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Recent Package Updates

2021-12-06: vim-8.2.3754-1 (Improved version of the editor "vi")
VIM adds many of the features that you would expect in an editor:
Unlimited undo, syntax coloring, split windows, visual selection,
graphical user interface (read: menus, mouse control, scrollbars,
text selection), and much much more.

commit log from Hisashi T Fujinaka (htodd@twofifty.com):

    Vim: Welcome to Vim-8.2.3754.
2021-12-06: vim-nox-8.2.3754-1 (Improved version of the editor "vi")
VIM adds many of the features that you would expect in an editor:
Unlimited undo, syntax coloring, split windows, visual selection,
graphical user interface (read: menus, mouse control, scrollbars,
text selection), and much much more.

commit log from Hisashi T Fujinaka (htodd@twofifty.com):

    Vim: Welcome to Vim-8.2.3754.
2021-12-05: contextual-return-pm5302-0.004014-1 (Different return values by caller context)
Different return values by caller context

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

    Contextual::Return: new version
2021-12-05: contextual-return-pm5282-0.004014-1 (Different return values by caller context)
Different return values by caller context

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

    Contextual::Return: new version
2021-12-05: contextual-return-pm5162-0.004014-1 (Different return values by caller context)
Different return values by caller context

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

    Contextual::Return: new version
2021-12-05: contextual-return-pm5303-0.004014-1 (Different return values by caller context)
Different return values by caller context

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

    Contextual::Return: new version
2021-12-05: contextual-return-pm5182-0.004014-1 (Different return values by caller context)
Different return values by caller context

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

    Contextual::Return: new version
2021-12-05: contextual-return-pm5184-0.004014-1 (Different return values by caller context)
Different return values by caller context

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

    Contextual::Return: new version
2021-12-05: maven-3.8.4-1 (Software project management tool)
Maven is a software project management and comprehension tool.
Based on the concept of a project object model (POM), Maven can
manage a project's build, reporting and documentation from a
central piece of information.

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

    maven: 3.8.4
2021-12-05: gdbm4-shlibs-1.14-4 (Shared libraries for gdbm4 package)
gdbm is the GNU implementation of the dbm database API.

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

    gdbm: missing BDep
2021-12-05: gdbm6-shlibs-1.22-1 (Shared libraries for gdbm6 package)
gdbm is the GNU implementation of the dbm database API.

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

    gdbm6: v1.22
    Bugfix for upstream bug 521
2021-12-05: gdbm3-shlibs-1.8.3-7 (Shared libraries for gdbm3 package)
gdbm is the GNU implementation of the dbm database API.

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

    gdbm*: sync package-layouts among libversions; keep gettext catalogs in sync with runtime files that use them
2021-12-04: tclap-1.2.5-1 (Templatized C++ Command Line Parser)
This is a simple templatized C++ library for parsing 
command line arguments. 
The library provides a simple, flexible object-oriented 
interface to the command line that automates argument 
parsing, USAGE creation and type casting.

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

    tclap: 1.2.5
2021-12-04: robin-map-0.6.3-1 (Fast hash map using robin hood hashing)
The robin-map library is a C++ implementation of a fast hash map and
hash set using open-addressing and linear robin hood hashing with
backward shift deletion to resolve collisions.

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

    robin-map: 0.6.3
2021-12-04: libopenimageio2.1-shlibs-2.1.20.0-1 (Library for reading and writing images)
OpenImageIO is a library for reading and writing images, and a bunch of 
related classes, utilities, and applications.  There is a particular 
emphasis on formats and functionality used in professional, large-scale 
animation and visual effects work for film.  OpenImageIO is used 
extensively in animation and VFX studios all over the world, and is also 
incorporated into several commercial products.

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

    libopenimageio: 2.1.20.0
2021-12-04: libmagickcore7.q16.9-shlibs-7.0.11.13-1 (ImageMagick core library (q16))
ImageMagick is a robust collection of tools and libraries to read, 
write, and manipulate an image in many image formats (over 68 major formats)
including popular formats like TIFF, JPEG, PNG, PDF, PhotoCD, and GIF.
With ImageMagick you can create images dynamically, making it 
suitable for Web applications. You can also resize, rotate, sharpen,
color reduce, or add special effects to an image and save your
completed work in the same or a different image format.

The "imagemagick" package installs the standard quantum-depth=16 suite.

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

    ImageMagick: 7.0.11-13
2021-12-03: samtools-1.13-1 (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: add upgrade note
2021-12-03: babel-py36-2.9.1-1 (Internationalization)
Babel provides access to the majority of the CLDR data. It simplifies
internationalization by doing the heavy lifting for you. It can format
dates, timespans and all kinds of number information. It simplifies
dealing with timezones and gives you access to the raw data (like
month and timezone names, how formatting works for different languages
and more).

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

    babel-py: 2.9.1
2021-12-03: mothur-1.46.1-1 (Microbial ecology software suite)
Microbial ecology software suite

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

    mothur: 1.56.1
2021-12-03: bedtools-2.30.0-1 (Utilities for comparing genomic features)
The BEDTools utilities allow one to address common genomics tasks such as 
finding feature overlaps and computing coverage. The utilities are largely 
based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. 
Using BEDTools, one can develop sophisticated pipelines that answer 
complicated research questions by "streaming" several BEDTools together. 
The following are examples of common questions that one can address with 
BEDTools.

    Intersecting two BED files in search of overlapping features.
    Culling/refining/computing coverage for BAM alignments based on genome 
features.
    Merging overlapping features.
    Screening for paired-end (PE) overlaps between PE sequences and 
existing genomic features.
    Calculating the depth and breadth of sequence coverage across defined 
"windows" in a genome.
    Screening for overlaps between "split" alignments and genomic features.

Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for 
comparing genomic features. Bioinformatics. 26, 6, pp. 841-842.

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

    bedtools: 2.30.0
2021-12-03: babel-py37-2.9.1-1 (Internationalization)
Babel provides access to the majority of the CLDR data. It simplifies
internationalization by doing the heavy lifting for you. It can format
dates, timespans and all kinds of number information. It simplifies
dealing with timezones and gives you access to the raw data (like
month and timezone names, how formatting works for different languages
and more).

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

    babel-py: 2.9.1
2021-12-03: breseq-0.36.1-1 (Mutation finder in microbe evolution)
breseq is a computational pipeline for finding mutations relative to a 
reference sequence in short-read DNA re-sequencing data intended for 
haploid microbial genomes (<20 Mb). breseq is a command line tool 
implemented in C++ and R.

It reports single-nucleotide mutations, point insertions and deletions, 
large deletions, and new junctions supported by mosaic reads (such as 
those produced by new mobile element insertions) in an annotated HTML 
format.

Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations
in laboratory-evolved microbes from next-generation sequencing
data using breseq. Methods Mol. Biol. 1151: 165-188.

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

    breseq: 0.36.1
2021-12-03: mafft-7.490-1 (Multiple sequence alignment program)
MAFFT is a multiple sequence alignment program for unix-like operating 
systems.  It offers a range of multiple alignment methods, L-INS-i 
(accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for
alignment of <~10,000 sequences), etc.

Katoh, Misawa, Kuma, Miyata 2002 (Nucleic Acids Res. 30:3059-3066)
MAFFT: a novel method for rapid multiple sequence alignment based 
on fast Fourier transform.

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

    mafft: 7.490
2021-12-03: pspp-1.4.1-1 (Statistical analysis program)
GNU PSPP interprets commands in the SPSS language, and produces tabular 
        output in ASCII, PostScript, or HTML format.

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

    use https
2021-12-03: eigen3-3.4.0-1 (C++ template library for linear algebra)
Eigen 3 is a C++ template library for linear algebra (vectors, matrices, and 
related algorithms). It is:
 * Versatile. Eigen handles both fixed-size and dynamic-size matrices and
  vectors, without code duplication, and in a completely integrated way. It
  aims to provide not only vectors and matrices but also many algorithms.
 * Fast. Expression templates remove temporaries and enable lazy evaluation.
  Explicit vectorization is performed for the SSE (2 and later) and AltiVec
  instruction sets, with graceful fallback to non-vectorized code. With
  fixed-size objects, dynamic memory allocation is avoided, and the loops
  are unrolled when that makes sense. For large matrices, special attention
  is paid to cache-friendliness. This Benchmark shows Eigen's outstanding
 performance.
 * Good API. Expression templates allow for a very clean and expressive API.
  Implementing an algorithm on top of Eigen feels like just copying
  pseudocode.

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

    eigen3: 3.4.0
2021-12-03: babel-py38-2.9.1-1 (Internationalization)
Babel provides access to the majority of the CLDR data. It simplifies
internationalization by doing the heavy lifting for you. It can format
dates, timespans and all kinds of number information. It simplifies
dealing with timezones and gives you access to the raw data (like
month and timezone names, how formatting works for different languages
and more).

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

    babel-py: 2.9.1
2021-12-03: libhts3-shlibs-1.14-1 (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.

HTSlib: C library for reading/writing high-throughput sequencing data
James K Bonfield, John Marshall, Petr Danecek, Heng Li, Valeriu Ohan,
Andrew Whitwham, Thomas Keane, Robert M Davies GigaScience, Volume 10,
Issue 2, February 2021, giab007,
https://doi.org/10.1093/gigascience/giab007

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

    libhts: 1.14
2021-12-03: babel-py34-2.9.1-1 (Internationalization)
Babel provides access to the majority of the CLDR data. It simplifies
internationalization by doing the heavy lifting for you. It can format
dates, timespans and all kinds of number information. It simplifies
dealing with timezones and gives you access to the raw data (like
month and timezone names, how formatting works for different languages
and more).

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

    babel-py: 2.9.1
2021-12-03: babel-py35-2.9.1-1 (Internationalization)
Babel provides access to the majority of the CLDR data. It simplifies
internationalization by doing the heavy lifting for you. It can format
dates, timespans and all kinds of number information. It simplifies
dealing with timezones and gives you access to the raw data (like
month and timezone names, how formatting works for different languages
and more).

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

    babel-py: 2.9.1
2021-12-03: bcftools-1.14-1 (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: 1.14
2021-12-03: tophat2-2.1.2-2 (Fast splice junction mapper for RNA-Seq reads)
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns 
RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput 
short read aligner Bowtie, and then analyzes the mapping results to 
identify splice junctions between exons.

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: 
accurate alignment of transcriptomes in the presence of insertions, 
deletions and gene fusions. Genome biology. 2013;14(4):R36. Epub 
2013/04/27. doi: 10.1186/gb-2013-14-4-r36. PubMed PMID: 23618408.

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

    tophat2: upgrade deps
2021-12-03: babel-py27-2.9.1-1 (Internationalization)
Babel provides access to the majority of the CLDR data. It simplifies
internationalization by doing the heavy lifting for you. It can format
dates, timespans and all kinds of number information. It simplifies
dealing with timezones and gives you access to the raw data (like
month and timezone names, how formatting works for different languages
and more).

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

    babel-py: 2.9.1
2021-12-03: libqalculate21-shlibs-3.20.0-1 (Math libary for expression evaluation)
Math libary for expression evaluation with units, variables and 
functions support and CAS functionality.

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

    libqalculate 3.20.0