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Recent Package Updates

2018-08-15: openssl100-dev-1.0.2p-1 (Secure Sockets Layer and Crypto Library)
OpenSSL is a free implementation of the Secure Sockets Layer (SSL)
and Transport Layer Security (TLS) protocols. It includes command line
utilities to manage certificates and a separate library implementing common
cryptograhic algorithms.

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream openssl100 1.0.2p
2018-08-15: pyopenssl-py37-18.0.0-1 (Python wrapper module around OpenSSL)
High-level wrapper around a subset of the OpenSSL library, includes

* SSL.Connection objects, wrapping the methods of Python's portable
  sockets
* Callbacks written in Python
* Extensive error-handling mechanism, mirroring OpenSSL's error codes
  ...  and much more ;)

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    Add py37 variant
2018-08-15: openssl110-dev-1.1.0i-1 (Secure Sockets Layer and Crypto Library)
OpenSSL is a free implementation of the Secure Sockets Layer (SSL)
and Transport Layer Security (TLS) protocols. It includes command line
utilities to manage certificates and a separate library implementing common
cryptograhic algorithms.

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream openssl110 1.1.0i
2018-08-15: cryptography-py27-2.3.1-1 (Cryptographic recipes for Python)
Cryptographic recipes for Python

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream cryptography-py 2.3.1 and py37 variant
2018-08-15: pyopenssl-py34-18.0.0-1 (Python wrapper module around OpenSSL)
High-level wrapper around a subset of the OpenSSL library, includes

* SSL.Connection objects, wrapping the methods of Python's portable
  sockets
* Callbacks written in Python
* Extensive error-handling mechanism, mirroring OpenSSL's error codes
  ...  and much more ;)

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    Add py37 variant
2018-08-15: cryptography-py36-2.3.1-1 (Cryptographic recipes for Python)
Cryptographic recipes for Python

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream cryptography-py 2.3.1 and py37 variant
2018-08-15: pyopenssl-py36-18.0.0-1 (Python wrapper module around OpenSSL)
High-level wrapper around a subset of the OpenSSL library, includes

* SSL.Connection objects, wrapping the methods of Python's portable
  sockets
* Callbacks written in Python
* Extensive error-handling mechanism, mirroring OpenSSL's error codes
  ...  and much more ;)

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    Add py37 variant
2018-08-15: pyopenssl-py27-18.0.0-1 (Python wrapper module around OpenSSL)
High-level wrapper around a subset of the OpenSSL library, includes

* SSL.Connection objects, wrapping the methods of Python's portable
  sockets
* Callbacks written in Python
* Extensive error-handling mechanism, mirroring OpenSSL's error codes
  ...  and much more ;)

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    Add py37 variant
2018-08-15: cryptography-py37-2.3.1-1 (Cryptographic recipes for Python)
Cryptographic recipes for Python

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream cryptography-py 2.3.1 and py37 variant
2018-08-15: cryptography-py35-2.3.1-1 (Cryptographic recipes for Python)
Cryptographic recipes for Python

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream cryptography-py 2.3.1 and py37 variant
2018-08-15: pyopenssl-py35-18.0.0-1 (Python wrapper module around OpenSSL)
High-level wrapper around a subset of the OpenSSL library, includes

* SSL.Connection objects, wrapping the methods of Python's portable
  sockets
* Callbacks written in Python
* Extensive error-handling mechanism, mirroring OpenSSL's error codes
  ...  and much more ;)

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    Add py37 variant
2018-08-15: cryptography-py34-2.3.1-1 (Cryptographic recipes for Python)
Cryptographic recipes for Python

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream cryptography-py 2.3.1 and py37 variant
2018-08-15: cffi-py35-1.11.5-1 (Foreign Function Intf for Python calling C)
Foreign Function Intf for Python calling C

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream cffi-py 1.11.5
2018-08-15: cffi-py37-1.11.5-1 (Foreign Function Intf for Python calling C)
Foreign Function Intf for Python calling C

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream cffi-py 1.11.5
2018-08-15: cffi-py27-1.11.5-1 (Foreign Function Intf for Python calling C)
Foreign Function Intf for Python calling C

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream cffi-py 1.11.5
2018-08-15: cffi-py36-1.11.5-1 (Foreign Function Intf for Python calling C)
Foreign Function Intf for Python calling C

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream cffi-py 1.11.5
2018-08-15: cffi-py34-1.11.5-1 (Foreign Function Intf for Python calling C)
Foreign Function Intf for Python calling C

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream cffi-py 1.11.5
2018-08-14: python-dateutil-py34-2.7.3-1 (Powerful extensions to datetime)
Powerful extensions to datetime

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New package python-dateutil-py 2.7.3
2018-08-14: python-dateutil-py36-2.7.3-1 (Powerful extensions to datetime)
Powerful extensions to datetime

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New package python-dateutil-py 2.7.3
2018-08-14: python-dateutil-py27-2.7.3-1 (Powerful extensions to datetime)
Powerful extensions to datetime

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New package python-dateutil-py 2.7.3
2018-08-14: python-dateutil-py35-2.7.3-1 (Powerful extensions to datetime)
Powerful extensions to datetime

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New package python-dateutil-py 2.7.3
2018-08-14: python-dateutil-py37-2.7.3-1 (Powerful extensions to datetime)
Powerful extensions to datetime

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New package python-dateutil-py 2.7.3
2018-08-14: lua53-5.3.5-1 (Small and fast embeddable scripting language)
Lua is a programming language originally designed for extending applications,
but also frequently used as a general-purpose, stand-alone language. Lua
combines simple procedural syntax (similar to Pascal) with powerful data
description constructs based on associative arrays and extensible semantics.
Lua is dynamically typed, interpreted from bytecodes, and has automatic 
memory management with garbage collection, making it ideal for 
configuration, scripting, and rapid prototyping. 

A fundamental concept in the design of Lua is to provide meta-mechanisms 
for implementing features, instead of providing a host of features directly in
the language. For example, although Lua is not a pure object-oriented
language, it does provide meta-mechanisms for implementing classes and
inheritance. Lua's meta-mechanisms bring an economy of concepts and keep the
language small, while allowing the semantics to be extended in unconventional
ways. Extensible semantics is a distinguishing feature of Lua. 

Lua is implemented as a small library of C functions, written in ANSI C, 
and compiles unmodified in all known platforms. The implementation goals 
are simplicity, efficiency, portability, and low embedding cost.

commit log from Karl-Michael Schindler (karl-michael.schindler@web.de):

    lua53: update to new upstream version (5.3.5)
2018-08-14: bedtools-2.27.1-1 (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 2.27.1
2018-08-13: vim-nox-8.1.280-1 (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-8.1.280.
2018-08-13: vim-8.1.280-1 (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-8.1.280.
2018-08-13: dulwich-py36-0.19.6-1 (Python implementation of Git)
Dulwich is a pure-Python implementation of the Git file formats
and protocols.

The project is named after the village in which Mr. and Mrs. Git live
in the Monty Python sketch.

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream dulwich-py 0.19.6
2018-08-13: xerces-j-2.11.0-2 (XML parser in Java)
The rich generating and validating capabilities allow the Xerces-J Parser to
        be used for:
        -  Building XML-savvy Web servers.
        -  The next generation of vertical applications which will use XML as their
           data format.
        -  On-the-fly validation for creating XML editors.
        -  Ensuring the integrity of e-business data expressed in XML.
        -  Building truly internationalized XML applications.

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

    java1.5 is not compatible with java8.
    Add upgrade note.
2018-08-13: xerces-j-docs-2.11.0-1 (Documentation for xerces-j)
Documentation for xerces-j

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

    Use main xerces-j patch to build headless.
    Still fails to finish building as before looking for java.lang
2018-08-13: dulwich-py34-0.19.6-1 (Python implementation of Git)
Dulwich is a pure-Python implementation of the Git file formats
and protocols.

The project is named after the village in which Mr. and Mrs. Git live
in the Monty Python sketch.

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream dulwich-py 0.19.6
2018-08-13: dulwich-py27-0.19.6-1 (Python implementation of Git)
Dulwich is a pure-Python implementation of the Git file formats
and protocols.

The project is named after the village in which Mr. and Mrs. Git live
in the Monty Python sketch.

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream dulwich-py 0.19.6
2018-08-13: dulwich-py35-0.19.6-1 (Python implementation of Git)
Dulwich is a pure-Python implementation of the Git file formats
and protocols.

The project is named after the village in which Mr. and Mrs. Git live
in the Monty Python sketch.

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream dulwich-py 0.19.6
2018-08-12: valgrind-3.13.0-10 (Debugging and profiling tool)
Valgrind is an award-winning instrumentation framework for building
dynamic analysis tools. There are Valgrind tools that can automatically
detect many memory management and threading bugs, and profile your
programs in detail. You can also use Valgrind to build new tools.

The Valgrind distribution currently includes six production-quality
tools: a memory error detector, two thread error detectors, a cache and
branch-prediction profiler, a call-graph generating cache profiler, and
a heap profiler. It also includes one experimental tool, which detects
out of bounds reads and writes of stack, global and heap arrays.

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    Use repo snapshot to fix build on Xcode 9 and 10.13
2018-08-12: hg-fastimport-py27-20180204-2 (Fastimport extension for mercurial)
The "fast import" format originates with Git, where it is used as the
        generic backend for converting other SCM repositories to git. It's
        generic enough that it can be used to feed a Mercurial repository as
        well, and that's what this extension does: read a "fast import" stream
        and turn it into changesets in a Mercurial repository. The potential of
        this extension is that any foreign SCM that can be converted to Git can
        also be converted to Mercurial, regardless of the capabilities of
        Mercurial's own ConvertExtension. The catch is that the conversion is a
        little cumbersome: first convert to a fast-import dump, then feed that
        dump to Mercurial.
        
        Add 'hgfastimport=' to the [extensions] section of ~/.hgrc to enable.

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    Fix hg-fastimport-py for hg 4.6+
2018-08-12: entrypoints-py34-0.2.3-2 (Discover and load entry points from packages)
Entry points are a way for Python packages to advertise objects with
some common interface. The most common examples are console_scripts
entry points, which define shell commands by identifying a Python
function to run.

commit log from Brendan Cully (brendan@cully.org):

    #222 entrypoints-py is missing a dep on configparser-py for py27
2018-08-12: entrypoints-py36-0.2.3-2 (Discover and load entry points from packages)
Entry points are a way for Python packages to advertise objects with
some common interface. The most common examples are console_scripts
entry points, which define shell commands by identifying a Python
function to run.

commit log from Brendan Cully (brendan@cully.org):

    #222 entrypoints-py is missing a dep on configparser-py for py27
2018-08-12: entrypoints-py35-0.2.3-2 (Discover and load entry points from packages)
Entry points are a way for Python packages to advertise objects with
some common interface. The most common examples are console_scripts
entry points, which define shell commands by identifying a Python
function to run.

commit log from Brendan Cully (brendan@cully.org):

    #222 entrypoints-py is missing a dep on configparser-py for py27
2018-08-12: entrypoints-py27-0.2.3-2 (Discover and load entry points from packages)
Entry points are a way for Python packages to advertise objects with
some common interface. The most common examples are console_scripts
entry points, which define shell commands by identifying a Python
function to run.

commit log from Brendan Cully (brendan@cully.org):

    #222 entrypoints-py is missing a dep on configparser-py for py27
2018-08-12: pysam-py27-0.15.0.1-1 (SAM/BAM sequence alignment python interface)
Module for reading and manipulating Samfiles. It's a lightweight
wrapper of the samtools C-API. Pysam also includes an interface
for tabix.

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

    samtools 1.9
2018-08-12: samtools-1.9-1 (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 1.9
2018-08-12: libhts2-shlibs-1.9-1 (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):

    samtools 1.9
2018-08-12: bcftools-1.9-1 (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):

    samtools 1.9
2018-08-12: libpng16-32bit-1.6.35-1 (PNG library (32-bit))
PNG library (32-bit)

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

    libpng 1.6.35
2018-08-12: libpng16-1.6.35-1 (PNG image format handling library)
PNG image format handling library

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

    libpng 1.6.35
2018-08-11: mercurial-py27-4.7-1 (Lightweight distributed SCM)
Mercurial is a fast, lightweight source control management 
system designed for efficient handling of very large 
distributed projects. Features include:

 * O(1) delta-compressed file storage and retrieval scheme
 * Complete cross-indexing of file and changesets for 
   efficient exploration of project history
 * Robust SHA1-based integrity checking and append-only 
   storage model
 * Decentralized development model with arbitrary merging 
   between trees
 * High-speed HTTP-based network merge protocol
 * Easy-to-use command-line interface
 * Integrated stand-alone web interface
 * Small Python codebase
 * GPL license

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream mercurial 4.7
2018-08-11: mercurial-4.7-1 (Lightweight distributed SCM)
Lightweight distributed SCM

commit log from Daniel Johnson (daniel@daniel-johnson.org):

    New upstream mercurial 4.7