[med-svn] [Git][med-team/abyss][master] 6 commits: routine-update: New upstream version

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Sat May 14 13:21:24 BST 2022



Étienne Mollier pushed to branch master at Debian Med / abyss


Commits:
b9fcf189 by Étienne Mollier at 2022-05-14T13:58:47+02:00
routine-update: New upstream version

- - - - -
aa19cce6 by Étienne Mollier at 2022-05-14T13:58:48+02:00
New upstream version 2.3.5+dfsg
- - - - -
e3366e74 by Étienne Mollier at 2022-05-14T13:58:52+02:00
Update upstream source from tag 'upstream/2.3.5+dfsg'

Update to upstream version '2.3.5+dfsg'
with Debian dir c217b039d79380d3d48daf46a8bbc8bce254171a
- - - - -
fe83eae5 by Étienne Mollier at 2022-05-14T13:58:52+02:00
routine-update: Standards-Version: 4.6.1

- - - - -
4fcef7f2 by Étienne Mollier at 2022-05-14T14:12:27+02:00
Add fix-privacy-breach.patch.

This is to avoid pinging a badges server while reading the offline
documentation.

- - - - -
7c278799 by Étienne Mollier at 2022-05-14T14:20:51+02:00
ready to upload to unstable

- - - - -


19 changed files:

- BloomDBG/bloom-dbg.h
- ChangeLog
- Common/Functional.h
- FilterGraph/FilterGraph.cc
- Graph/ContigGraphAlgorithms.h
- Graph/ExtendPath.h
- Konnector/konnector.cc
- Misc/samtobreak.hs
- PathOverlap/PathOverlap.cpp
- SimpleGraph/SimpleGraph.cpp
- bin/abyss-pe
- configure.ac
- debian/changelog
- debian/control
- + debian/patches/fix-privacy-breach.patch
- debian/patches/series
- doc/ABYSS.1
- doc/abyss-pe.1
- doc/abyss-tofastq.1


Changes:

=====================================
BloomDBG/bloom-dbg.h
=====================================
@@ -175,6 +175,7 @@ seedTypeStr(const SeedType& type)
 		break;
 	}
 	assert(false);
+	return "";
 }
 
 /**
@@ -288,6 +289,7 @@ readResultStr(const ReadResult& result)
 		break;
 	}
 	assert(false);
+	return "";
 }
 
 /**
@@ -460,7 +462,7 @@ printContig(
     unsigned k,
     std::ostream& out)
 {
-	assert(seq.length() >= k);
+	assert(seq.length() >= k); (void)k;
 
 	FastaRecord contig;
 


=====================================
ChangeLog
=====================================
@@ -1,3 +1,12 @@
+2022-05-11 Vladimir Nikolic <vnikolic at bcgsc.ca>
+
+  * Release version 2.3.5
+
+    General:
+	* Fixed compile errors when using the -DNDEBUG flag.
+	* Removed deprecated C++ features.
+
+
 2021-12-20 Vladimir Nikolic <vnikolic at bcgsc.ca>
 
   * Release version 2.3.4


=====================================
Common/Functional.h
=====================================
@@ -5,16 +5,22 @@
 
 /** A functor that always returns true. */
 template <typename Arg>
-struct True : std::unary_function<Arg, bool> {
+struct True {
 	bool operator()(const Arg&) const { return true; }
+
+	typedef Arg argument_type;
+	typedef bool result_type;
 };
 
 /** A functor to adapt a pointer to a member variable. */
 template <typename Arg, typename Result>
-struct MemVar : std::unary_function<Arg, Result>
+struct MemVar
 {
 	MemVar(Result Arg::* p) : m_p(p) { }
 	Result operator()(const Arg& arg) const { return arg.*m_p; }
+
+	typedef Arg argument_type;
+	typedef Result result_type;
   private:
 	Result Arg::* m_p;
 };
@@ -28,8 +34,7 @@ MemVar<Arg, Result> mem_var(Result Arg::* p)
 
 /** A functor, f1(f2(x)). */
 template <typename F1, typename F2>
-struct unary_compose : std::unary_function <
-		typename F2::argument_type, typename F1::result_type>
+struct unary_compose
 {
 	unary_compose(const F1& f1, const F2& f2) : f1(f1), f2(f2) { }
 	typename F1::result_type operator()(
@@ -37,6 +42,9 @@ struct unary_compose : std::unary_function <
 	{
 		return f1(f2(x));
 	}
+
+	typedef typename F2::argument_type argument_type;
+	typedef typename F1::result_type result_type;
   private:
 	F1 f1;
 	F2 f2;
@@ -51,8 +59,7 @@ unary_compose<F1, F2> compose1(const F1& f1, const F2& f2)
 
 /** A functor, f(g1(x), g2(x)). */
 template <typename F, typename G1, typename G2>
-struct binary_compose : std::unary_function <
-		typename G1::argument_type, typename F::result_type>
+struct binary_compose
 {
 	binary_compose(const F& f, const G1& g1, const G2& g2)
 		: f(f), g1(g1), g2(g2) { }
@@ -61,6 +68,9 @@ struct binary_compose : std::unary_function <
 	{
 		return f(g1(x), g2(x));
 	}
+
+	typedef typename G1::argument_type argument_type;
+	typedef typename G1::result_type result_type;
   private:
 	F f;
 	G1 g1;


=====================================
FilterGraph/FilterGraph.cc
=====================================
@@ -382,7 +382,7 @@ removeContigs(Graph& g, vector<vertex_descriptor>& sc)
 }
 
 /** Return the value of the bit at the specified index. */
-struct Marked : unary_function<vertex_descriptor, bool>
+struct Marked
 {
 	typedef vector<bool> Data;
 	Marked(const Graph& g, const Data& data)
@@ -391,6 +391,9 @@ struct Marked : unary_function<vertex_descriptor, bool>
 	{}
 	bool operator()(vertex_descriptor u) const { return m_data[get(vertex_contig_index, m_g, u)]; }
 
+	typedef vertex_descriptor argument_type;
+	typedef bool result_type;
+
   private:
 	const Graph& m_g;
 	const Data& m_data;
@@ -434,7 +437,7 @@ struct sortContigs
 	}
 };
 
-struct ShorterThanX : unary_function<vertex_descriptor, bool>
+struct ShorterThanX
 {
 	const Graph& g;
 	const vector<bool>& seen;
@@ -451,9 +454,12 @@ struct ShorterThanX : unary_function<vertex_descriptor, bool>
 		return g[y].length < x && !get(vertex_removed, g, y) &&
 		       !seen[get(vertex_contig_index, g, y)];
 	}
+
+	typedef vertex_descriptor argument_type;
+	typedef bool result_type;
 };
 
-struct LongerThanX : unary_function<vertex_descriptor, bool>
+struct LongerThanX
 {
 	const Graph& g;
 	const vector<bool>& seen;
@@ -470,9 +476,12 @@ struct LongerThanX : unary_function<vertex_descriptor, bool>
 		return g[y].length > x && !get(vertex_removed, g, y) &&
 		       !seen[get(vertex_contig_index, g, y)];
 	}
+
+	typedef vertex_descriptor argument_type;
+	typedef bool result_type;
 };
 
-struct CoverageLessThan : unary_function<vertex_descriptor, bool>
+struct CoverageLessThan
 {
 	const Graph& g;
 	const vector<bool>& seen;
@@ -491,6 +500,9 @@ struct CoverageLessThan : unary_function<vertex_descriptor, bool>
 		return meanCoverage < minCov && !get(vertex_removed, g, u) &&
 		       !seen[get(vertex_contig_index, g, u)];
 	}
+
+	typedef vertex_descriptor argument_type;
+	typedef bool result_type;
 };
 
 static void
@@ -549,7 +561,7 @@ getSequence(const Graph& g, vertex_descriptor u)
 }
 
 /** Return whether the specified edge is inconsistent. */
-struct is_edge_inconsistent : unary_function<edge_descriptor, bool>
+struct is_edge_inconsistent
 {
 	const Graph& g;
 
@@ -574,6 +586,9 @@ struct is_edge_inconsistent : unary_function<edge_descriptor, bool>
 				return true;
 		return false;
 	}
+
+	typedef edge_descriptor argument_type;
+	typedef bool result_type;
 };
 
 template<typename It>


=====================================
Graph/ContigGraphAlgorithms.h
=====================================
@@ -18,7 +18,7 @@ using boost::graph_traits;
 
 /** Return true if the edge e is a palindrome. */
 template<typename Graph>
-struct IsPalindrome : std::unary_function<typename graph_traits<Graph>::edge_descriptor, bool>
+struct IsPalindrome
 {
 	IsPalindrome(const Graph& g)
 	  : m_g(g)
@@ -28,6 +28,9 @@ struct IsPalindrome : std::unary_function<typename graph_traits<Graph>::edge_des
 		return source(e, m_g) == get(vertex_complement, m_g, target(e, m_g));
 	}
 
+	typedef typename graph_traits<Graph>::edge_descriptor argument_type;
+	typedef bool result_type;
+
   private:
 	const Graph& m_g;
 };
@@ -223,7 +226,7 @@ assemble(Graph& g, OutIt out)
 
 /** Return true if the edge e is +ve sense. */
 template<typename Graph>
-struct IsPositive : std::unary_function<typename graph_traits<Graph>::edge_descriptor, bool>
+struct IsPositive
 {
 	IsPositive(const Graph& g)
 	  : m_g(g)
@@ -233,6 +236,9 @@ struct IsPositive : std::unary_function<typename graph_traits<Graph>::edge_descr
 		return !get(vertex_sense, m_g, source(e, m_g)) && !get(vertex_sense, m_g, target(e, m_g));
 	}
 
+	typedef typename graph_traits<Graph>::edge_descriptor argument_type;
+	typedef bool result_type;
+
   private:
 	const Graph& m_g;
 };
@@ -284,7 +290,7 @@ pruneTips_if(Graph& g, OutputIt result, Pred p)
 
 /** Return true if the vertex is a normal 1-in 0-out tip. */
 template<typename Graph>
-struct IsTip : std::unary_function<typename graph_traits<Graph>::vertex_descriptor, bool>
+struct IsTip
 {
 	IsTip(const Graph& g)
 	  : m_g(g)
@@ -294,6 +300,9 @@ struct IsTip : std::unary_function<typename graph_traits<Graph>::vertex_descript
 		return in_degree(v, m_g) == 1;
 	}
 
+	typedef typename graph_traits<Graph>::vertex_descriptor argument_type;
+	typedef bool result_type;
+
   private:
 	const Graph& m_g;
 };


=====================================
Graph/ExtendPath.h
=====================================
@@ -76,6 +76,7 @@ static inline const char* pathExtensionResultStr(PathExtensionResultCode result)
 	default:
 		assert(false);
 	}
+	return "";
 }
 
 /** length of path extension (in vertices) and reason for stopping */


=====================================
Konnector/konnector.cc
=====================================
@@ -457,7 +457,7 @@ static inline string calcQual(const FastqRecord& orig,
 	unsigned extendedRight)
 {
 	assert(extended.length() == orig.seq.length() +
-		extendedLeft + extendedRight);
+		extendedLeft + extendedRight); (void)extendedRight;
 
 	unsigned char correctedQual = opt::qualityOffset + opt::correctedQual;
 	string qual(extended.length(), correctedQual);


=====================================
Misc/samtobreak.hs
=====================================
@@ -279,7 +279,7 @@ parseArgs = do
   where
   help = putStr (usageInfo usage options) >> exitSuccess
   tryHelp = "Try 'abyss-samtobreak --help' for more information."
-  version = "abyss-samtobreak (ABySS) 2.3.4\n"
+  version = "abyss-samtobreak (ABySS) 2.3.5\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 


=====================================
PathOverlap/PathOverlap.cpp
=====================================
@@ -507,7 +507,7 @@ mergePaths(const Paths& paths, const OverlapMap& overlaps, const ContigPath& mer
 }
 
 /** Return true if the edge e is a path overlap. */
-struct IsPathOverlap : unary_function<edge_descriptor, bool>
+struct IsPathOverlap
 {
 	IsPathOverlap(const Graph& g, const OverlapMap& pmap, const IsPositive<Graph>& pred)
 	  : m_g(g)
@@ -522,6 +522,9 @@ struct IsPathOverlap : unary_function<edge_descriptor, bool>
 		return stranded && getOverlap(m_pmap, source(e, m_g), target(e, m_g));
 	}
 
+	typedef edge_descriptor argument_type;
+	typedef bool result_type;
+
   private:
 	const Graph& m_g;
 	const OverlapMap& m_pmap;


=====================================
SimpleGraph/SimpleGraph.cpp
=====================================
@@ -305,7 +305,6 @@ static unsigned calculatePathLength(const Graph& g,
 
 /** Compare the lengths of two paths. */
 struct ComparePathLength
-		: binary_function<ContigPath, ContigPath, bool>
 {
 	ComparePathLength(const Graph& g, const ContigNode& origin)
 		: m_g(g), m_origin(origin) { }
@@ -315,6 +314,10 @@ struct ComparePathLength
 		return lenA < lenB
 			|| (lenA == lenB && a.size() < b.size());
 	}
+
+	typedef ContigPath first_argument_type;
+	typedef ContigPath second_argument_type;
+	typedef bool result_type;
   private:
 	const Graph& m_g;
 	const ContigNode& m_origin;


=====================================
bin/abyss-pe
=====================================
@@ -414,7 +414,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users at bcgsc.ca.'
 
 version:
-	@echo "abyss-pe (ABySS) 2.3.4"
+	@echo "abyss-pe (ABySS) 2.3.5"
 	@echo "Written by Shaun Jackman and Anthony Raymond."
 	@echo
 	@echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"


=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
 AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.3.4, abyss-users at bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.3.5, abyss-users at bcgsc.ca, abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 
 AC_CONFIG_MACRO_DIR([m4])


=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+abyss (2.3.5+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Standards-Version: 4.6.1 (routine-update)
+  * Add fix-privacy-breach.patch; this is to avoid pinging a badges server
+    while reading the offline documentation.
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 14 May 2022 14:19:36 +0200
+
 abyss (2.3.4+dfsg-1) unstable; urgency=medium
 
   * Upstream declares that only 64bit architectures are supported


=====================================
debian/control
=====================================
@@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13),
                pkg-config,
                help2man,
                debhelper
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/abyss
 Vcs-Git: https://salsa.debian.org/med-team/abyss.git
 Homepage: https://github.com/bcgsc/abyss


=====================================
debian/patches/fix-privacy-breach.patch
=====================================
@@ -0,0 +1,18 @@
+Description: fix privacy generic breaches in the README file
+ they are caused by inclusion of badges from remote locations.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: not-needed
+Last-Update: 2022-05-14
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- abyss.orig/README.md
++++ abyss/README.md
+@@ -1,8 +1,3 @@
+-[![Release](https://img.shields.io/github/release/bcgsc/abyss.svg)](https://github.com/bcgsc/abyss/releases)
+-[![Downloads](https://img.shields.io/github/downloads/bcgsc/abyss/total?logo=github)](https://github.com/bcgsc/abyss/releases/download/2.2.3/abyss-2.2.3.tar.gz)
+-[![Conda](https://img.shields.io/conda/dn/bioconda/abyss?label=Conda)](https://anaconda.org/bioconda/abyss)
+-[![Issues](https://img.shields.io/github/issues/bcgsc/abyss.svg)](https://github.com/bcgsc/abyss/issues)
+-
+ ABySS
+ ================================================================================
+ 


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 abyss-pe.patch
 # gtest.patch
 #abyss-32-bit.patch
+fix-privacy-breach.patch


=====================================
doc/ABYSS.1
=====================================
@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.4" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.5" "User Commands"
 .SH NAME
 ABYSS \- assemble short reads into contigs
 .SH SYNOPSIS


=====================================
doc/abyss-pe.1
=====================================
@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.4" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.5" "User Commands"
 .SH NAME
 abyss-pe - assemble reads into contigs
 .SH SYNOPSIS


=====================================
doc/abyss-tofastq.1
=====================================
@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.4" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.5" "User Commands"
 .SH NAME
 abyss-tofastq \- convert various file formats to FASTQ format
 .br



View it on GitLab: https://salsa.debian.org/med-team/abyss/-/compare/6bf6c9b6aaf6da2efe1e2274ee5f9529c50db7b7...7c27879992997096cf99b7e5d96e4e09b6b48c90

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View it on GitLab: https://salsa.debian.org/med-team/abyss/-/compare/6bf6c9b6aaf6da2efe1e2274ee5f9529c50db7b7...7c27879992997096cf99b7e5d96e4e09b6b48c90
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