CVS commit: pkgsrc/devel/matio

["Niclas Rosenvik" <nros%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   nros
Date:           Sun Nov  7 10:50:38 UTC 2021

Modified Files:
        pkgsrc/devel/matio: Makefile PLIST distinfo
Added Files:
        pkgsrc/devel/matio: buildlink3.mk
        pkgsrc/devel/matio/patches: patch-documentation_Makefile.in

Log Message:
Update devel/matio to version 1.5.12

Pkgsrc changes:
Set license
Buildlink file added

Changes from NEWS file:

Changes in 1.5.21 (25 March 2021)
* Fixed: Avoid usage of strlen when creating MAT_T_UTF8 encoded
  character array (regression of v1.5.20)
* Fixed reading of compression flag from HDF5 MAT file

Changes in 1.5.20 (21 March 2021)
* Added support for writing MAT_T_UTF8 encoded character array
  to HDF5 MAT file (by conversion to UTF-16 if in BMP)
* Updated cmake-conan to version 0.16.1
* Fixed bug with size_t arguments of logging function calls
* Fixed bug reading past EOF from (crafted) MAT file
* Fixed bug writing MAT_T_UTF8 encoded character array to v5
  MAT file
* Fixed printing of MAT_T_UTF8 encoded character array
* Several other fixes, for example for memory leaks

Changes in 1.5.19 (6 November 2020)
* Fixed support for CMake (>= v3.19.0) build system
* Fixed bug reading variable from v4 MAT file
  (regression of v1.5.18)

Changes in 1.5.18 (17 September 2020)
* Added support of HDF5 v1.12.x
* Added support for UTF-8 encoded file name on Windows (MSVC)
  (requires HDF5 >= v1.11.6 for HDF5 MAT file)
* Added support for reading uncompressed v5 MAT file generated
  by SWAN
* Added error codes to public interface
* Added support for CMake build system
* Fixed read performance of numeric array from compressed v5
  MAT file
* Fixed support for VS2005 and VS2008 (MSVC)
  (regression of v1.5.15)
* Fixed mktemp linker warning when using GNU linker
* Fixed bug writing struct array to uncompressed v5 MAT file
  on big endian architecture (regression of v1.5.10)
* Fixed bug writing cell array to uncompressed v5 MAT file
  on big endian architecture
* Fixed bug reading variable name from v4 MAT file
  (CVE-2019-17533)
* Fixed bug reading variable name from (crafted) compressed v5
  MAT file
  (CVE-2020-19497)
* Fixed bug reading dimensions from (crafted) compressed v5 MAT
  file (CVE-2019-20017, CVE-2019-20018, CVE-2019-20020,
  CVE-2019-20052)

Changes in 1.5.17 (18 July 2019)
* Fixed bug reading struct array with packed field names from v5
  MAT file
* Fixed bug reading past EOF from (crafted) uncompressed v5 MAT
  file

Changes in 1.5.16 (25 June 2019)
* Fixed error handling on integer addition/multiplication
  overflows (CVE-2019-13107)

Changes in 1.5.15 (29 March 2019)
* Added new API function Mat_GetHeader to retrieve header string
  of a MAT file
* Fixed integer multiplication overflows when calculating total
  number of elements from (crafted) MAT file
* Fixed bug reading character array from (compressed) v5 MAT
  file (regression of v1.5.14)
* Fixed number of variables for repeated calls of Mat_GetDir
* Fixed memory leak in Mat_VarFree for function class

Changes in 1.5.14 (11 March 2019)
* Deprecated usage of Mat_VarWriteInfo/Mat_VarWriteData in favor
  of Mat_VarWrite/Mat_VarWriteAppend
* Fixed bug reading dimensions from (crafted) compressed v5 MAT
  file (CVE-2019-9026, CVE-2019-9027, CVE-2019-9028,
  CVE-2019-9029, CVE-2019-9030, CVE-2019-9031, CVE-2019-9032,
  CVE-2019-9033, CVE-2019-9034, CVE-2019-9035, CVE-2019-9036,
  CVE-2019-9038)
* Fixed bug reading name (> 24 characters) from v5 MAT file
  (regression of v1.5.13)
* Fixed bug printing datatype in Mat_VarPrint (CVE-2019-9037)

Changes in 1.5.13 (22 October 2018)
* Fixed bug calculating size for zero-rank variables in
  Mat_VarGetSize
* Fixed bug reading dimensions from (crafted) v5 MAT file
* Fixed bug reading tag and class from (crafted) v5 MAT file
* Fixed integer multiplication overflows
* Fixed HDF5 compatibility in Mat_Open and Mat_Create for
  HDF5 > v1.10.1

Changes in 1.5.12 (7 March 2018)
* Updated Mat_VarWriteAppend: Added support to append a
  variable to a previously written struct array in HDF5
  MAT file
* Fixed bug reading MAT_T_UINT16 encoded character array
  from HDF5 MAT file
* Fixed bug reading MAT_T_UTF16 encoded character array
  from compressed v5 MAT file
* Fixed bug writing MAT_T_UTF16 encoded character array
  to HDF5 MAT file
* Fixed buffer overflow in Mat_VarGetCells/Mat_VarGetStructs

Changes in 1.5.11 (22 October 2017)
* Added new API function Mat_VarWriteAppend to append a
  numeric array to a previously written variable in HDF5
  MAT file
* Fixed bug calculating sizes of cell/struct array with
  empty cells/fields in Mat_VarGetSize
* Fixed bug writing cell/struct array with empty cells/fields
  to v5 MAT file
* Fixed bug writing cell/struct array with empty cells/fields
  to HDF5 MAT file
* Fixed read performance of cell/struct array with empty
  cells/fields from v5 MAT file
* Fixed read performance of numeric array from uncompressed
  v5 MAT file
* Fixed testsuite (if configured with the MATLAB application)
* Updated man pages

Changes in 1.5.10 (14 February 2017)
* Added new API function Mat_GetDir to retrieve all variable
  names of a MAT file
* Fixed performance of repeated calls to Mat_VarWrite
  (regression of v1.5.7)
* Fixed bugs reading (hyperslabs of) numeric array where the
  variable data type differs from the desired output data type
* Increased testsuite coverage

Changes in 1.5.9 (22 October 2016)
* Fixed resource leak when reading character array from HDF5
  MAT file
* Fixed bug writing struct to HDF5 MAT file: Mat_VarWrite
  never returned 0 on success
* Fixed bug writing sparse logical array to HDF5 MAT file
* Fixed bug calculating array sizes of struct, cell, complex
  and sparse array in Mat_VarGetSize
* Fixed bug duplicating sparse array with empty data in
  Mat_VarDuplicate
* Fixed segmentation fault when reading compressed v5 MAT
  file with opaque class
* Updated support of HDF5 v1.10.x: No longer depend on
  deprecated v1.8.x symbols

Changes in 1.5.8 (30 June 2016)
* Fixed bug writing array to v4 MAT file on big endian
  architecture (regression of v1.5.7)

Changes in 1.5.7 (22 June 2016)
* Added support for MAT_T_UTF16 when reading character array
  from v5 MAT file
* Added support of HDF5 v1.10.x (with deprecated v1.8.x
  symbols exported)
* Added warning on unsupported character data types when
  reading v5 MAT file
* Added error check if variable already exists when writing
  to MAT file
* Fixed support of custom log functions:
    Moved log levels to the public interface
* Fixed bug creating v4 and v5 MAT file:
    Open in write+update mode
* Fixed bug creating v5 and HDF5 MAT file:
    Set BOF marker to 128
* Fixed bug in Mat_VarDelete:
    Rewind file before looping over variables
* Fixed bug writing cell array with empty struct fields to
  compressed v5 MAT file
* Fixed bug reading empty character array from HDF5 MAT file
* Fixed bug iterating through links in a group of HDF5
  MAT file
* Fixed bug iterating on #subsystem# group of HDF5 MAT file
* Fixed compilation out of source directory
* Fixed C++ compilation on MinGW
* Restructured testsuite
* Fixed testsuite if hdf5 dependency is missing
* Increased testsuite coverage
* Various fixes for variable scopes that cause compilers to
  issue diagnostics

Changes in 1.5.6 (23 February 2016)
* Fixed bug writing array to v4 MAT file on big endian
  architecture
* Fixed bug writing header with more than 127 characters
  to v5 or HDF5 MAT file

Changes in 1.5.5 (19 February 2016)
* Added support of reading sparse array from v4 MAT file
* Added support of writing sparse array to v4 MAT file
* Added support of writing character array to v4 MAT file
* Added support of autogen.sh on Darwin
* Added missing Visual Studio project files for test_mat
* Added missing Visual Studio resource file
* Enabled C++ compilation
* Updated snprintf.c to C99 snprintf v1.1
* Increased testsuite coverage
* Fixed bug writing complex array to v4 MAT file
* Fixed bug writing cell containing a struct with fields
  but empty array to compressed v5 MAT file
* Fixed bug reading hyperslabs of cells and struct fields
  from compressed v5 MAT file (regression of v1.5.3)
* Fixed bug writing empty character array to uncompressed
  v5 MAT file
* Fixed bug reading cells and struct fields from HDF5 MAT file
* Fixed bug printing array dimensions in Mat_VarPrint on MinGW
* Fixed bug calculating array sizes of structs in Mat_VarGetSize
* Fixed bug duplicating sparse array in Mat_VarDuplicate
* Fixed testsuite if zlib/hdf5 dependencies are missing
* Several other fixes, especially for memory leaks

Changes in 1.5.3 (11 January 2016)
* Added support for writing numeric array to v4 MAT file
* Added Visual Studio project for test_mat
* Added new API functions Mat_CalcSingleSubscript2 and
  Mat_CalcSubscripts2 that work on size_t type
* Fixed memory consumption reading compressed v5 MAT file
* Fixed bug writing compressed v5 MAT file
* Fixed bug in Mat_VarReadNextInfo5 where freed variable
  was not set to NULL
* Fixed several bugs in Mat_VarDelete
* Fixed bug writing empty struct to HDF5 MAT file
* Fixed bug writing character array to HDF5 MAT file
* Fixed bug writing character array to compressed v5 MAT file
* Updated Visual Studio solution and project files to work
  with newer HDF5 and Visual Studio versions
* Various fixes for unused variables, unnecessary
  initializations, etc. that
  cause compilers to issue diagnostics
* Several other fixes, especially for memory leaks

Changes in 1.5.2 (31 July 2013)
* Added support for linear data read for v4 and HDF5 MAT file
* Fixed bug reading slices of variables in matdump
* Fixed feof calls so they compile on platforms that
  dereference the argument in a macro
* More robust checking that file is MAT file and eliminates
  some segmentation faults
* Various fixes for unused variables, unnecessary
  initializations, etc. that cause compilers to issue
  diagnostics
* Several other fixes

Changes in 1.5.1 (10 March 2013)
* Fixed bug writing compressed HDF5 file
* Fixed bug reading cell array elements written with
  a non-empty variable name
* Fixed bug writing complex sparse matrices as struct
  fields or cell elements to uncompressed v5 MAT file
* Fixed a number of potential issues identified via
  static analysis
* Fixed uninitialized pointers when creating
  structures through Mat_VarCreateStruct, and fix a
  bug in the struct API testsuite
* Fixed extended sparse support in v7.3 MAT file
* Added 64-bit integer support for v5 MAT file
* Added missing support for reading hyperslabs from
  HDF5 MAT file
* Added variable indexing notation support to
  matdump to display subsets of variables
* Added tests for extended sparse support in testsuite
* Added missing enumerations or default case in
  switch statements

Changes in 1.5.0 (15 April 2012)
* Changed licensing from the GNU Lesser General Public
  License to the BSD-2-Clause License
* Added support for reading/writing HDF5 MAT file
* Bug fixes for compressed variables that caused issues
  with matio reading them
* Upgraded dimensions in matvar_t structure to size_t
  enabling support for large arrays
* Added a testsuite


To generate a diff of this commit:
cvs rdiff -u -r1.5 -r1.6 pkgsrc/devel/matio/Makefile
cvs rdiff -u -r1.1.1.1 -r1.2 pkgsrc/devel/matio/PLIST
cvs rdiff -u -r0 -r1.3 pkgsrc/devel/matio/buildlink3.mk
cvs rdiff -u -r1.4 -r1.5 pkgsrc/devel/matio/distinfo
cvs rdiff -u -r0 -r1.1 \
    pkgsrc/devel/matio/patches/patch-documentation_Makefile.in

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/devel/matio/Makefile
diff -u pkgsrc/devel/matio/Makefile:1.5 pkgsrc/devel/matio/Makefile:1.6
--- pkgsrc/devel/matio/Makefile:1.5     Sun Jun 14 10:07:48 2020
+++ pkgsrc/devel/matio/Makefile Sun Nov  7 10:50:38 2021
@@ -1,12 +1,13 @@
-# $NetBSD: Makefile,v 1.5 2020/06/14 10:07:48 nia Exp $
+# $NetBSD: Makefile,v 1.6 2021/11/07 10:50:38 nros Exp $
 
-DISTNAME=              matio-1.3.3
+DISTNAME=              matio-1.5.21
 CATEGORIES=            devel
 MASTER_SITES=          ${MASTER_SITE_SOURCEFORGE:=matio/}
 
 MAINTAINER=            pkgsrc-users%NetBSD.org@localhost
 HOMEPAGE=              https://sourceforge.net/projects/matio/
 COMMENT=               Matlab MAT file I/O library
+LICENSE=               2-clause-bsd
 
 GNU_CONFIGURE=         yes
 # we need a fortran90 compiler for pkgsrc before we can
@@ -18,5 +19,6 @@ USE_LIBTOOL=          yes
 
 PKGCONFIG_OVERRIDE=    matio.pc.in
 
+.include "../../devel/hdf5/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/devel/matio/PLIST
diff -u pkgsrc/devel/matio/PLIST:1.1.1.1 pkgsrc/devel/matio/PLIST:1.2
--- pkgsrc/devel/matio/PLIST:1.1.1.1    Fri May 15 23:08:14 2009
+++ pkgsrc/devel/matio/PLIST    Sun Nov  7 10:50:38 2021
@@ -1,5 +1,32 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2009/05/15 23:08:14 dmcmahill Exp $
+@comment $NetBSD: PLIST,v 1.2 2021/11/07 10:50:38 nros Exp $
+bin/matdump
 include/matio.h
-include/matioConfig.h
+include/matio_pubconf.h
 lib/libmatio.la
 lib/pkgconfig/matio.pc
+man/man3/Mat_Close.3
+man/man3/Mat_CreateVer.3
+man/man3/Mat_GetDir.3
+man/man3/Mat_GetFilename.3
+man/man3/Mat_GetHeader.3
+man/man3/Mat_GetLibraryVersion.3
+man/man3/Mat_GetVersion.3
+man/man3/Mat_Open.3
+man/man3/Mat_Rewind.3
+man/man3/Mat_VarAddStructField.3
+man/man3/Mat_VarCreate.3
+man/man3/Mat_VarCreateStruct.3
+man/man3/Mat_VarDelete.3
+man/man3/Mat_VarFree.3
+man/man3/Mat_VarGetNumberOfFields.3
+man/man3/Mat_VarGetSize.3
+man/man3/Mat_VarGetStructFieldnames.3
+man/man3/Mat_VarGetStructs.3
+man/man3/Mat_VarGetStructsLinear.3
+man/man3/Mat_VarPrint.3
+man/man3/Mat_VarRead.3
+man/man3/Mat_VarReadInfo.3
+man/man3/Mat_VarReadNext.3
+man/man3/Mat_VarReadNextInfo.3
+man/man3/Mat_VarWrite.3
+man/man3/Mat_VarWriteAppend.3

Index: pkgsrc/devel/matio/distinfo
diff -u pkgsrc/devel/matio/distinfo:1.4 pkgsrc/devel/matio/distinfo:1.5
--- pkgsrc/devel/matio/distinfo:1.4     Tue Oct 26 10:15:39 2021
+++ pkgsrc/devel/matio/distinfo Sun Nov  7 10:50:38 2021
@@ -1,5 +1,6 @@
-$NetBSD: distinfo,v 1.4 2021/10/26 10:15:39 nia Exp $
+$NetBSD: distinfo,v 1.5 2021/11/07 10:50:38 nros Exp $
 
-BLAKE2s (matio-1.3.3.tar.gz) = f89dc46955cbfd7dee8be1857762da36f50bb39f72919c56ceec3223494674d7
-SHA512 (matio-1.3.3.tar.gz) = 8766f4c77dc276b7f60473f29e7f3ecb63bdbfa96f08647b015819a1e38a4b624d616f95c00f29966dba701a7aa9c479a87af09b9e2b14aa7dabbeeb64cae959
-Size (matio-1.3.3.tar.gz) = 418794 bytes
+BLAKE2s (matio-1.5.21.tar.gz) = 436f7155f889be58d38a53b8c1c7ffcf5ef933b89003ad92bdf24b3abd5de134
+SHA512 (matio-1.5.21.tar.gz) = b00bcad807e6a7e10afa656eb77a0e3e9fb08d9cecc3e94ba41ef91ce60367d6686e6d387a874bbb83eb2f895d4a97caac554a70e7f5f6f5cb750052702d411c
+Size (matio-1.5.21.tar.gz) = 10110430 bytes
+SHA1 (patch-documentation_Makefile.in) = 0f31d828464a09d061e24482e432422f4e5003df

Added files:

Index: pkgsrc/devel/matio/buildlink3.mk
diff -u /dev/null pkgsrc/devel/matio/buildlink3.mk:1.3
--- /dev/null   Sun Nov  7 10:50:38 2021
+++ pkgsrc/devel/matio/buildlink3.mk    Sun Nov  7 10:50:38 2021
@@ -0,0 +1,16 @@
+# $NetBSD: buildlink3.mk,v 1.3 2021/11/07 10:50:38 nros Exp $
+
+BUILDLINK_TREE+=       matio
+
+.if !defined(MATIO_BUILDLINK3_MK)
+MATIO_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.matio+=  matio>=1.5.12
+BUILDLINK_PKGSRCDIR.matio?=    ../../devel/matio
+
+# matio.pc refer to these libs
+.include "../../devel/hdf5/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.endif # MATIO_BUILDLINK3_MK
+
+BUILDLINK_TREE+=       -matio

Index: pkgsrc/devel/matio/patches/patch-documentation_Makefile.in
diff -u /dev/null pkgsrc/devel/matio/patches/patch-documentation_Makefile.in:1.1
--- /dev/null   Sun Nov  7 10:50:38 2021
+++ pkgsrc/devel/matio/patches/patch-documentation_Makefile.in  Sun Nov  7 10:50:38 2021
@@ -0,0 +1,16 @@
+$NetBSD: patch-documentation_Makefile.in,v 1.1 2021/11/07 10:50:38 nros Exp $
+
+* don't try to install info files, they are not generated even with
+  TEXINFO_REQD set to the latest version.
+
+--- documentation/Makefile.in.orig     2021-11-07 12:33:51.390164116 +0000
++++ documentation/Makefile.in
+@@ -693,7 +693,7 @@ info: info-am
+ 
+ info-am: $(INFO_DEPS)
+ 
+-install-data-am: install-info-am install-man
++install-data-am: install-man
+ 
+ install-dvi: install-dvi-am
+