[med-svn] [Git][med-team/libmaus2][master] 8 commits: d/watch: adjust repack suffix from dfsg to ds
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Oct 24 14:45:33 BST 2021
Étienne Mollier pushed to branch master at Debian Med / libmaus2
Commits:
014bb2df by Étienne Mollier at 2021-10-24T12:21:21+02:00
d/watch: adjust repack suffix from dfsg to ds
Files-Exclude are so for technical reasons, not for licensing
concerns.
- - - - -
7396a414 by Étienne Mollier at 2021-10-24T12:23:07+02:00
update changelog
- - - - -
629b27cf by Étienne Mollier at 2021-10-24T12:23:51+02:00
routine-update: New upstream version
- - - - -
3b6cb162 by Étienne Mollier at 2021-10-24T12:23:52+02:00
New upstream version 2.0.806+ds
- - - - -
e990df60 by Étienne Mollier at 2021-10-24T12:24:04+02:00
Update upstream source from tag 'upstream/2.0.806+ds'
Update to upstream version '2.0.806+ds'
with Debian dir 41a2f26d5fb99e6532141225f9993c0386a8759e
- - - - -
9bdfc174 by Étienne Mollier at 2021-10-24T12:24:05+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
e853876a by Étienne Mollier at 2021-10-24T15:02:15+02:00
d/changelog: New upstream version (Closes: #997199)
- - - - -
0aabdb10 by Étienne Mollier at 2021-10-24T15:44:52+02:00
ready for upload to unstable
- - - - -
20 changed files:
- ChangeLog
- configure.ac
- debian/changelog
- debian/control
- debian/watch
- src/libmaus2/aio/SecrecyOutputStreamFactory.cpp
- src/libmaus2/avl/AVLSet.hpp
- src/libmaus2/bambam/parallel/ScramCramEncoding.cpp
- src/libmaus2/dazzler/align/SortingOverlapOutputBuffer.hpp
- src/libmaus2/math/Convolution.hpp
- src/libmaus2/math/Matrix.hpp
- src/libmaus2/parallel/AtomicPtrStack.hpp
- src/libmaus2/parallel/threadpool/cram/CramEnqueuePackageDataHandler.hpp
- src/libmaus2/sorting/RankSearch.hpp
- src/libmaus2/sorting/SortingBufferedOutputFile.hpp
- src/libmaus2/util/OctetString.cpp
- src/libmaus2/util/OctetString.hpp
- src/libmaus2/util/Utf8String.cpp
- src/libmaus2/util/Utf8String.hpp
- src/test/testThreadPoolCramEncode.cpp
Changes:
=====================================
ChangeLog
=====================================
@@ -1,3 +1,29 @@
+libmaus2 (2.0.806-1) unstable; urgency=medium
+
+ * Add missing include directive required for gcc 11
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Sat, 16 Oct 2021 17:30:12 +0200
+
+libmaus2 (2.0.805-1) unstable; urgency=medium
+
+ * Fix compilation on w64
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Wed, 15 Sep 2021 11:04:58 +0200
+
+libmaus2 (2.0.804-1) unstable; urgency=medium
+
+ * Fix some warnings when compiling without io_lib
+ * Remove -std=c++17 from cflags reported by libsecrecy as flag is not accepted by clang when compiling .c files
+ * Fix warning when compiling without openmp support
+ * Change external template statements in OctectString and Utf8String from class to struct
+ * Fix check for calling toupper in src/test/testThreadPoolCramEncode.cpp
+ * Fix include guard in CramEnqueuePackageDataHandler.hpp
+ * Change bool const & to bool in return type of AtomicPtrStack::top
+ * Fix infinite loop in SecrecyOutputStreamFactory::constructShared()
+ * Remove nonsense identity variable assignments in configure.ac
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Mon, 13 Sep 2021 14:27:49 +0200
+
libmaus2 (2.0.803-1) unstable; urgency=medium
* Reduce size of test in testsort as it does not compile on x86
=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
-AC_INIT(libmaus2,2.0.803,[germant at miltenyibiotec.de],[libmaus2],[https://gitlab.com/german.tischler/libmaus2])
-LIBRARY_VERSION=2:803:0
+AC_INIT(libmaus2,2.0.806,[germant at miltenyibiotec.de],[libmaus2],[https://gitlab.com/german.tischler/libmaus2])
+LIBRARY_VERSION=2:806:0
AC_MSG_NOTICE([Configuring for source in directory ${srcdir}])
AC_CANONICAL_SYSTEM
AC_CANONICAL_HOST
@@ -1978,12 +1978,10 @@ fi
AC_LANG_PUSH([C++])
CPPFLAGS_SAVE="${CPPFLAGS}"
-CPPFLAGS="${CPPFLAGS}"
if test "${seventeen}" = "yes" ; then
CPPFLAGS="${CPPFLAGS} -std=c++17"
fi
LIBS_SAVE="${LIBS}"
-LIBS="${LIBS}"
AC_MSG_CHECKING([whether std::unique_ptr exists])
AC_LINK_IFELSE([AC_LANG_SOURCE([#include <memory>
@@ -2006,12 +2004,10 @@ fi
AC_LANG_PUSH([C++])
CPPFLAGS_SAVE="${CPPFLAGS}"
-CPPFLAGS="${CPPFLAGS}"
if test "${seventeen}" = "yes" ; then
CPPFLAGS="${CPPFLAGS} -std=c++17"
fi
LIBS_SAVE="${LIBS}"
-LIBS="${LIBS}"
AC_MSG_CHECKING([whether std::shared_ptr exists])
AC_LINK_IFELSE([AC_LANG_SOURCE([#include <memory>
@@ -2048,12 +2044,10 @@ fi
AC_LANG_PUSH([C++])
CPPFLAGS_SAVE="${CPPFLAGS}"
-CPPFLAGS="${CPPFLAGS}"
if test "${seventeen}" = "yes" ; then
CPPFLAGS="${CPPFLAGS} -std=c++17"
fi
LIBS_SAVE="${LIBS}"
-LIBS="${LIBS}"
AC_MSG_CHECKING([whether std::unordered_map exists])
AC_LINK_IFELSE([AC_LANG_SOURCE([#include <unordered_map>
@@ -2072,12 +2066,10 @@ AC_LANG_POP
AC_LANG_PUSH([C++])
CPPFLAGS_SAVE="${CPPFLAGS}"
-CPPFLAGS="${CPPFLAGS}"
if test "${seventeen}" = "yes" ; then
CPPFLAGS="${CPPFLAGS} -std=c++17"
fi
LIBS_SAVE="${LIBS}"
-LIBS="${LIBS}"
AC_MSG_CHECKING([whether std::unordered_set exists])
AC_LINK_IFELSE([AC_LANG_SOURCE([#include <unordered_set>
@@ -2108,12 +2100,10 @@ fi
AC_LANG_PUSH([C++])
CPPFLAGS_SAVE="${CPPFLAGS}"
-CPPFLAGS="${CPPFLAGS}"
if test "${seventeen}" = "yes" ; then
CPPFLAGS="${CPPFLAGS} -std=c++17"
fi
LIBS_SAVE="${LIBS}"
-LIBS="${LIBS}"
AC_MSG_CHECKING([whether std::move exists])
AC_LINK_IFELSE([AC_LANG_SOURCE([#include <tuple>
@@ -3037,7 +3027,8 @@ if test "${with_libsecrecy}" != "no" ; then
if test "${libsecrecy}" = "yes" ; then
LIBMAUS2_HAVE_LIBSECRECY="#define LIBMAUS2_HAVE_LIBSECRECY"
LIBMAUS2_LIBSECRECY_LIBS="${libsecrecy_LIBS}"
- LIBMAUS2_LIBSECRECY_CPPFLAGS="${libsecrecy_CFLAGS}"
+ LIBMAUS2_LIBSECRECY_CPPFLAGS=$(echo "${libsecrecy_CFLAGS}" | sed -e "s|-std=c++17||")
+ dnl AC_MSG_NOTICE([Using LIBMAUS2_LIBSECRECY_CPPFLAGS=${LIBMAUS2_LIBSECRECY_CPPFLAGS}])
LIBMAUS2_LIBSECRECY_REQ="libsecrecy"
fi
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+libmaus2 (2.0.806+ds-1) unstable; urgency=medium
+
+ * d/watch: adjust repack suffix from dfsg to ds; Files-Exclude are so for
+ technical reasons, not for licensing concerns.
+ * New upstream version (Closes: #997199)
+ * Standards-Version: 4.6.0 (routine-update)
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 24 Oct 2021 15:05:44 +0200
+
libmaus2 (2.0.803+dfsg-1) unstable; urgency=medium
* New upstream version 2.0.803+dfsg
=====================================
debian/control
=====================================
@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),
libsecrecy-dev,
pkg-config,
zlib1g-dev
-Standards-Version: 4.6.0.1
+Standards-Version: 4.6.0
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
=====================================
debian/watch
=====================================
@@ -1,5 +1,5 @@
version=4
-opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
+opts="repacksuffix=+ds,dversionmangle=auto,repack,compression=xz" \
https://gitlab.com/german.tischler/libmaus2/tags?sort=updated_desc \
.*/archive/.*/libmaus2- at ANY_VERSION@-release-\d+ at ARCHIVE_EXT@
=====================================
src/libmaus2/aio/SecrecyOutputStreamFactory.cpp
=====================================
@@ -84,7 +84,7 @@ libmaus2::aio::OutputStream::shared_ptr_type libmaus2::aio::SecrecyOutputStreamF
libmaus2::aio::OutputStream::shared_ptr_type libmaus2::aio::SecrecyOutputStreamFactory::constructShared(std::string const & filename)
{
- return constructShared(filename);
+ return constructShared(filename,std::string());
}
void libmaus2::aio::SecrecyOutputStreamFactory::rename(std::string const & from, std::string const & to)
=====================================
src/libmaus2/avl/AVLSet.hpp
=====================================
@@ -23,6 +23,7 @@
#include <vector>
#include <cassert>
#include <ostream>
+#include <limits>
// #define AVL_TREE_DEBUG
=====================================
src/libmaus2/bambam/parallel/ScramCramEncoding.cpp
=====================================
@@ -176,7 +176,17 @@ int libmaus2::bambam::parallel::ScramCramEncoding::io_lib_cram_process_work_pack
#endif
}
-int libmaus2::bambam::parallel::ScramCramEncoding::io_lib_cram_set_seqs_per_slice(void * context, size_t const seqsperslice)
+int libmaus2::bambam::parallel::ScramCramEncoding::io_lib_cram_set_seqs_per_slice(
+ void *
+ #if defined(LIBMAUS2_HAVE_IO_LIB)
+ context
+ #endif
+ ,
+ size_t const
+ #if defined(LIBMAUS2_HAVE_IO_LIB)
+ seqsperslice
+ #endif
+)
{
#if defined(LIBMAUS2_HAVE_IO_LIB)
return libmaus2_bambam_scram_cram_set_seqs_per_slice(context,seqsperslice);
@@ -188,7 +198,17 @@ int libmaus2::bambam::parallel::ScramCramEncoding::io_lib_cram_set_seqs_per_slic
#endif
}
-int libmaus2::bambam::parallel::ScramCramEncoding::io_lib_cram_set_bases_per_slice(void * context, size_t const basesperslice)
+int libmaus2::bambam::parallel::ScramCramEncoding::io_lib_cram_set_bases_per_slice(
+ void *
+ #if defined(LIBMAUS2_HAVE_IO_LIB)
+ context
+ #endif
+ ,
+ size_t const
+ #if defined(LIBMAUS2_HAVE_IO_LIB)
+ basesperslice
+ #endif
+)
{
#if defined(LIBMAUS2_HAVE_IO_LIB)
return libmaus2_bambam_scram_cram_set_bases_per_slice(context,basesperslice);
@@ -201,7 +221,17 @@ int libmaus2::bambam::parallel::ScramCramEncoding::io_lib_cram_set_bases_per_sli
}
-int libmaus2::bambam::parallel::ScramCramEncoding::io_lib_cram_set_version(void * context, std::string const & version)
+int libmaus2::bambam::parallel::ScramCramEncoding::io_lib_cram_set_version(
+ void *
+ #if defined(LIBMAUS2_HAVE_IO_LIB)
+ context
+ #endif
+ ,
+ std::string const &
+ #if defined(LIBMAUS2_HAVE_IO_LIB)
+ version
+ #endif
+)
{
#if defined(LIBMAUS2_HAVE_IO_LIB)
return libmaus2_bambam_scram_cram_set_version(context,version.c_str());
=====================================
src/libmaus2/dazzler/align/SortingOverlapOutputBuffer.hpp
=====================================
@@ -724,7 +724,12 @@ namespace libmaus2
std::string const & outputfilename,
std::string const & tmpfilebase,
uint64_t const mergefanin = getDefaultMergeFanIn(),
- uint64_t const numsortthreads = 1,
+ uint64_t const
+ #if defined(_OPENMP)
+ numsortthreads
+ #endif
+ = 1
+ ,
uint64_t const nummergethreads = 1,
comparator_type comparator = comparator_type())
{
=====================================
src/libmaus2/math/Convolution.hpp
=====================================
@@ -258,7 +258,11 @@ namespace libmaus2
PowerCacheRussian(
std::vector < double > const & P_I,
unsigned int const l, unsigned int const s,
- uint64_t const numthreads,
+ uint64_t const
+ #if defined(_OPENMP)
+ numthreads
+ #endif
+ ,
double const re = std::numeric_limits<double>::min()
)
: n(1ull << l), A(n), e(re)
=====================================
src/libmaus2/math/Matrix.hpp
=====================================
@@ -278,7 +278,14 @@ namespace libmaus2
return R;
}
- template<typename N> Matrix<N> multiply(Matrix<N> const & A, Matrix<N> const & B, uint64_t const threads)
+ template<typename N> Matrix<N> multiply(
+ Matrix<N> const & A,
+ Matrix<N> const & B,
+ uint64_t const
+ #if defined(_OPENMP)
+ threads
+ #endif
+ )
{
assert ( A.c == B.r );
=====================================
src/libmaus2/parallel/AtomicPtrStack.hpp
=====================================
@@ -132,7 +132,7 @@ namespace libmaus2
return p.load().get()[i].store(ptr);
}
- bool const & top(libmaus2::util::shared_ptr<type> & T) const
+ bool top(libmaus2::util::shared_ptr<type> & T) const
{
std::lock_guard<decltype(lock)> slock(lock);
=====================================
src/libmaus2/parallel/threadpool/cram/CramEnqueuePackageDataHandler.hpp
=====================================
@@ -15,7 +15,7 @@
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>..
*/
-#if ! defined(LIBMAUS2_PARALLEL_THREADPOOL_BAM_CRAMENQUEPACKAGEDATAHANDLERB_HPP)
+#if ! defined(LIBMAUS2_PARALLEL_THREADPOOL_BAM_CRAMENQUEPACKAGEDATAHANDLER_HPP)
#define LIBMAUS2_PARALLEL_THREADPOOL_BAM_CRAMENQUEPACKAGEDATAHANDLER_HPP
#include <libmaus2/parallel/threadpool/bam/ThreadPoolBamParseControl.hpp>
=====================================
src/libmaus2/sorting/RankSearch.hpp
=====================================
@@ -1593,7 +1593,12 @@ namespace libmaus2
{
std::vector < std::vector < std::shared_ptr<SortOp> > > Vop;
- void dispatchOMP(std::size_t const threads)
+ void dispatchOMP(
+ std::size_t const
+ #if defined(_OPENMP)
+ threads
+ #endif
+ )
{
std::atomic<int> parfailed(0);
=====================================
src/libmaus2/sorting/SortingBufferedOutputFile.hpp
=====================================
@@ -572,7 +572,11 @@ namespace libmaus2
}
Merger(
- uint64_t const numthreads,
+ uint64_t const
+ #if defined(_OPENMP)
+ numthreads
+ #endif
+ ,
libmaus2::autoarray::AutoArray < sorter_ptr_type > & ASO,
std::vector<std::string> const & rVfn,
order_type & order,
@@ -815,7 +819,15 @@ namespace libmaus2
}
- std::string reduceParallel(uint64_t const numthreads, uint64_t const backblocksize = 1024ull, uint64_t const maxfan = 16ull)
+ std::string reduceParallel(
+ uint64_t const
+ #if defined(_OPENMP)
+ numthreads
+ #endif
+ ,
+ uint64_t const backblocksize = 1024ull,
+ uint64_t const maxfan = 16ull
+ )
{
struct MergeObject
{
@@ -900,7 +912,16 @@ namespace libmaus2
}
- std::string reduceUniqueParallel(IndexCallback & indexer, uint64_t const numthreads, uint64_t const backblocksize = 1024ull, uint64_t const maxfan = 16ull)
+ std::string reduceUniqueParallel(
+ IndexCallback & indexer,
+ uint64_t const
+ #if defined(_OPENMP)
+ numthreads
+ #endif
+ ,
+ uint64_t const backblocksize = 1024ull,
+ uint64_t const maxfan = 16ull
+ )
{
struct MergeObject
{
@@ -995,7 +1016,15 @@ namespace libmaus2
}
- std::string reduceUniqueParallel(uint64_t const numthreads, uint64_t const backblocksize = 1024ull, uint64_t const maxfan = 16ull)
+ std::string reduceUniqueParallel(
+ uint64_t const
+ #if defined(_OPENMP)
+ numthreads
+ #endif
+ ,
+ uint64_t const backblocksize = 1024ull,
+ uint64_t const maxfan = 16ull
+ )
{
struct MergeObject
{
@@ -1180,7 +1209,16 @@ namespace libmaus2
}
- std::string reduceParallel(uint64_t const numthreads, IndexCallback & indexer, uint64_t const backblocksize = 1024ull, uint64_t const maxfan = 16ull)
+ std::string reduceParallel(
+ uint64_t const
+ #if defined(_OPENMP)
+ numthreads
+ #endif
+ ,
+ IndexCallback & indexer,
+ uint64_t const backblocksize = 1024ull,
+ uint64_t const maxfan = 16ull
+ )
{
libmaus2::autoarray::AutoArray < typename sorter_type::merger_ptr_type > AME(Vfn.size());
=====================================
src/libmaus2/util/OctetString.cpp
=====================================
@@ -196,5 +196,5 @@ template<unsigned int wordsize>
return SA;
}
-template class libmaus2::util::OctetString<32>;
-template class libmaus2::util::OctetString<64>;
+template struct libmaus2::util::OctetString<32>;
+template struct libmaus2::util::OctetString<64>;
=====================================
src/libmaus2/util/OctetString.hpp
=====================================
@@ -140,8 +140,8 @@ namespace libmaus2
computeSuffixArray(bool const parallel = false) const;
};
- extern template class OctetString<32>;
- extern template class OctetString<64>;
+ extern template struct OctetString<32>;
+ extern template struct OctetString<64>;
}
}
#endif
=====================================
src/libmaus2/util/Utf8String.cpp
=====================================
@@ -424,5 +424,5 @@ template<unsigned int wordsize>
return SA;
}
-template class libmaus2::util::Utf8String<32>;
-template class libmaus2::util::Utf8String<64>;
+template struct libmaus2::util::Utf8String<32>;
+template struct libmaus2::util::Utf8String<64>;
=====================================
src/libmaus2/util/Utf8String.hpp
=====================================
@@ -163,8 +163,8 @@ namespace libmaus2
computeSuffixArray(bool const parallel = false) const;
};
- extern template class Utf8String<32>;
- extern template class Utf8String<64>;
+ extern template struct Utf8String<32>;
+ extern template struct Utf8String<64>;
}
}
#endif
=====================================
src/test/testThreadPoolCramEncode.cpp
=====================================
@@ -99,7 +99,7 @@ int main(int argc, char * argv[])
std::size_t o = 0;
std::string & s = pat.spattern;
for ( std::size_t i = 0; i < s.size(); ++i )
- if ( i >= 33 || i <= 126 )
+ if ( (i >= 33) && (i <= 126) )
s[o++] = ::toupper(s[i]);
s.resize(o);
@@ -116,7 +116,7 @@ int main(int argc, char * argv[])
dictpath /= digest;
std::cerr << "[V] writing " << dictpath << " for " << pat.sid << " in " << ref << std::endl;
- libmaus2::aio::OutputStreamInstance OSI(static_cast<std::string>(dictpath));
+ libmaus2::aio::OutputStreamInstance OSI(dictpath.string());
OSI << s;
OSI.flush();
}
View it on GitLab: https://salsa.debian.org/med-team/libmaus2/-/compare/f084ae20fc24b5bc60adeb5f7caea0d2ded8b70a...0aabdb103932dcc5bd77e8731ce4a95512611a92
--
View it on GitLab: https://salsa.debian.org/med-team/libmaus2/-/compare/f084ae20fc24b5bc60adeb5f7caea0d2ded8b70a...0aabdb103932dcc5bd77e8731ce4a95512611a92
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