Commit graph

284201 commits

Author SHA1 Message Date
minskim
d06af8d43f Update path to math/py-tables 2018-07-05 01:21:05 +00:00
adam
dbcfeed81a Updated multimedia/bitstream 2018-07-04 21:46:27 +00:00
adam
7f89bbfcec bitstream: updated to 1.4
1.4:
Add RTCP helpers
2018-07-04 21:45:54 +00:00
fhajny
dbd8268a3a doc: Updated www/passenger to 5.3.3 2018-07-04 14:41:28 +00:00
fhajny
c76479b3de www/*passenger: Update to 5.3.3.
- [Apache, Nginx] Fixes the passenger-install-*-module scripts.
- [Nginx] Fixed nginx module building on CentOS 6.
2018-07-04 14:41:18 +00:00
bsiegert
b0b9e94900 Patch SV 51159 in GNU Make.
Hopefully this will fix the problems joerg@ and others encountered last
time gmake was updated to 4.2.1. Description of the patch:

[SV 51159] Use a non-blocking read with pselect to avoid hangs.
* posixos.c (set_blocking): Set blocking on a file descriptor.
(jobserver_setup): Set non-blocking on the jobserver read side.
(jobserver_parse_auth): Ditto.
(jobserver_acquire_all): Set blocking to avoid a busy-wait loop.
(jobserver_acquire): If the non-blocking read() returns without
taking a token then try again.
2018-07-04 14:09:07 +00:00
jperkin
5393242c73 *: Move SUBST_STAGE from post-patch to pre-configure
Performing substitutions during post-patch breaks tools such as mkpatches,
making it very difficult to regenerate correct patches after making changes,
and often leading to substituted string replacements being committed.
2018-07-04 13:40:07 +00:00
wen
68640d6240 Updated devel/p5-MooseX-Emulate-Class-Accessor-Fast to 0.009032 2018-07-04 13:27:41 +00:00
wen
e8a3909d77 Update to 0.009032
Upstream changes:
0.009032 - 2018-07-03
          - Releasing as stable

0.009_031 - 2018-06-22
          - Repackaged with ExtUtils::MakeMaker (and Distar) rather than
            Module::Install
          - enabled previously TODO test for attribute named meta
2018-07-04 13:26:38 +00:00
wen
324374fd7b Updated devel/p5-Module-CoreList to 5.20180626 2018-07-04 12:57:54 +00:00
wen
461179f574 Update to 5.20180626
Upstream changes:
5.20180626
  - Updated for v5.29.0
2018-07-04 12:54:32 +00:00
adam
24f3c1924a Updated security/gpgme 2018-07-04 12:54:31 +00:00
wen
e090db3036 Updated devel/p5-Modern-Perl to 1.20180701 2018-07-04 12:52:20 +00:00
wen
1e6988ae3c Update to 1.20180701
Upstream changes:
1.20180701 2018-07-01 10:34:32-07:00 America/Los_Angeles
    - added support for Perl 5.26 and 5.28
2018-07-04 12:51:11 +00:00
wen
ec1a424e08 Updated lang/yabasic to 2.79.2 2018-07-04 12:47:29 +00:00
adam
43a07b11e2 gpgme: updated to 1.11.1
version 1.11.1:
* Fixed build problems in the 1.11.0 release.
* Added C++ interfaces which were planned for 1.11.0.

version 1.11.0:
* New encryption API to support direct key specification including
  hidden recipients option and taking keys from a file.  This also
  allows to enforce the use of a subkey.
* New encryption flag for the new API to enforce the use of plain
  mail addresses (addr-spec).
* The import API can now tell whether v3 keys are skipped.  These old
  and basically broken keys are not anymore supported by GnuPG 2.1.
* The decrypt and verify API will now return the MIME flag as
  specified by RFC-4880bis.
* The offline mode now has an effect on gpg by disabling all network
  access.
* A failed OpenPGP verification how returns the fingerprint of the
  intended key if a recent gpg version was used for signature
  creation.
* New tool gpgme-json as native messaging server for web browsers.
  As of now public key encryption and decryption is supported.
  Requires Libgpg-error 1.29.
* New context flag "request-origin" which has an effect when used
  with GnuPG 2.2.6 or later.
* New context flag "no-symkey-cache" which has an effect when used
  with GnuPG 2.2.7 or later.
* New convenience constant GPGME_KEYLIST_MODE_LOCATE.
* Improved the Python documentation.
* Fixed a potential regression with GnuPG 2.2.6 or later.
* Fixed a crash in the Python bindings on 32 bit platforms.
* Various minor fixes.
2018-07-04 12:46:29 +00:00
wen
cf735c2bd8 Update to 2.79.2
Upstream changes:
Version 2.79.2, May 13, 2018

    No changes over 2.79.1
    Advanced patchlevel to get in line with tagging again

Version 2.79.0, April 21, 2018

    Introduced new peeks "secondsrunning" and "millisrunning"
    Bugfixes regarding the switch statement
2018-07-04 12:45:57 +00:00
bsiegert
9ad9c4c52a gmake-4.2.1 2018-07-04 09:44:01 +00:00
bsiegert
a3a1053c89 Update GNU make to 4.2.1.
Version 4.2.1 (10 Jun 2016)

A complete list of bugs fixed in this version is available here:

http://sv.gnu.org/bugs/index.php?group=make&report_id=111&fix_release_id=107&set=custom

This release is a bug-fix release.


Version 4.2 (22 May 2016)

A complete list of bugs fixed in this version is available here:

http://sv.gnu.org/bugs/index.php?group=make&report_id=111&fix_release_id=106&set=custom

* New variable: $(.SHELLSTATUS) is set to the exit status of the last != or
  $(shell ...) function invoked in this instance of make.  This will be "0" if
  successful or not "0" if not successful.  The variable value is unset if no
  != or $(shell ...) function has been invoked.

* The $(file ...) function can now read from a file with $(file <FILE).
  The function is expanded to the contents of the file.  The contents are
  expanded verbatim except that the final newline, if any, is stripped.

* The makefile line numbers shown by GNU make now point directly to the
  specific line in the recipe where the failure or warning occurred.
  Sample changes suggested by Brian Vandenberg <phantall@gmail.com>

* The interface to GNU make's "jobserver" is stable as documented in the
  manual, for tools which may want to access it.

  WARNING: Backward-incompatibility! The internal-only command line option
  --jobserver-fds has been renamed for publishing, to --jobserver-auth.

* The amount of parallelism can be determined by querying MAKEFLAGS, even when
  the job server is enabled (previously MAKEFLAGS would always contain only
  "-j", with no number, when job server was enabled).
2018-07-04 09:42:56 +00:00
adam
b0abdb4d35 Updated devel/py-pbr, www/py-model_mommy 2018-07-04 09:08:08 +00:00
adam
d8f64bf9fb py-model_mommy: updated to 1.6.0
1.6.0
- Support for Postgres' CI fields types
- NullBooleanField using gen_boolean generator
- Remove dependency with Django from model_mommy.random_gen module
- New paramenter `_refresh_after_create` added to `model_mommy.make` method (defaults to `False`)
2018-07-04 09:07:45 +00:00
adam
ef33659cc4 py-pbr: updated to 4.0.4
4.0.4
* Revert "Remove win32/nt checks for wrapper script gen"

4.0.3
* Don't poke in pip for requests
* Fix builddoc with sphinx <= 1.6

4.0.1
* add lower-constraints job
* Explicitly read setup.cfg as utf-8 on Python 3

4.0.0
* builddoc: Treat '[pbr] autodoc\_tree\_excludes' as a multi-line opt
* update parse test to use reliable comparison
* Better Sem-Ver header handling
* Make docs on env vars a little clearer
* Updated from global requirements
* Updated from global requirements
* future-proof invocation of apidoc
* emit warning correctly
* Updated from global requirements
* deprecations: Deprecate support for '-py{N}' requirements
* doc: Minor rework of usage doc
* doc: Rework features doc
* Support v<semver> version
* Deprecate testr and nose integration
* tests: Increase coverage of requirements parsing
* trivial: Move packaging tests to test\_packaging
* Put test-requirements into an extra named 'test'
* Support Description-Content-Type metadata
* Avoid tox\_install.sh for constraints support
* Test on Python 3.6
* Support PEP 345 Project-URL metadata
* Remove setting of version/release from releasenotes
* Updated from global requirements
* Use 'build\_reno' setuptools extension if available
* Remove unnecessary 'if True'
* Discover Distribution through the class hierarchy
* Add reno for release notes management
* Remove support for command hooks
* Remove dead code
* Deprecate support for Sphinx < 1.6
* builddoc: Use '[sphinx\_build] builders' with Sphinx < 1.6
* Remove win32/nt checks for wrapper script gen
* Updated from global requirements
* Remove py26 support
* Updated from global requirements
* Updated from global requirements
* Updated from global requirements
* Update URLs in documents according to document migration
* Updated from global requirements
* gitignore: Ignore .venv
* switch from oslosphinx to openstackdocstheme
* Trivial: Fix docstring
* turn on warning-as-error flag for doc build
* rearrange existing documentation using the new standard layout
2018-07-04 09:05:16 +00:00
wen
a7acd42f86 Updated devel/R-bit to 1.1.14 2018-07-04 08:15:51 +00:00
wen
ce7143f932 Update to 1.1.14
Upstream changes:
CHANGES IN bit VERSION 1.1-14

BUG FIXES

    o bit[i] and bit[i]<-v now check for non-positive integers
      which prevents a segfault when bit[NA] or bit[NA]<-v



        CHANGES IN bit VERSION 1.1-13

USER VISIBLE CHANGES

    o logical NA is now mapped to bit FALSE as in ff booleans
    o extractor function '[.bit' with positive numeric subscripts
	  (integer, double, bitwhich) now behaves like '[.logical' and returns
	  NA for out-of-bound requests and no element for 0
    o extractor function '[[.bit' with positive numeric (integer, double,
      bitwhich) subscripts now behaves like '[[.logical' and throws an error
      for out-of-bound requests
    o extractor function '[.bit' with range index subscripts (ri)
      subscripts now behaves like '[[.bit' and throws an error
      for out-of-bound requests
    o assignment functions '[<-.bit' and '[[<-.bit' with positive numeric
      (integer, double, bitwhich) subscripts now behave like '[<-.logical' and
      '[[<-.logical' and silently increase vector length if necessary
    o assignment function '[<-.bit' with range index subscripts (ri) now
      behaves like '[[<-.bit' and silently increases vector length if necessary
    o rlepack() is now a generic with a method for class 'integer'
    o rleunpack() is now a generic with a method for class 'rlepack'
    o unique.rlepack() now gives correct results for unordered sequences
    o anyDuplicated.rlepack() now returns the position of the first
	  duplicate and gives correct results for unordered sequences

TUNING

    o The package can now compiled with 64bit words instead of 32bit words,
      since we only measured a minor speedup, we left 32bit as the default.

BUG FIXES

    o extractor and assignment functions now check for legal (positive)
      subscript bounds, hence illegally large subscripts or zero no longer
      cause memory violations
2018-07-04 08:13:59 +00:00
adam
ce0cd65bcb Updated devel/py-serpent, math/py-numexpr 2018-07-04 08:10:53 +00:00
adam
190ee55663 py-numexpr: updated to 2.6.5
Changes from 2.6.4 to 2.6.5
- The maximum thread count can now be set at import-time by setting the
  environment variable 'NUMEXPR_MAX_THREADS'. The default number of
  max threads was lowered from 4096 (which was deemed excessive) to 64.
- A number of imports were removed (pkg_resources) or made lazy (cpuinfo) in
  order to speed load-times for downstream packages (such as pandas, sympy,
  and tables). Import time has dropped from about 330 ms to 90 ms. Thanks to
  Jason Sachs for pointing out the source of the slow-down.
- Thanks to Alvaro Lopez Ortega for updates to benchmarks to be compatible with
  Python 3.
- Travis and AppVeyor now fail if the test module fails or errors.
- Thanks to Mahdi Ben Jelloul for a patch that removed a bug where constants
  in where calls would raise a ValueError.
- Fixed a bug whereby all-constant power operations would lead to infinite
  recursion.
2018-07-04 08:10:07 +00:00
wen
6a08a78aa2 Updated devel/p5-File-ShareDir to 1.116 2018-07-04 08:06:37 +00:00
adam
7c9a16fbed py-serpent: updated to 1.25
1.25:
LICENSE file included in release.
2018-07-04 08:06:23 +00:00
wen
6111c0f55d Update to 1.116
Upstream changes:
1.116   2018-06-24
    - fix fail-test which incorrectly read without permission
      ==> introduce new CI test proving this (Thanks to Ville
          Skyttä <ville.skytta@iki.fi>)
    - spelling fixes (Thanks to Ville Skyttä <ville.skytta@iki.fi>)
    - fix author tests when run without recommended dependencies
      (reported by Mohammed Anwar & Wesley Schwengle)
    - add a test proving and reporting dependencies
2018-07-04 08:05:25 +00:00
wen
47a1944bbb Updated devel/p5-Event-RPC to 1.10 2018-07-04 08:01:27 +00:00
wen
9f6e102004 Update to 1.10
Upstream changes:
1.10 Wed Jun 27, 2018, joern
    Bugfixes:
    - Test suite failed on newer Perl versions which
      do not have . in @INC anymore.

1.09 Mon Jun 25, 2018, joern
    Features:
    - Event::RPC::Server->prepare() to support having
      control over the Event loop yourself.

    Bugfixes:
    - SSL tests failed due to expired CA certificate.
      Just created new certificates with 30 year
      expiration and put a gen.sh script inside to
      easily generate new certificates after that
      period ;)
    - Removed unused code. Thanks for the hint to
      ppisar AT redhat.com.
2018-07-04 08:00:29 +00:00
wen
c2347e0461 Updated devel/p5-CPAN-Perl-Releases to 3.68 2018-07-04 07:48:51 +00:00
wen
6331b994d6 Update to 3.68
Upstream changes:
version 3.68 at 2018-06-27 00:55:44 +0000
-----------------------------------------

  Change: 56da5405ec89c9b7690bdf8325f7373af97cd2d7
  Author: Chris 'BinGOs' Williams <chris@bingosnet.co.uk>
  Date : 2018-06-27 01:55:44 +0000

    Updated for v5.29.0
2018-07-04 07:48:02 +00:00
wen
549b60f350 Updated devel/p5-Class-Accessor-Grouped to 0.10014 2018-07-04 07:44:55 +00:00
wen
520120a3eb Update to 0.10014
Upstream changes:
0.10014 2018-07-01 19:25 (UTC)
    - releasing 0.10013_01 as stable

0.10013_01 2018-05-28 13:37 (UTC)
    - convert packaging from Module::Install to plain ExtUtils::MakeMaker
    - fix running Makefile.PL when @INC does not contain '.' (perl 5.26).
    - don't run author tests at all for user installs
2018-07-04 07:43:59 +00:00
wen
4c7332f3bd Updated math/R to 3.5.1 2018-07-04 07:28:31 +00:00
wen
bfed5c726f Update to 3.5.1
Upstream changes:
CHANGES IN R 3.5.1
BUG FIXES

    file("stdin") is no longer considered seekable.

    dput() and dump() are no longer truncating when options(deparse.max.lines = *) is set.

    Calls with an S3 class are no longer evaluated when printed, fixing part of PR#17398, thanks to a patch from Lionel Henry.

    Allow file argument of Rscript to include space even when it is first on the command line.

    callNextMethod() uses the generic from the environment of the calling method. Reported by Hervé Pagès with well documented examples.

    Compressed file connections are marked as blocking.

    optim(*, lower = c(-Inf, -Inf)) no longer warns (and switches the method), thanks to a suggestion by John Nash.

    predict(fm, newdata) is now correct also for models where the formula has terms such as splines::ns(..) or stats::poly(..), fixing PR#17414, based on a patch from Duncan Murdoch.

    simulate.lm(glm(*, gaussian(link = <non-default>))) has been corrected, fixing PR#17415 thanks to Alex Courtiol.

    unlist(x) no longer fails in some cases of nested empty lists. Reported by Steven Nydick.

    qr.coef(qr(<all 0, w/ colnames>)) now works. Reported by Kun Ren.

    The radix sort is robust to vectors with >1 billion elements (but long vectors are still unsupported). Thanks to Matt Dowle for the fix.

    Terminal connections (e.g., stdin) are no longer buffered. Fixes PR#17432.

    deparse(x), dput(x) and dump() now respect c()'s argument names recursive and use.names, e.g., for x <- setNames(0, "recursive"), thanks to Suharto Anggono's PR#17427.

    Unbuffered connections now work with encoding conversion. Reported by Stephen Berman.

    ‘.Renviron’ on Windows with Rgui is again by default searched for in user documents directory when invoked via the launcher icon. Reported by Jeroen Ooms.

    printCoefmat() now also works with explicit right=TRUE.

    print.noquote() now also works with explicit quote=FALSE.

    The default method for pairs(.., horInd=*, verInd=*) now gets the correct order, thanks to reports by Chris Andrews and Gerrit Eichner. Additionally, when horInd or verInd contain only a subset of variables, all the axes are labeled correctly now.

    agrep("..|..", .., fixed=FALSE) now matches when it should, thanks to a reminder by Andreas Kolter.

    str(ch) now works for more invalid multibyte strings.
2018-07-04 07:27:13 +00:00
adam
70d8223782 py-pandas: revbump for py-tables 2018-07-04 06:50:04 +00:00
adam
896dd5005b Updated math/py-tables to 3.4.4 2018-07-04 06:49:04 +00:00
adam
2a4c1ea8b6 py-tables: (ex py-pytables) updated to 3.4.4
Changes from 3.4.3 to 3.4.4

Improvements

Environment variable to control the use of embedded libraries.
Include citation in repository. gh-690.

Bugs fixed

Fixed import error with numexpr 2.6.5.dev0 gh-685.
Fixed linter warnings.
Fixed for re.split() is version detection. gh-687.
Fixed test failures with Python 2.7 and NumPy 1.14.3 gh-688 & gh-689.
2018-07-04 06:46:49 +00:00
minskim
26fc30e30d doc: Added databases/py-lmdb version 0.94 2018-07-04 05:18:31 +00:00
minskim
9d9fc05bcb databases/Makefile: Add py-lmdb 2018-07-04 05:18:15 +00:00
minskim
d329ee7342 databases/py-lmdb: Import version 0.94
Provides Python binding for the LMDB "Lightning" Database.
2018-07-04 05:18:06 +00:00
adam
a9694032be Updated security/py-asyncssh, www/py-gunicorn, databases/py-peewee, devel/py-test-testmon 2018-07-04 04:00:03 +00:00
adam
a8528a7094 py-test-testmon: updated to 0.9.12
0.9.12:
Fixing some nasty bugs
2018-07-04 03:58:42 +00:00
adam
0bab6d11b1 py-peewee: updated to 3.5.2
3.5.2:

New guide to using window functions in Peewee.
New and improved table name auto-generation. This feature is not backwards compatible, so it is disabled by default. To enable, set legacy_table_names=False in your model's Meta options. For more details, see table names documentation.
Allow passing single fields/columns to window function order_by and partition_by arguments.
Support for FILTER (WHERE...) clauses with window functions and aggregates.
Added IdentityField class suitable for use with Postgres 10's new identity column type. It can be used anywhere AutoField or BigAutoField was being used previously.
Fixed bug creating indexes on tables that are in attached databases (SQLite).
Fixed obscure bug when using prefetch() and ModelAlias to populate a back-reference related model.


3.5.1:

New features
------------
New documentation for working with relationships in Peewee.
Improved tests and documentation for MySQL upsert functionality.
Allow database parameter to be specified with ModelSelect.get() method.
Add QualifiedNames helper to peewee module exports.
Add temporary= meta option to support temporary tables.
Allow a Database object to be passed to constructor of DataSet helper.

Bug fixes
---------
Fixed edge-case where attempting to alias a field to it's underlying column-name (when different), Peewee would not respect the alias and use the field name instead.
Raise a ValueError when joining and aliasing the join to a foreign-key's object_id_name descriptor. Should prevent accidentally introducing O(n) queries or silently ignoring data from a joined-instance.
Fixed bug for MySQL when creating a foreign-key to a model which used the BigAutoField for it's primary-key.
Fixed bugs in the implementation of user-defined aggregates and extensions with the APSW SQLite driver.
Fixed regression introduced in 3.5.0 which ignored custom Model __repr__().
Fixed regression from 2.x in which inserting from a query using a SQL() was no longer working.
2018-07-04 03:56:46 +00:00
adam
6e5a313b92 py-gunicorn: updated to 19.9.0
19.9.0:
* fix: address a regression that prevented syslog support from working
* fix: correctly set REMOTE_ADDR on versions of Python 3 affected by
  Python Issue 30205 <https://bugs.python.org/issue30205>_
* fix: show zero response length correctly in access log
* fix: prevent raising :exc:AttributeError when --reload is not passed
  in case of a :exc:SyntaxError raised from the WSGI application.
* The internal module gunicorn.workers.async was renamed to gunicorn.workers.base_async
  since async is now a reserved word in Python 3.7.
2018-07-04 03:43:12 +00:00
adam
e0d767d0f5 py-asyncssh: updated to 1.13.2
Release 1.13.2:
Added support for accessing client host keys via the OpenSSH ssh-keysign program when doing host-based authentication. If ssh-keysign is present and enabled on the system, an AsyncSSH based SSH client can use host-based authentication without access to the host private keys.
Added support for using pathlib path objects when reading and writing private and public keys and certificates.
Added support for auth_completed() callback in the SSHServer class which runs when authentication completes successfully on each new connection.
Fixed host-based authentication unit tests to mock out calls to getnameinfo() to avoid failures on systems with restricted network functionality.
2018-07-04 03:38:34 +00:00
markd
8cd03fcda8 tex-xcolor: add some dependencies used under certain options. 2018-07-03 21:11:46 +00:00
jperkin
31bfbbe432 doc: Updated pkgtools/pkgin to 0.11.4 2018-07-03 17:39:45 +00:00