBinary-should-not-be-inline.patch
+hardening.patch
+spelling.patch