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Recent Package Updates

2020-12-01: gshhg-2.3.7-1 (Global dataset of shorelines, rivers, borders)
This package provides five different resolution versions of the GSHHG
        (Global Self-consistent Hierarchical High-resolution Geography)
        data base: course, low, intermediate, high, and full resolution.
        GSHHG combines the World Vector Shoreline and World Data Base II
        products into a single quality-checked hierarchical data base at
        5 resolutions.

        These tiled GSHHG files in netCDF4 format are intended for use by
        the Genetic Mapping Tools (GMT).

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    update homepage
2020-12-01: libapr.0-shlibs-1.7.0-1 (Apache Portable Runtime shared libraries)
The mission of the Apache Portable Runtime (APR) project is to create and
  maintain software libraries that provide a predictable and consistent
  interface to underlying platform-specific implementations. The primary goal
  is to provide an API to which software developers may code and be assured
  of predictable if not identical behaviour regardless of the platform on
  which their software is built, relieving them of the need to code
  special-case conditions to work around or take advantage of
  platform-specific deficiencies or features.

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    Big Sur and Xcode12 fixes
    See #687
2020-11-29: mysql-unified-5.0.96-5 (Open Source SQL database)
Open Source SQL database

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    macOS10.14 and Xcode12 fixes
2020-11-29: qca2-x11-2.2.1-3 (Cross-platform Crypto API)
Taking a hint from the similarly-named Java Cryptography Architecture,
QCA aims to provide a straightforward and cross-platform crypto API,
using Qt datatypes and conventions.  QCA separates the API from the
implementation, using plugins known as Providers.  The advantage of
this model is to allow applications to avoid linking to or explicitly
depending on any particular cryptographic library.  This allows one
to easily change or upgrade crypto implementations without even
needing to recompile the application!

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    Use latest release for cyrus-sasl dep
2020-11-29: qca2-mac-2.2.1-3 (Cross-platform Crypto API)
Taking a hint from the similarly-named Java Cryptography Architecture,
QCA aims to provide a straightforward and cross-platform crypto API,
using Qt datatypes and conventions.  QCA separates the API from the
implementation, using plugins known as Providers.  The advantage of
this model is to allow applications to avoid linking to or explicitly
depending on any particular cryptographic library.  This allows one
to easily change or upgrade crypto implementations without even
needing to recompile the application!

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    Use latest release for cyrus-sasl dep
2020-11-29: qca2-qt5-mac-2.3.1-3 (Cross-platform Crypto API)
Taking a hint from the similarly-named Java Cryptography Architecture,
QCA aims to provide a straightforward and cross-platform crypto API,
using Qt datatypes and conventions.  QCA separates the API from the
implementation, using plugins known as Providers.  The advantage of
this model is to allow applications to avoid linking to or explicitly
depending on any particular cryptographic library.  This allows one
to easily change or upgrade crypto implementations without even
needing to recompile the application!

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    Use latest release for cyrus-sasl dep
2020-11-29: mpv-0.33.0-2 (Multimedia player)
Movie player based on MPlayer and mplayer2. It supports a 
wide variety of video file formats, audio and video codecs, 
and subtitle types.

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    Use Debian's waf script so that we can edit it.
    This lets us change it to have absolute -I paths so that f-p-p works.
2020-11-28: mtools-4.0.26-1 (Collection of tools to manipulate MSDOS files)
Mtools is a collection of programs to allow unix systems to read, write,
and manipulate files on an MSDOS filesystem. Each program attempts to
emulate the MSDOS eqivalent command as closely as practical.

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    mtools 4.0.26
2020-11-27: libhts2-shlibs-1.9-2 (Library for high-throughput sequencing data)
HTSlib is an implementation of a unified C library for accessing common 
file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput 
sequencing data.  It is the core library used by samtools and bcftools.

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    libhts: 1.11 release
    new libN=3
2020-11-27: libhts3-shlibs-1.11-1 (Library for high-throughput sequencing data)
HTSlib is an implementation of a unified C library for accessing common 
file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput 
sequencing data.  It is the core library used by samtools and bcftools.

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    libhts: 1.11 release
    new libN=3
2020-11-27: bcftools-1.11-1 (Tools for VCF/BCF files)
BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All commands
work transparently with both VCFs and BCFs, both uncompressed and
BGZF-compressed.

Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF will
work in all situations. Un-indexed VCF and BCF and streams will work in
most, but not all situations. In general, whenever multiple VCFs are
read simultaneously, they must be indexed and therefore also compressed.

BCFtools is designed to work on a stream. It regards an input file "-"
as the standard input (stdin) and outputs to the standard output
(stdout). Several commands can thus be combined with Unix pipes.

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    bcftools: 1.11
2020-11-27: samtools-1.11-1 (Tools for SAM alignment files)
SAM Tools provide various utilities for manipulating alignments in 
the SAM format, including sorting, merging, indexing and generating 
alignments in a per-position format.

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    samtools 1.11
2020-11-27: cufflinks-2.2.1-5 (RNA-Seq assembler and expression tester)
Cufflinks assembles transcripts, estimates their abundances, and tests for 
differential expression and regulation in RNA-Seq samples. It accepts 
aligned RNA-Seq reads and assembles the alignments into a parsimonious set 
of transcripts. Cufflinks then estimates the relative abundances of these 
transcripts based on how many reads support each one, taking into account 
biases in library preparation protocols.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. 
Differential gene and transcript expression analysis of RNA-seq 
experiments with TopHat and Cufflinks. Nat Protoc. 2012;7(3):562-78. Epub 
2012/03/03. doi: 10.1038/nprot.2012.016. PubMed PMID: 22383036; PubMed 
Central PMCID: PMC3334321.

commit log from Hanspeter Niederstrasser (nieder@users.sourceforge.net):

    bump linked libhts version
2020-11-26: algorithm-diff-pm-1.20.00-2 (Computes differences between two texts)
Computes differences between two texts

commit log from Daniel Macks (dmacks@netspace.org):

    Fix .pod syntax errors
2020-11-26: test-numeric-pm5162-0.3-4 (Testing utilities for numbers)
This module contains utilities to test numbers to determine if data is
  numeric, if numbers are even or odd, test for integers, formatted, etc.

commit log from Daniel Macks (dmacks@netspace.org):

    Scrap MANIFEST file (TOC of distro)
2020-11-26: device-serialport-pm5282-1.04-2 (Perl5 interface to serial ports)
This module is a POSIX emulation of the Win32::SerialPort module.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix .pod syntax errors
2020-11-26: test-numeric-pm5184-0.3-4 (Testing utilities for numbers)
This module contains utilities to test numbers to determine if data is
  numeric, if numbers are even or odd, test for integers, formatted, etc.

commit log from Daniel Macks (dmacks@netspace.org):

    Scrap MANIFEST file (TOC of distro)
2020-11-26: shout2-pm5162-2.1-2 (Libshout2 perl module extension)
Libshout2 perl module extension

commit log from Daniel Macks (dmacks@netspace.org):

    Scrap MANIFEST file (TOC of distro)
2020-11-26: device-serialport-pm5182-1.04-2 (Perl5 interface to serial ports)
This module is a POSIX emulation of the Win32::SerialPort module.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix .pod syntax errors
2020-11-26: test-numeric-pm5182-0.3-4 (Testing utilities for numbers)
This module contains utilities to test numbers to determine if data is
  numeric, if numbers are even or odd, test for integers, formatted, etc.

commit log from Daniel Macks (dmacks@netspace.org):

    Scrap MANIFEST file (TOC of distro)
2020-11-26: test-numeric-pm5282-0.3-4 (Testing utilities for numbers)
This module contains utilities to test numbers to determine if data is
  numeric, if numbers are even or odd, test for integers, formatted, etc.

commit log from Daniel Macks (dmacks@netspace.org):

    Scrap MANIFEST file (TOC of distro)
2020-11-26: shout2-pm5184-2.1-2 (Libshout2 perl module extension)
Libshout2 perl module extension

commit log from Daniel Macks (dmacks@netspace.org):

    Scrap MANIFEST file (TOC of distro)
2020-11-26: shout2-pm5282-2.1-2 (Libshout2 perl module extension)
Libshout2 perl module extension

commit log from Daniel Macks (dmacks@netspace.org):

    Scrap MANIFEST file (TOC of distro)
2020-11-26: device-serialport-pm5162-1.04-2 (Perl5 interface to serial ports)
This module is a POSIX emulation of the Win32::SerialPort module.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix .pod syntax errors
2020-11-26: device-serialport-pm5184-1.04-2 (Perl5 interface to serial ports)
This module is a POSIX emulation of the Win32::SerialPort module.

commit log from Daniel Macks (dmacks@netspace.org):

    Fix .pod syntax errors
2020-11-26: shout2-pm5182-2.1-2 (Libshout2 perl module extension)
Libshout2 perl module extension

commit log from Daniel Macks (dmacks@netspace.org):

    Scrap MANIFEST file (TOC of distro)
2020-11-26: text-delimmatch-pm-1.06a-2 (Perl module finding regexp delimited strings)
DelimMatch allows you to match delimited substrings in a buffer.
The delimiters can be specified with any regular expression and
the start and end delimiters need not be the same.  If the
delimited text is properly nested, entire nested groups are
returned.

In addition, you may specify quoting and escaping characters that
contribute to the recognition of start and end delimiters.

commit log from Daniel Macks (dmacks@netspace.org):

    Scrap MANIFEST file (TOC of distro)