Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.
OK wiz@
Gnumeric 1.12.40
Andreas:
* Fix histogram tool for the case of no labels. [#795475]
Dean McCarron:
* Introspection fixes.
Morten:
* Add floating-point environment sanity check. [#794515]
* Before saving, verify that files hasn't changed on disk. [#334024]
* Add GUI for comparing sheets.
* Introspection fixes.
* Clean up workbook view construction.
* Test suite improvements.
* Fix problems with boxed types.
* Avoid most punting for object properties.
* Fix paste from LibreOffice.
* Fix paste to LibreOffice -- use Biff8. [#795280]
* Allow inter-process paste-special. [#346630]
* Fix ssconvert --merge-to problem with names. [#795408]
* Fix problem with image pasting.
* Allow pasting an image into Gnumeric. [#366816]
* Full-column paste includes column width. [#121722]
* Auto-fix shared array formulas in gnumeric files.
* No-net-access doc build. [#790226]
* No-net test suite fixes.
dbus 1.12.8 (2018-04-30)
========================
The “golden super-velociraptor” release.
Enhancements:
• The Devhelp documentation index is now in version 2 format
(fd.o #106186, Simon McVittie)
• Give the dbus-daemon man page some scarier warnings about
<allow_anonymous/> and non-local TCP, which are insecure and should
not be used, particularly for the standard system and session buses
(fd.o #106004, Simon McVittie)
Fixes:
• Fix installation of Ducktype documentation with newer yelp-build
versions (fd.o #106171, Simon McVittie)
D-Bus Python Bindings 1.2.8 (2018-05-04)
========================================
The “cursed ice surface” release.
Dependencies:
• Documentation requires Sphinx and the readthedocs theme
• Documentation no longer requires epydoc
Enhancements:
• Build documentation with Sphinx instead of epydoc
• Remove obsolete COMPAT.txt, documenting compatibility breaks in
versions over a decade old
Fixes:
• Make sure $(builddir)/test exists before creating .test files there
• Add PKG-INFO and egg_info to dist tarballs so they can be uploaded
to PyPI again
- version: 3.23.0
date: 2018-05-04
new features:
- title: "Kobo driver: Add support for new firmware"
- title: "Book polishing: Add an option to upgrade EPUB 2 to EPUB 3"
- title: "DOCX Input: Convert text written with dingbat fonts such as Wingding or Symbol correctly."
- title: "When choosing the page to use as a cover from a PDF file, add a button to render more pages, if needed"
- title: "TXT Input: Add support for embedded images that use relative URLs when converting markdown or textile. Note that this will only work if you are converting using the ebook-convert command line tool as the main calibre program moves files around, so relative references will not be valid."
- title: "Edit book: Insert special character: Add an option to select if searching should match all words or any of the words"
- title: 'Edit book: Insert special character: When searching by name match prefixes in addition to whole words. So you can now type "horiz" to match "horizontal".'
- title: "Linux installer: Simplify the command used to install calibre and add support for Ubuntu 18.04 which is missing a default python executable"
- title: "When upgrading EPUB 2 to EPUB 3 add the 'epub' namespace to all HTML files, for convenience."
bug fixes:
- title: "Edit Book: Fix an error caused by a landmark entry in EPUB 3 files that has an <a> tag without an href attribute."
- title: "Edit Book: Fix names for some control characters not being displayed in the status bar"
- title: "Searching: Fix A (B) not being treated as A AND (B)"
- title: "Kobo driver: Add an option to not maintain bookmarks/read status/etc. when resending a book already on the device."
- title: "DOCX Input: Ignore complex script font styles. Fixes conversion of documents that specify only complex script styles and no simple script styles."
- title: "When updating EPUB 2 to EPUB 3 ensure only a single dc:date element is present in the OPF"
Changes:
Documentation
-------------
- bpo-17232: Clarify docs for -O and -OO. Patch by Terry Reedy.
- bpo-32800: Update link to w3c doc for xml default namespaces.
- bpo-8722: Document __getattr__() behavior when property get() method raises
AttributeError.
- bpo-32614: Modify RE examples in documentation to use raw strings to
prevent DeprecationWarning and add text to REGEX HOWTO to
highlight the deprecation.
- bpo-31972: Improve docstrings for pathlib.PurePath subclasses.
- bpo-17799: Explain real behaviour of sys.settrace and sys.setprofile and
their C-API counterparts regarding which type of events are
received in each function. Patch by Pablo Galindo Salgado.
pkgsrc changes:
- Fix an error pointed out by gcc-6.4.0 via
patches/patch-filter_pdftoopvp_OPVPOutputDev.cxx:
filter/pdftoopvp/OPVPOutputDev.cxx: In member function 'void OPVPOutputDev::doUpdateFont(GfxState*)':
filter/pdftoopvp/OPVPOutputDev.cxx:532:46: error: invalid conversion from 'const Ref*' to 'Ref*' [-fpermissive]
id = new SplashOutFontFileID(gfxFont->getID());
~~~~~~~~~~~~~~^~
filter/pdftoopvp/OPVPOutputDev.cxx:69:3: note: initializing argument 1 of 'SplashOutFontFileID::SplashOutFontFileID(Ref*)'
SplashOutFontFileID(Ref *rA) { r = *rA; substIdx = -1; }
^~~~~~~~~~~~~~~~~~~
Changes:
1.20.3
------
- braille: Do not remove read permission on cups-brf. Thanks
to Samuel Thibault for this patch (Pull request #32).
- braille: Get braille table descriptions from liblouis
metadata. Thanks to Samuel Thibault for this patch (Pull
request #31).
- braille: Select liblouis tables based on metadata before
using file names. Thanks to Samuel Thibault for this patch
(Pull request #30).
- cups-browsed: The new method of identifying remote CUPS
queues via the "printer-type" TXT record field does not work
for printers discovered by legacy CUPS broadcast (CUPS 1.5.x
or older). Now consider also printers without TXT record
(not discovered via DNS-SD) as remote CUPS queues (Issue
#34).
- gstoraster: Improved detection whether input is PostScript
or PDF by skipping over possible headers. Thanks to Rod
Schmidt (schmidtrod at q dot com) for the patch.
1.20.2
------
- cups-browsed: If the user modifies/overwrites a print queue
created by cups-browsed, it will now automatically released
from the control of cups-browsed, so the modified queue does
not get removed by cups-browsed on shutdown. (Ubuntu bug
#1731417).
- cups-browsed: The configuration setting
"CreateIPPPrinterQueues LocalOnly" suppressed also the
automatic generation of local queues for remote CUPS
printers whereas this option is only intended for physical
IPP printers.
- cups-browsed: Identify remote CUPS queues by the
"printer-type" TXT record entry and not by the
"ipp(s)://<host>/printers/<name>" URIs, there are also IPP
network printers with such URIs (HP LaserJet Professional
M1212nf MFP in Ubuntu bug #1731417).
- .gitignore: Added filter/braille/filters/brftopagedbrf
- cups-browsed, foomatic-rip: Fixed several typos. Thanks to
Didier Raboud for the patches.
Upstream changes:
Features
- Add --with-libhiredis, unbound support for a new cachedb
backend that uses a Redis server as the storage. This
implementation depends on the hiredis client library
(https://redislabs.com/lp/hiredis/).
And unbound should be built with both --enable-cachedb and
--with-libhiredis[=PATH] (where $PATH/include/hiredis/hiredis.h
should exist). Patch from Jinmei Tatuya (Infoblox).
- Create additional tls service interfaces by opening them on other
portnumbers and listing the portnumbers as additional-tls-port: nr.
- ED448 support.
- num.query.authzone.up and num.query.authzone.down statistics counters.
- Accept both option names with and without colon for get_option
and set_option.
- low-rtt and low-rtt-pct in unbound.conf enable the server selection
of fast servers for some percentage of the time.
- num.query.aggressive.NOERROR and num.query.aggressive.NXDOMAIN
statistics counters.
- allow-notify: config statement for auth-zones.
- Can set tls authentication with forward-addr: IP#tls.auth.name
And put the public cert bundle in tls-cert-bundle: "ca-bundle.pem".
such as forward-addr: 9.9.9.9@853#dns.quad9.net or
1.1.1.1@853#cloudflare-dns.com
- list_auth_zones unbound-control command.
- Added root-key-sentinel support
Bug Fixes
- Fix#3727: Protocol name is TLS, options have been renamed but
documentation is not consistent.
- Check IXFR start serial.
- Fix typo in documentation.
- Fix#3736: Fix 0 TTL domains stuck on SERVFAIL unless manually
flushed with serve-expired on.
- Fix#3817: core dump happens in libunbound delete, when queued
servfail hits deleted message queue.
- corrected a minor typo in the changelog.
- move htobe64/be64toh portability code to cachedb.c.
- iana port update.
- Do not use cached NSEC records to generate negative answers for
domains under DNSSEC Negative Trust Anchors.
- Fix unbound-control get_option aggressive-nsec
- Check "result" in dup_all(), by Florian Obser.
- Fix#4043: make test fails due to v6 presentation issue in macOS.
- Fix unable to resolve after new WLAN connection, due to auth-zone
failing with a forwarder set. Now, auth-zone is only used for
answers (not referrals) when a forwarder is set.
- Combine write of tcp length and tcp query for dns over tls.
- nitpick fixes in example.conf.
- Fix above stub queries for type NS and useless delegation point.
- Fix unbound-control over pipe with openssl 1.1.1, the TLSv1.3
tls_choose_sigalg routine does not allow the ciphers for the pipe,
so use TLSv1.2.
- Fix that flush_zone sets prefetch ttl expired, so that with
serve-expired enabled it'll start prefetching those entries.
- Fix downstream auth zone, only fallback when auth zone fails to
answer and fallback is enabled.
- Fix for max include depth for authzones.
- Fix memory free on fail for $INCLUDE in authzone.
- Fix that an internal error to look up the wrong rr type for
auth zone gets stopped, before trying to send there.
- Fix auth zone target lookup iterator.
- Fix auth-zone retry timer to be on schedule with retry timeout,
with backoff. Also time a refresh at the zone expiry.
- Fix#658: unbound using TLS in a forwarding configuration does not
verify the server's certificate (RFC 8310 support).
- For addr with #authname and no @port notation, the default is 853.
- man page documentation for dns-over-tls forward-addr '#' notation.
- removed free from failed parse case.
- Fix#4091: Fix that reload of auth-zone does not merge the zonefile
with the previous contents.
- Delete auth zone when removed from config.
- makedist uses bz2 for expat code, instead of tar.gz.
- Fix#4092: libunbound: use-caps-for-id lacks colon in
config_set_option.
- auth zone http download stores exact copy of downloaded file,
including comments in the file.
- Fix sldns parse failure for CDS alternate delete syntax empty hex.
- Attempt for auth zone fix; add of callback in mesh gets from
callback does not skip callback of result.
- Fix cname classification with qname minimisation enabled.
- Fix contrib/fastrpz.patch for this release.
- Fix auth https for libev.
- Fix memory leak when caching wildcard records for aggressive NSEC use
- Fix for crash in daemon_cleanup with dnstap during reload,
from Saksham Manchanda.
- Also that for dnscrypt.
From nia in PR 53266.
New in version 2.28:
Improvements to the FreeBSD startup script. (Craig Leres)
Minor portability tweak in mmc.c.
Fix to buffer overrun bug in htpasswd. Reported by Alessio Santoru as CVE-2017-17663.
New in version 2.27:
Stats syslogs changed from LOG_INFO to LOG_NOTICE.
Use memmove() for self-overlapping string copies instead of strcpy().
Couple of subroutine name changes for consistency.
* Changes in Wget 1.19.5
* Fix cookie injection (CVE-2018-0494)
* Enable TLS1.3 with recent OpenSSL environment
* New option --ciphers to set GnuTLS / OpenSSL ciphers directly
* Updated CSS grammar to CSS 2.2
* Fixed several memleaks found by OSS-Fuzz
* Fixed several buffer overflows found by OSS-Fuzz
* Fixed several integer overflows found by OSS-Fuzz
* Several minor bug fixes
* Changes in Wget 1.19.4
* A major bug that caused GZip'ed pages to never be decompressed has been fixed
* Support for Content-Encoding and Transfer-Encoding have been marked as
experimental and disabled by default
* Changes in Wget 1.19.3
* Prevent erroneous decompression of .gz and .tgz files with broken servers
* Added support for HTTP 308 Permanent Redirect response
* Fix a segfault in some cases where the Content-Type header is not sent
* Support OpenSSL 1.1 builds without using deprecated features
* Fix netrc file detection on Windows
* Several minor bug fixes
binary files. I verified the output from both microcode-20180312.tgz's
microcode.dat and intel-ucode/??-??-?? are the same.
This change is required for microcode-20180425.tgz.
From the release notes:
Added:
* Ethereum: --txnocoverage cli argument to suppress coverage based analysis halting criteria
* Ethereum: Support added for more Solidity features (imports, uint/int types, function types)
Fixed:
* Numerous Ethereum ABI fixes
* Linux and x86/64 emulation fixes
* Solver performance issue
Attention: Syncthing now advertises continuous watching support in
the GUI. If you enable this on NetBSD, you'll run out of file
descriptors and syncthing won't work. At least that's what happened
to me... so take care.
Bugfixes:
#4815: Local host header check is too restrictive
#4833: Unclear error message about failed watcher when running out of inotify watches
#4870: Don't show a warning when a file from a paused folder is requested
#4875: Zeroed local/global "state" (local files untouched) and remote file deletion with root Windows symlink
Enhancements:
#4516: Bandwidth throttling per remote device
#4552: Add UI for filesystem watcher
#4823: Don't show ignored files in the "global changes" list
#4828: Global change log should indicate folder
Other issues:
#4749: Make all tests Go 1.10 caching compatible
#4868: Docker Documentation
In some cases, if an installed package's source directory did not
exist, pkg_rr could invoke "make clean" at top-level of pkgsrc. Bug
report and fix by Andreas Gustafsson in PR pkg/53157.
