[med-svn] [Git][med-team/libmaus2][master] 7 commits: routine-update: New upstream version

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Sun Jan 1 19:52:27 GMT 2023 


Étienne Mollier pushed to branch master at Debian Med / libmaus2


Commits:
fc683a1b by Étienne Mollier at 2023-01-01T17:57:50+01:00
routine-update: New upstream version

- - - - -
cee4cd3e by Étienne Mollier at 2023-01-01T17:57:51+01:00
New upstream version 2.0.813+ds
- - - - -
56a7743b by Étienne Mollier at 2023-01-01T17:58:05+01:00
Update upstream source from tag 'upstream/2.0.813+ds'

Update to upstream version '2.0.813+ds'
with Debian dir 33c1653dff8a66068c2cdf8ac0858c889ed5fa3c
- - - - -
d814d161 by Étienne Mollier at 2023-01-01T17:58:06+01:00
routine-update: Standards-Version: 4.6.2

- - - - -
76f8dd80 by Étienne Mollier at 2023-01-01T17:58:21+01:00
Set upstream metadata fields: Bug-Database.

Changes-By: lintian-brush

- - - - -
72e4efe2 by Étienne Mollier at 2023-01-01T20:43:07+01:00
d/copyright: bump copyright year.

- - - - -
4efc6b01 by Étienne Mollier at 2023-01-01T20:50:07+01:00
ready to upload to unstable.

- - - - -


12 changed files:

- ChangeLog
- config.h.in
- configure.ac
- debian/changelog
- debian/control
- debian/copyright
- debian/upstream/metadata
- src/libmaus2/fastx/RefPathTokenVector.hpp
- src/libmaus2/gtf/ExonSubInfo.hpp
- src/libmaus2/util/DirectoryStructure.hpp
- src/libmaus2/util/MemUsage.cpp
- src/libmaus2/util/OutputFileNameTools.cpp


Changes:

=====================================
ChangeLog
=====================================
@@ -1,3 +1,10 @@
+libmaus2 (2.0.813-1) unstable; urgency=medium
+
+  * Add range checks in DirectoryStructure
+  * Add missing includes required for gcc13
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de>  Sat, 10 Dec 2022 18:30:06 +0100
+
 libmaus2 (2.0.812-1) unstable; urgency=medium
 
   * Add BamAlignmentTagOnlyComparator class


=====================================
config.h.in
=====================================
@@ -12,12 +12,12 @@
 /* Define to 1 if you have the <inttypes.h> header file. */
 #undef HAVE_INTTYPES_H
 
-/* Define to 1 if you have the <memory.h> header file. */
-#undef HAVE_MEMORY_H
-
 /* Define to 1 if you have the <stdint.h> header file. */
 #undef HAVE_STDINT_H
 
+/* Define to 1 if you have the <stdio.h> header file. */
+#undef HAVE_STDIO_H
+
 /* Define to 1 if you have the <stdlib.h> header file. */
 #undef HAVE_STDLIB_H
 
@@ -63,7 +63,9 @@
 /* The size of `unsigned long', as computed by sizeof. */
 #undef SIZEOF_UNSIGNED_LONG
 
-/* Define to 1 if you have the ANSI C header files. */
+/* Define to 1 if all of the C90 standard headers exist (not just the ones
+   required in a freestanding environment). This macro is provided for
+   backward compatibility; new code need not use it. */
 #undef STDC_HEADERS
 
 /* Version number of package */
@@ -81,11 +83,6 @@
 # endif
 #endif
 
-/* Enable large inode numbers on Mac OS X 10.5.  */
-#ifndef _DARWIN_USE_64_BIT_INODE
-# define _DARWIN_USE_64_BIT_INODE 1
-#endif
-
 /* Number of bits in a file offset, on hosts where this is settable. */
 #undef _FILE_OFFSET_BITS
 


=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
-AC_INIT(libmaus2,2.0.812,[germant at miltenyibiotec.de],[libmaus2],[https://gitlab.com/german.tischler/libmaus2])
-LIBRARY_VERSION=2:812:0
+AC_INIT(libmaus2,2.0.813,[germant at miltenyibiotec.de],[libmaus2],[https://gitlab.com/german.tischler/libmaus2])
+LIBRARY_VERSION=2:813:0
 AC_MSG_NOTICE([Configuring for source in directory ${srcdir}])
 AC_CANONICAL_SYSTEM
 AC_CANONICAL_HOST


=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+libmaus2 (2.0.813+ds-1) unstable; urgency=medium
+
+  * New upstream version
+  * Standards-Version: 4.6.2 (routine-update)
+  * Set upstream metadata fields: Bug-Database.
+  * d/copyright: bump copyright year.
+
+ -- Étienne Mollier <emollier at debian.org>  Sun, 01 Jan 2023 20:49:39 +0100
+
 libmaus2 (2.0.812+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: 4.6.1
+Standards-Version: 4.6.2
 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/copyright
=====================================
@@ -151,7 +151,7 @@ License: GPL-3+
 Files: debian/*
 Copyright: 2019-2020 Andreas Tille <tille at debian.org>
            2019-2020 Steffen Moeller <moeller at debian.org>
-           2020-2022 Étienne Mollier <emollier at debian.org>
+           2020-2023 Étienne Mollier <emollier at debian.org>
 License: GPL-3+
 
 License: MIT


=====================================
debian/upstream/metadata
=====================================
@@ -7,6 +7,6 @@ Registry:
   Entry: libmaus
   Comment: No refereral to a version 2
 Bug-Submit: tischler at mpi-cbg.de
-Bug-Database: https://gitlab.com/german.tischler/libmaus2/issues
+Bug-Database: https://gitlab.com/german.tischler/libmaus2/-/issues
 Repository: https://gitlab.com/german.tischler/libmaus2.git
 Repository-Browse: https://gitlab.com/german.tischler/libmaus2


=====================================
src/libmaus2/fastx/RefPathTokenVector.hpp
=====================================
@@ -19,6 +19,7 @@
 #if ! defined(LIBMAUS2_FASTX_REFPATHTOKENVECTOR_HPP)
 #define LIBMAUS2_FASTX_REFPATHTOKENVECTOR_HPP
 
+#include <cstdint>
 #include <libmaus2/fastx/RefPathToken.hpp>
 #include <vector>
 #include <limits>


=====================================
src/libmaus2/gtf/ExonSubInfo.hpp
=====================================
@@ -18,6 +18,7 @@
 #if ! defined(LIBMAUS2_GTF_EXONSUBINFO_HPP)
 #define LIBMAUS2_GTF_EXONSUBINFO_HPP
 
+#include <cstdint>
 #include <ostream>
 
 namespace libmaus2


=====================================
src/libmaus2/util/DirectoryStructure.hpp
=====================================
@@ -105,6 +105,13 @@ namespace libmaus2
 
 			std::vector<uint64_t> getVector(uint64_t const i) const
 			{
+				if ( ! (i<n) ) {
+					libmaus2::exception::LibMausException lme;
+					lme.getStream() << "[E] libmaus2::util::DirectoryStructure::getVector: i=" << i << " is out of range for n=" << n << std::endl;
+					lme.finish();
+					throw lme;
+				}
+
 				std::vector<uint64_t> V;
 
 				uint64_t z = i;
@@ -130,6 +137,13 @@ namespace libmaus2
 			 **/
 			std::string operator[](uint64_t const i) const
 			{
+				if ( ! (i<n) ) {
+					libmaus2::exception::LibMausException lme;
+					lme.getStream() << "[E] libmaus2::util::DirectoryStructure::operator[]: i=" << i << " is out of range for n=" << n << std::endl;
+					lme.finish();
+					throw lme;
+				}
+
 				std::vector<uint64_t> V = getVector(i);
 
 				DirectoryEntry DS(prefix,V);
@@ -146,6 +160,13 @@ namespace libmaus2
 			 **/
 			std::string getDirectoryFor(uint64_t const i) const
 			{
+				if ( ! (i<n) ) {
+					libmaus2::exception::LibMausException lme;
+					lme.getStream() << "[E] libmaus2::util::DirectoryStructure::getDirectoryFor: i=" << i << " is out of range for n=" << n << std::endl;
+					lme.finish();
+					throw lme;
+				}
+
 				std::vector<uint64_t> V = getVector(i);
 
 				DirectoryEntry DS(prefix,V);


=====================================
src/libmaus2/util/MemUsage.cpp
=====================================
@@ -16,7 +16,7 @@
     You should have received a copy of the GNU General Public License
     along with this program.  If not, see <http://www.gnu.org/licenses/>..
 */
-
+#include <cstdint>
 #include <libmaus2/util/MemUsage.hpp>
 #include <libmaus2/util/MemoryStatistics.hpp>
 #include <libmaus2/posix/PosixFunctions.hpp>


=====================================
src/libmaus2/util/OutputFileNameTools.cpp
=====================================
@@ -17,6 +17,7 @@
     along with this program.  If not, see <http://www.gnu.org/licenses/>..
 */
 
+#include <cstdint>
 #include <libmaus2/util/OutputFileNameTools.hpp>
 
 std::string libmaus2::util::OutputFileNameTools::lcp(std::string const & a, std::string const & b)



View it on GitLab: https://salsa.debian.org/med-team/libmaus2/-/compare/2254d3314d84fc4a834dd394025aac8cdfe12f09...4efc6b010fed0f1a29fb939a509c96a8ff625da7

-- 
View it on GitLab: https://salsa.debian.org/med-team/libmaus2/-/compare/2254d3314d84fc4a834dd394025aac8cdfe12f09...4efc6b010fed0f1a29fb939a509c96a8ff625da7
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