[med-svn] [Git][med-team/libmaus2][master] 5 commits: New upstream version 2.0.811+ds
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Sep 15 20:00:08 BST 2022
Étienne Mollier pushed to branch master at Debian Med / libmaus2
Commits:
a44d6230 by Étienne Mollier at 2022-09-15T20:35:43+02:00
New upstream version 2.0.811+ds
- - - - -
f85df75e by Étienne Mollier at 2022-09-15T20:35:43+02:00
routine-update: New upstream version
- - - - -
83d5d397 by Étienne Mollier at 2022-09-15T20:35:48+02:00
Update upstream source from tag 'upstream/2.0.811+ds'
Update to upstream version '2.0.811+ds'
with Debian dir 6aa93ef1d13d995d8116697fbbd2433f66b94392
- - - - -
b925bc31 by Étienne Mollier at 2022-09-15T20:35:49+02:00
routine-update: Standards-Version: 4.6.1
- - - - -
141abfe2 by Étienne Mollier at 2022-09-15T20:53:58+02:00
routine-update: Ready to upload to unstable
- - - - -
15 changed files:
- ChangeLog
- configure.ac
- debian/changelog
- debian/control
- src/libmaus2/aio/PutOutputIterator.hpp
- src/libmaus2/autoarray/AutoArray.hpp
- src/libmaus2/avl/AVLSet.hpp
- src/libmaus2/avl/AtomicAVLKeyPtrSet.hpp
- src/libmaus2/avl/AtomicAVLMap.hpp
- src/libmaus2/avl/AtomicAVLPtrValueMap.hpp
- src/libmaus2/avl/AtomicAVLSet.hpp
- src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
- src/libmaus2/util/ArgParser.hpp
- src/libmaus2/util/UnsignedIntegerIndexIterator.hpp
- src/libmaus2/util/iterator.hpp
Changes:
=====================================
ChangeLog
=====================================
@@ -1,3 +1,9 @@
+libmaus2 (2.0.811-1) unstable; urgency=medium
+
+ * Fix some warnings about std::iterator being deprecated
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Wed, 07 Sep 2022 12:44:58 +0200
+
libmaus2 (2.0.810-1) unstable; urgency=medium
* Apply some improvements in BWT construction
=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
-AC_INIT(libmaus2,2.0.810,[germant at miltenyibiotec.de],[libmaus2],[https://gitlab.com/german.tischler/libmaus2])
-LIBRARY_VERSION=2:810:0
+AC_INIT(libmaus2,2.0.811,[germant at miltenyibiotec.de],[libmaus2],[https://gitlab.com/german.tischler/libmaus2])
+LIBRARY_VERSION=2:811:0
AC_MSG_NOTICE([Configuring for source in directory ${srcdir}])
AC_CANONICAL_SYSTEM
AC_CANONICAL_HOST
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+libmaus2 (2.0.811+ds-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.6.1 (routine-update)
+
+ -- Étienne Mollier <emollier at debian.org> Thu, 15 Sep 2022 20:36:02 +0200
+
libmaus2 (2.0.810+ds-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),
libsecrecy-dev,
pkg-config,
zlib1g-dev
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/libmaus2
Vcs-Git: https://salsa.debian.org/med-team/libmaus2.git
Homepage: https://gitlab.com/german.tischler/libmaus2
=====================================
src/libmaus2/aio/PutOutputIterator.hpp
=====================================
@@ -30,7 +30,7 @@ namespace libmaus2
* output iterator using an objects put function
**/
template<typename _data_type, typename _owner_type>
- struct PutOutputIterator : public ::std::iterator< ::std::output_iterator_tag, _data_type>
+ struct PutOutputIterator
{
//! data type
typedef _data_type data_type;
@@ -39,16 +39,12 @@ namespace libmaus2
//! this type
typedef PutOutputIterator<data_type,owner_type> this_type;
- //! iterator category
- typedef ::std::output_iterator_tag iterator_category;
- //! value type
- typedef typename ::std::iterator< ::std::output_iterator_tag, data_type>::value_type value_type;
- //! difference type
- typedef typename ::std::iterator< ::std::output_iterator_tag, data_type>::difference_type difference_type;
- //! reference type
- typedef typename ::std::iterator< ::std::output_iterator_tag, data_type>::reference reference;
- //! pointer type
- typedef typename ::std::iterator< ::std::output_iterator_tag, data_type>::pointer pointer;
+
+ using iterator_category = ::std::output_iterator_tag;
+ using value_type = data_type;
+ using difference_type = std::intptr_t;
+ using pointer = data_type *;
+ using reference = data_type &;
//! owner object used for actual output
owner_type * SGOP;
=====================================
src/libmaus2/autoarray/AutoArray.hpp
=====================================
@@ -44,6 +44,10 @@
#include <mutex>
#include <sstream>
+#if defined(__INTEL_COMPILER)
+#include <aligned_new>
+#endif
+
#include <libmaus2/serialize/Serialize.hpp>
#include <libmaus2/util/MemoryStatistics.hpp>
=====================================
src/libmaus2/avl/AVLSet.hpp
=====================================
@@ -61,7 +61,7 @@ namespace libmaus2
typedef key_type const & reference;
typedef key_type const * pointer;
typedef key_type value_type;
- typedef typename ::std::iterator< ::std::forward_iterator_tag, key_type>::difference_type difference_type;
+ using difference_type = std::intptr_t;
tree_type const * tree;
index_type cur;
@@ -158,7 +158,7 @@ namespace libmaus2
typedef key_type const & reference;
typedef key_type const * pointer;
typedef key_type value_type;
- typedef typename ::std::iterator< ::std::forward_iterator_tag, key_type>::difference_type difference_type;
+ using difference_type = std::intptr_t;
tree_type const * tree;
index_type cur;
=====================================
src/libmaus2/avl/AtomicAVLKeyPtrSet.hpp
=====================================
@@ -75,7 +75,7 @@ namespace libmaus2
typedef libmaus2::util::atomic_shared_ptr<key_type> const & reference;
typedef libmaus2::util::atomic_shared_ptr<key_type> const * pointer;
typedef libmaus2::util::atomic_shared_ptr<key_type> value_type;
- typedef typename ::std::iterator< ::std::forward_iterator_tag, key_type>::difference_type difference_type;
+ using difference_type = std::intptr_t;
tree_type const * tree;
index_type cur;
@@ -172,7 +172,7 @@ namespace libmaus2
typedef libmaus2::util::atomic_shared_ptr<key_type> const & reference;
typedef libmaus2::util::atomic_shared_ptr<key_type> const * pointer;
typedef libmaus2::util::atomic_shared_ptr<key_type> value_type;
- typedef typename ::std::iterator< ::std::forward_iterator_tag, key_type>::difference_type difference_type;
+ using difference_type = std::intptr_t;
tree_type const * tree;
index_type cur;
=====================================
src/libmaus2/avl/AtomicAVLMap.hpp
=====================================
@@ -82,7 +82,7 @@ namespace libmaus2
typedef pair_type * pointer;
typedef _key_type key_type;
typedef _value_type value_type;
- typedef typename ::std::iterator< ::std::forward_iterator_tag, pair_type>::difference_type difference_type;
+ using difference_type = std::intptr_t;
tree_type * tree;
index_type cur;
@@ -184,7 +184,7 @@ namespace libmaus2
typedef pair_type const * pointer;
typedef _key_type key_type;
typedef _value_type value_type;
- typedef typename ::std::iterator< ::std::forward_iterator_tag, pair_type>::difference_type difference_type;
+ using difference_type = std::intptr_t;
tree_type const * tree;
index_type cur;
@@ -286,7 +286,7 @@ namespace libmaus2
typedef pair_type const * pointer;
typedef _key_type key_type;
typedef _value_type value_type;
- typedef typename ::std::iterator< ::std::forward_iterator_tag, pair_type>::difference_type difference_type;
+ using difference_type = std::intptr_t;
tree_type const * tree;
index_type cur;
=====================================
src/libmaus2/avl/AtomicAVLPtrValueMap.hpp
=====================================
@@ -82,7 +82,7 @@ namespace libmaus2
typedef pair_type const * pointer;
typedef _key_type key_type;
typedef _value_type value_type;
- typedef typename ::std::iterator< ::std::forward_iterator_tag, pair_type>::difference_type difference_type;
+ using difference_type = std::intptr_t;
tree_type const * tree;
index_type cur;
@@ -184,7 +184,7 @@ namespace libmaus2
typedef pair_type const * pointer;
typedef _key_type key_type;
typedef _value_type value_type;
- typedef typename ::std::iterator< ::std::forward_iterator_tag, pair_type>::difference_type difference_type;
+ using difference_type = std::intptr_t;
tree_type const * tree;
index_type cur;
=====================================
src/libmaus2/avl/AtomicAVLSet.hpp
=====================================
@@ -75,7 +75,7 @@ namespace libmaus2
typedef key_type const & reference;
typedef key_type const * pointer;
typedef key_type value_type;
- typedef typename ::std::iterator< ::std::forward_iterator_tag, key_type>::difference_type difference_type;
+ using difference_type = std::intptr_t;
tree_type const * tree;
index_type cur;
@@ -172,7 +172,7 @@ namespace libmaus2
typedef key_type const & reference;
typedef key_type const * pointer;
typedef key_type value_type;
- typedef typename ::std::iterator< ::std::forward_iterator_tag, key_type>::difference_type difference_type;
+ using difference_type = std::intptr_t;
tree_type const * tree;
index_type cur;
=====================================
src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
=====================================
@@ -1809,7 +1809,7 @@ namespace libmaus2
sequence_type gp = G.getOffsetSequence(low);
uint64_t s = 0;
- for ( uint64_t i = low; i < high; ++i )
+ for ( uint64_t j = low; j < high; ++j )
s += gp.get();
P[i] = s;
=====================================
src/libmaus2/util/ArgParser.hpp
=====================================
@@ -84,9 +84,9 @@ namespace libmaus2
{
std::string const s = args[i];
- for ( uint64_t i = 0; i < s.size(); ++i )
+ for ( uint64_t j = 0; j < s.size(); ++j )
{
- int const c = static_cast<unsigned char>(s[i]);
+ int const c = static_cast<unsigned char>(s[j]);
if (
::isalnum(c)
=====================================
src/libmaus2/util/UnsignedIntegerIndexIterator.hpp
=====================================
@@ -28,7 +28,7 @@ namespace libmaus2
namespace util
{
template<typename _owner_type, typename _data_type, size_t _k>
- struct UnsignedIntegerIndexIterator : public ::std::iterator< ::std::random_access_iterator_tag, _data_type>
+ struct UnsignedIntegerIndexIterator
{
typedef _owner_type owner_type;
typedef _data_type data_type;
@@ -37,11 +37,12 @@ namespace libmaus2
typedef libmaus2::math::UnsignedInteger<k> index_type;
- typedef ::std::random_access_iterator_tag iterator_category;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::value_type value_type;
- typedef index_type difference_type;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::reference reference;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::pointer pointer;
+
+ using iterator_category = ::std::random_access_iterator_tag;
+ using value_type = data_type;
+ using difference_type = index_type;
+ using pointer = data_type *;
+ using reference = data_type &;
owner_type const * owner;
index_type i;
=====================================
src/libmaus2/util/iterator.hpp
=====================================
@@ -68,11 +68,11 @@ namespace libmaus2
typedef AssignmentProxy<owner_type,data_type> proxy_type;
typedef AssignmentProxyIterator<owner_type,data_type> this_type;
- typedef std::random_access_iterator_tag iterator_category;
- typedef proxy_type reference;
- typedef proxy_type * pointer;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::value_type value_type;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::difference_type difference_type;
+ using iterator_category = ::std::random_access_iterator_tag;
+ using value_type = data_type;
+ using difference_type = std::intptr_t;
+ using pointer = proxy_type *;
+ using reference = proxy_type;
owner_type * owner;
int64_t i;
@@ -180,7 +180,7 @@ namespace libmaus2
}
template<typename _owner_type, typename _data_type, typename _index_type = int64_t>
- struct ConstIterator : public ::std::iterator< ::std::random_access_iterator_tag, _data_type>
+ struct ConstIterator
{
typedef _owner_type owner_type;
typedef _data_type data_type;
@@ -188,11 +188,11 @@ namespace libmaus2
typedef ConstIterator<owner_type,data_type,index_type> this_type;
typedef AssignmentProxyIterator<owner_type,data_type> iterator;
- typedef ::std::random_access_iterator_tag iterator_category;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::value_type value_type;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::difference_type difference_type;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::reference reference;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::pointer pointer;
+ using iterator_category = ::std::random_access_iterator_tag;
+ using value_type = data_type;
+ using difference_type = std::intptr_t;
+ using pointer = data_type *;
+ using reference = data_type &;
owner_type const * owner;
index_type i;
@@ -309,7 +309,7 @@ namespace libmaus2
}
template<typename _owner_type, typename _data_type, typename _index_type = int64_t, typename _difference_type = int64_t>
- struct ConstIteratorDiff : public ::std::iterator< ::std::random_access_iterator_tag, _data_type>
+ struct ConstIteratorDiff
{
typedef _owner_type owner_type;
typedef _data_type data_type;
@@ -317,11 +317,11 @@ namespace libmaus2
typedef ConstIteratorDiff<owner_type,data_type,index_type,_difference_type> this_type;
typedef AssignmentProxyIterator<owner_type,data_type> iterator;
- typedef ::std::random_access_iterator_tag iterator_category;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::value_type value_type;
- typedef _difference_type difference_type;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::reference reference;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::pointer pointer;
+ using iterator_category = ::std::random_access_iterator_tag;
+ using value_type = data_type;
+ using difference_type = _difference_type;
+ using pointer = data_type *;
+ using reference = data_type &;
owner_type const * owner;
index_type i;
@@ -437,18 +437,18 @@ namespace libmaus2
}
template<typename _owner_type, typename _data_type>
- struct ConstIteratorSharedPointer : public ::std::iterator< ::std::random_access_iterator_tag, _data_type>
+ struct ConstIteratorSharedPointer
{
typedef _owner_type owner_type;
typedef _data_type data_type;
typedef ConstIteratorSharedPointer<owner_type,data_type> this_type;
typedef typename owner_type::shared_ptr_type owner_ptr_type;
- typedef ::std::random_access_iterator_tag iterator_category;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::value_type value_type;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::difference_type difference_type;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::reference reference;
- typedef typename ::std::iterator< ::std::random_access_iterator_tag, data_type>::pointer pointer;
+ using iterator_category = ::std::random_access_iterator_tag;
+ using value_type = data_type;
+ using difference_type = std::intptr_t;
+ using pointer = data_type *;
+ using reference = data_type &;
owner_ptr_type owner;
int64_t i;
View it on GitLab: https://salsa.debian.org/med-team/libmaus2/-/compare/665d425f57ae2ceacb27ecaa5766d97e701f9858...141abfe2ec43ff51f6acbb968fd6d2d7968234c4
--
View it on GitLab: https://salsa.debian.org/med-team/libmaus2/-/compare/665d425f57ae2ceacb27ecaa5766d97e701f9858...141abfe2ec43ff51f6acbb968fd6d2d7968234c4
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