[med-svn] [Git][med-team/velvet][master] 14 commits: drop unneeded get-orig-source target
Andreas Tille
gitlab at salsa.debian.org
Thu Jul 5 09:46:34 BST 2018
Andreas Tille pushed to branch master at Debian Med / velvet
Commits:
b3999b2d by Andreas Tille at 2018-07-05T09:23:24+02:00
drop unneeded get-orig-source target
- - - - -
08b56571 by Andreas Tille at 2018-07-05T09:23:40+02:00
debhelper 11
- - - - -
89518555 by Andreas Tille at 2018-07-05T09:24:12+02:00
Point Vcs fields to salsa.debian.org
- - - - -
637675d5 by Andreas Tille at 2018-07-05T09:24:12+02:00
Standards-Version: 4.1.4
- - - - -
c530b9f3 by Andreas Tille at 2018-07-05T09:28:58+02:00
--no-parallel is needed to build successfully
- - - - -
e4c37345 by Andreas Tille at 2018-07-05T09:36:28+02:00
Drop unnecessary Testsuite field
- - - - -
1779d3c5 by Andreas Tille at 2018-07-05T09:46:05+02:00
Provide manpages for versions with MAXKMERLENGTH = 127
- - - - -
0a0a54c7 by Andreas Tille at 2018-07-05T09:47:20+02:00
Propagate hardening options
- - - - -
1ce67a52 by Andreas Tille at 2018-07-05T09:53:28+02:00
Install all manpages
- - - - -
e9ac3f05 by Andreas Tille at 2018-07-05T09:57:58+02:00
Fix spelling
- - - - -
8f871ea9 by Andreas Tille at 2018-07-05T09:58:45+02:00
Secure URI in watch file
- - - - -
69812c79 by Andreas Tille at 2018-07-05T10:00:20+02:00
Remove unused lintian override
- - - - -
b0573e6f by Andreas Tille at 2018-07-05T10:17:29+02:00
Fix manpages installation
- - - - -
b3e56c6c by Andreas Tille at 2018-07-05T10:21:45+02:00
Upload to unstable
- - - - -
25 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/createmanpages
- debian/manpages/velvetg.1
- debian/manpages/velvetg_127.1
- debian/manpages/velvetg_127_long.1
- debian/manpages/velvetg_63.1
- debian/manpages/velvetg_63_long.1
- debian/manpages/velvetg_de.1
- debian/manpages/velvetg_long.1
- debian/manpages/velveth.1
- debian/manpages/velveth_127.1
- debian/manpages/velveth_127_long.1
- debian/manpages/velveth_63.1
- debian/manpages/velveth_63_long.1
- debian/manpages/velveth_de.1
- debian/manpages/velveth_long.1
- + debian/patches/hardening.patch
- debian/patches/series
- + debian/patches/spelling.patch
- debian/rules
- debian/velvet-long.manpages
- − debian/velvet-tests.lintian-overrides
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,21 @@
-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 at 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 at debian.org> Thu, 05 Jul 2018 10:17:41 +0200
velvet (1.2.10+dfsg1-4) experimental; urgency=medium
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -3,15 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at 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
=====================================
--- a/debian/createmanpages
+++ b/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
=====================================
--- a/debian/manpages/velvetg.1
+++ b/debian/manpages/velvetg.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velvetg_127.1
+++ b/debian/manpages/velvetg_127.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velvetg_127_long.1
+++ b/debian/manpages/velvetg_127_long.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velvetg_63.1
+++ b/debian/manpages/velvetg_63.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velvetg_63_long.1
+++ b/debian/manpages/velvetg_63_long.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velvetg_de.1
+++ b/debian/manpages/velvetg_de.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velvetg_long.1
+++ b/debian/manpages/velvetg_long.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velveth.1
+++ b/debian/manpages/velveth.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velveth_127.1
+++ b/debian/manpages/velveth_127.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velveth_127_long.1
+++ b/debian/manpages/velveth_127_long.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velveth_63.1
+++ b/debian/manpages/velveth_63.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velveth_63_long.1
+++ b/debian/manpages/velveth_63_long.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velveth_de.1
+++ b/debian/manpages/velveth_de.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- a/debian/manpages/velveth_long.1
+++ b/debian/manpages/velveth_long.1
@@ -1,5 +1,5 @@
-.\" 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
=====================================
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,13 @@
+Author: Andreas Tille <tille at 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
=====================================
--- a/debian/patches/series
+++ b/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
=====================================
debian/patches/spelling.patch
=====================================
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,26 @@
+Description: Fix spelling
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 05 Jul 2018 09:22:07 +0200
+
+--- a/src/correctedGraph.c
++++ b/src/correctedGraph.c
+@@ -2384,7 +2384,7 @@ static void initializeTodoLists()
+ }
+ }
+
+- velvetLog("Done with initilization\n");
++ velvetLog("Done with initialization\n");
+ }
+
+ static void tourBusNode(Node * node)
+--- a/src/kmerOccurenceTable.c
++++ b/src/kmerOccurenceTable.c
+@@ -161,7 +161,7 @@ void sortKmerOccurenceTable(KmerOccurenc
+ IDnum kmerOccurenceIndex;
+ KmerOccurence * kmerOccurence, * previous;
+
+- velvetLog("Sorting kmer occurence table ... \n");
++ velvetLog("Sorting kmer occurrence table ... \n");
+
+ qsort(table->kmerTable, table->kmerTableSize, sizeof(KmerOccurence),
+ compareKmerOccurences);
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -4,7 +4,7 @@
#export DH_VERBOSE=1
%:
- dh $@
+ dh $@ --no-parallel
pkg=velvet
@@ -73,6 +73,3 @@ override_dh_compress :
override_dh_pysupport :
#Not needed, Python scripts are just for examples
-
-get-orig-source:
- uscan --verbose --force-download --repack --compression xz
=====================================
debian/velvet-long.manpages
=====================================
--- a/debian/velvet-long.manpages
+++ b/debian/velvet-long.manpages
@@ -1,2 +1,3 @@
debian/manpages/*63.1
+debian/manpages/*127.1
debian/manpages/*long.1
=====================================
debian/velvet-tests.lintian-overrides deleted
=====================================
--- a/debian/velvet-tests.lintian-overrides
+++ /dev/null
@@ -1,2 +0,0 @@
-# Ignore false positives about verbose copies of *.gz files from upstream source
-velvet-tests: package-contains-timestamped-gzip usr/share/doc/velvet/tests/read*.f*.gz
=====================================
debian/watch
=====================================
--- a/debian/watch
+++ b/debian/watch
@@ -1,3 +1,4 @@
-version=3
+version=4
+
opts="dversionmangle=s/([~+]dfsg|~nozlibcopy)\d/$1/,uversionmangle=s/$/+dfsg/" \
- http://www.ebi.ac.uk/~zerbino/velvet/velvet_([.\d]*).tgz
+ https://www.ebi.ac.uk/~zerbino/velvet/velvet_([.\d]*).tgz
View it on GitLab: https://salsa.debian.org/med-team/velvet/compare/13b6ed139d6f9a39ce5dadb39881efa337b17dff...b3e56c6c80392815df65efb36bdef1ad142b8bd3
--
View it on GitLab: https://salsa.debian.org/med-team/velvet/compare/13b6ed139d6f9a39ce5dadb39881efa337b17dff...b3e56c6c80392815df65efb36bdef1ad142b8bd3
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