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Fix issue https://github.com/SDL-Hercules-390/hyperion/issues/525
which can cause a segfault if networking is used.
Created a patch file from an upstream commit, therefore it patches multiple
files. It should be possible to remove it at the next release.
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<ChangeLog>
*) Bugfix: an error might occur when reading PROXY protocol version 2
header with large number of TLVs.
*) Bugfix: a segmentation fault might occur in a worker process if SSI
was used to process subrequests created by other modules.
Thanks to Ciel Zhao.
*) Workaround: when a hostname used in the "listen" directive resolves
to multiple addresses, nginx now ignores duplicates within these
addresses.
*) Bugfix: nginx might hog CPU during unbuffered proxying if SSL
connections to backends were used.
</ChangeLog>
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Format consistency in comment.
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Move fix out of hacks.mk and generalise for all systems, the problem is that
NetBSD unzip behaves differently to other implementations, which is why we end
up with these problems. Also make it pkglint clean while here.
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bugfixes and minor improvements
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(instead buildlinking textproc/discount), and it sometimes contains
macOS xattrs that break extraction as root on other systems.
Fixes "Cannot restore extended attributes: com.apple.quarantine
com.apple.quarantine" seen with pkg_comp(8) on NetBSD/amd64 9.3.
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1.16.1
Bug fixes:
Fixed a bug with the template-coordinate sort which caused incorrect ordering when using threads, or processing large files that don't fit completely in memory.
Fixed a crash that occurred when trying to use samtools merge in template-coordinate mode.
1.16
New work and changes:
samtools reference command added. This subcommand extracts the embedded reference out of a CRAM file.
samtools import now adds grouped by query-name to the header.
Made samtools view read error messages more generic. Former error message would claim that there was a "truncated file or corrupt BAM index file" with no real justification. Also reset errno in stream_view which could lead to confusing error messages.
Make samtools view -p also clear mqual, tlen and cigar.
Add bedcov option -c to report read count.
Add UMI/barcode handling to samtools markdup.
Add a new template coordinate sort order to samtools sort and samtools merge. This is useful when working with unique molecular identifiers (UMIs).
Rename mpileup --ignore-overlaps to --ignore-overlaps-removal or --disable-overlap-removal. The previous name was ambiguous and was often read as an option to enable removal of overlapping bases, while in reality this is on by default and the option turns off the ability to remove overlapping bases.
The dict command can now read BWA's .alt file and add AH:* tags indicating reference sequences that represent alternate loci.
The samtools index command can now accept multiple alignment filenames with the new -M option, and will index each of them separately. (Specifying the output index filename via out.index or the new -o option is currently only applicable when there is only one alignment file to be indexed.)
Allow samtools fastq -T "*". This allows all tags from SAM records to be written to fastq headers. This is a counterpart to samtools import -T "*".
Bug Fixes:
Re-enable --reference option for samtools depth. The reference is not used but this makes the command line usage compatible with older releases.
Fix regex coordinate bug in samtools markdup.
Fix divide by zero in plot-bamstats -m, on unmapped data.
Fix missing RG headers when using samtools merge -r.
Fix a possible unaligned access in samtools reference.
Documentation:
Add documentation on CRAM compression profiles and some of the newer options that appear in CRAM 3.1 and above.
Add sclen filter expression keyword documentation.
Extend FILTER EXPRESSION man page section to match the changes made in HTSlib.
Non user-visible changes and build improvements:
Ensure generated test files are ignored (by git) and cleaned (by make testclean)
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1.16
Make hfile_s3 refresh AWS credentials on expiry in order to make HTSlib work better with AWS IAM credentials, which have a limited lifespan.
Allow BAM headers between 2GB and 4GB in size once more. This is not permitted in the BAM specification but was allowed in an earlier version of HTSlib. There is now a warning at 2GB and a hard failure at 4GB.
Improve error message when failing to load an index.
Permit MM (base modification) tags containing . and ? suffixes. These define implicit vs explicit coordinates. See the SAM tags specification for details.
Warn if spaces instead of tabs are detected in a VCF file to prevent confusion.
Add an sclen filter expression keyword. This is the length of a soft-clip, both left and right end. It may be combined with qlen (qlen-sclen) to obtain the number of bases in the query sequence that have been aligned to the genome ie it provides a way to compare local-alignment vs global-alignment length.
Improve error messages for CRAM reference mismatches. If the user specifies the wrong reference, the CRAM slice header MD5sum checks fail. We now report the SQ line M5 string too so it is possible to validate against the whole chr in the ref.fa file. The error message has also been improved to report the reference name instead of #num. Finally, we now hint at the likely cause, which counters the misleading samtools supplied error of "truncated or corrupt" file.
Expose more of the CRAM API and add new functionality to extract the reference from a CRAM file.
Improvements to the implementation of embedded references in CRAM where no external reference is specified.
The CRAM writer now allows alignment records with RG:Z: aux tags that don't have a corresponding @RG ID in the file header. Previously these tags would have been silently dropped. HTSlib will complain whenever it has to add one though, as such tags do not conform to recommended practice for the SAM, BAM and CRAM formats.
Set tab delimiter in man page for tabix GFF3 sort.
When using libdeflate, the 1...9 scale of BGZF compression levels is now remapped to the 1...12 range used by libdeflate instead of being passed directly. In particular, HTSlib levels 8 and 9 now map to libdeflate levels 10 and 12, so it is possible to select the highest (but slowest) compression offered by libdeflate.
The VCF variant API has been extended so that it can return separate flags for INS and DEL variants as well as the existing INDEL one. These flags have not been added to the old bcf_get_variant_types() interface as it could break existing users. To access them, it is necessary to use new functions bcf_has_variant_type() and bcf_has_variant_types().
The missing, but trivial, le_to_u8() function has been added to hts_endian.
bcf_format_gt() now works properly on big-endian platforms.
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security/py-google-auth-oauthlib, devel/pcre2
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Version 10.42 11-December-2022
------------------------------
1. Change 19 of 10.41 wasn't quite right; it put the definition of a default,
empty value for PCRE2_CALL_CONVENTION in src/pcre2posix.c instead of
src/pcre2posix.h, which meant that programs that included pcre2posix.h but not
pcre2.h failed to compile.
2. To catch similar issues to the above in future, a new small test program
that includes pcre2posix.h but not pcre2.h has been added to the test suite.
3. When the -S option of pcre2test was used to set a stack size greater than
the allowed maximum, the error message displayed the hard limit incorrectly.
This was pointed out on GitHub pull request 171, but the suggested patch
didn't cope with all cases. Some further modification was required.
4. Supplying an ovector count of more than 65535 to pcre2_match_data_create()
caused a crash because the field in the match data block is only 16 bits. A
maximum of 65535 is now silently applied.
5. Merged @carenas patch 175 which fixes 86 - segfault on aarch64 (ARM),
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0.8.0 (2022-12-08)
Features
Add support for Python 3.11
Introduce granted scopes to credentials
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5.7.1
Bugs fixed
- fix: some descriptors raise AttributeError
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Redis 7.0.6
===========
Upgrade urgency: MODERATE, Contains fixes for a few non-critical or unlikely bugs,
and some dramatic optimizations to Geo, EVAL, and Sorted sets commands.
Potentially Breaking Bug Fixes for new Redis 7.0 features
=======================================================
* RM_ResetDataset module API should not clear the functions
* RM_Call module API used with the "C" flag to run scripts, would now cause
the commands in the script to check ACL with the designated user
Performance and resource utilization improvements
=================================================
* Geo commands speedups
* Fix EVAL command performance regression from Redis 7.0
* Reduce EXPIRE commands performance regression from Redis 7.0
* Optimize commands returning double values, mainly affecting zset commands
* Optimize Lua parsing of some command responses
* Optimize client memory usage tracking operation while client eviction is disabled
Platform / toolchain support related improvements
=================================================
* Fix compilation on Solaris
Module API changes
==================
* RM_SetContextUser, RM_SetModuleUserACLString, RM_GetModuleUserACLString
* Fix crash in CLIENT_CHANGE event, when the selected database is not 0
Changes in CLI tools
====================
* redis-benchmark avoid aborting on NOPERM from CONFIG GET
Bug Fixes
=========
* Avoid hang of diskless replication fork child when parent crashes
* Fix crash with module API of list iterator and RM_ListDelete
* Fix TLS error handling to avoid connection drops on timeouts
* Fix runtime changes to cluster-announce-*-port to take effect on the local node too
* Fix sentinel function that compares hostnames if failed resolve
* Fix MIGRATE with AUTH set to "keys" is getting wrong key names leading to MOVED or ACL errors
Fixes for issues in previous releases of Redis 7.0
--------------------------------------------------
* Fix command line startup --sentinel problem
* Fis missing FCALL commands in monitor
* Fix CLUSTER SHARDS showing empty hostname
* Replica that asks for rdb-only could have missed the EOF and hang
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Add deromanize subcommand to convert Roman numeral chromosome IDs
fastx-stats: Report standard deviation for read length
Changes: https://github.com/auerlab/biolibc-tools/releases
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This release delivers upstream two changes we've been shipping in Solaris
for many years - a fix to the command line handling to allow specifying
IPv6 addresses directly ("xhost +2001:DB8::11") and the use of gettext()
to allow localizing output & error messages. Unfortunately, this release
only includes the changes to use gettext, but does not include any
translations.
Alan Coopersmith (6):
gitlab CI: add a basic build test
Build xz tarballs instead of bzip2
Recognize raw IPv6 numeric address
Use gettext() to localize messages if available
Simplify i18n of 'unable to get ... address for ...' error message
xhost 1.0.9
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Bump pkgsrc version.
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Git 2.38.2 Release Notes
========================
This is to backport various fixes accumulated during the development
towards Git 2.39, the next feature release.
Fixes since v2.38.1
-------------------
* Update CodingGuidelines to clarify what features to use and avoid
in C99.
* The codepath that reads from the index v4 had unaligned memory
accesses, which has been corrected.
* "git remote rename" failed to rename a remote without fetch
refspec, which has been corrected.
* "git clone" did not like to see the "--bare" and the "--origin"
options used together without a good reason.
* Fix messages incorrectly marked for translation.
* "git fsck" failed to release contents of tree objects already used
from the memory, which has been fixed.
* "git rebase -i" can mistakenly attempt to apply a fixup to a commit
itself, which has been corrected.
* In read-only repositories, "git merge-tree" tried to come up with a
merge result tree object, which it failed (which is not wrong) and
led to a segfault (which is bad), which has been corrected.
* Force C locale while running tests around httpd to make sure we can
find expected error messages in the log.
* Fix a logic in "mailinfo -b" that miscomputed the length of a
substring, which lead to an out-of-bounds access.
* The codepath to sign learned to report errors when it fails to read
from "ssh-keygen".
* "GIT_EDITOR=: git branch --edit-description" resulted in failure,
which has been corrected.
* Documentation on various Boolean GIT_* environment variables have
been clarified.
* "git multi-pack-index repack/expire" used to repack unreachable
cruft into a new pack, which have been corrected.
* The code to clean temporary object directories (used for
quarantine) tried to remove them inside its signal handler, which
was a no-no.
* "git branch --edit-description" on an unborh branch misleadingly
said that no such branch exists, which has been corrected.
* GitHub CI settings have been adjusted to recent reality, merging
and cherry-picking necessary topics that have been prepared for Git
2.39.
* `git rebase --update-refs` would delete references when all `update-ref`
commands in the sequencer were removed, which has been corrected.
Also contains various documentation updates and code clean-ups.
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Parlatype is a minimal audio player for manual speech transcription,
written for the GNOME desktop environment. It plays audio sources
to transcribe them in your favourite text application.
It's intended to be useful for journalists, students, scientists
and whoever needs to transcribe audio files.
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