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Author SHA1 Message Date
Jason W. Bacon
a156fdcf52 biology/subread: Read alignment, quantification and mutation discovery 
The Subread package comprises a suite of software programs for processing
next-gen sequencing read data including:

    Subread: a general-purpose read aligner
    Subjunc: a read aligner developed for aligning RNA-seq reads
    featureCounts: a software program developed for counting reads to genomic
    features such as genes, exons, promoters and genomic bins.
    Sublong: a long-read aligner that is designed based on seed-and-vote.
    exactSNP: discovers SNPs by testing signals against local background noise.
 2020-06-05 01:55:49 +00:00
Wen Heping
6220495836 - Fix the name of py-django30 in my previous commit 
Spotted by:	dan@langille.org
 2020-06-04 23:43:25 +00:00
Glen Barber
ff129e2cb3 Attempt to fix build. 
Sponsored by:	Rubicon Communications, LLC (netgate.com)
 2020-06-04 23:31:29 +00:00
Jose Alonso Cardenas Marquez
eda8dacdab - Modify some entries into pkg-message file 
- Bump PORTREVISION
 2020-06-04 22:59:09 +00:00
Jose Alonso Cardenas Marquez
1a5ac0c4c0 - Add shells/bash as dependency 
- Bump PORTREVISION

PR:		246662
Submitted by:	kaltheat at gmail.com
 2020-06-04 22:58:07 +00:00
Lev A. Serebryakov
070fb7fcab Update to last toolchain & committ. 2020-06-04 22:56:17 +00:00
Jose Alonso Cardenas Marquez
46723471a2 - Update to 8.8.7 
Security:	c5ec57a9-9c2b-11ea-82b8-4c72b94353b5
 2020-06-04 22:50:31 +00:00
Jose Alonso Cardenas Marquez
d8cafe0a73 - Update c5ec57a9-9c2b-11ea-82b8-4c72b94353b5 entry. Add drupal 8.8.6 2020-06-04 22:49:54 +00:00
Xin LI
e3029cb10f devel/py-ujson: update to 3.0.0. 2020-06-04 22:47:09 +00:00
Lev A. Serebryakov
a809c12c7b Update to latest release 2020q2-update 2020-06-04 22:45:34 +00:00
Romain Tartière
9956b7dcee Update to 3.5.0 
With hat:	puppet
 2020-06-04 22:41:44 +00:00
Romain Tartière
c69be90c57 Update to 1.8.0 
With hat:	puppet
 2020-06-04 22:41:25 +00:00
Romain Tartière
b6f1e2ddad Upadte to 5.2.15 
With hat:	puppet
 2020-06-04 22:41:00 +00:00
Romain Tartière
88bd6d6843 Update to 6.11.0 (for real this time) 
Release notes:
https://puppet.com/docs/puppetdb/latest/release_notes.html#puppetdb-6110

With hat:	puppet
 2020-06-04 22:40:15 +00:00
Romain Tartière
a7b4e5fd77 Update to 6.11.0 
Release notes:
https://puppet.com/docs/puppetdb/latest/release_notes.html#puppetdb-6110

With hat:	puppet
 2020-06-04 22:26:06 +00:00
Romain Tartière
f87f1271e1 Update to 6.12.0 
Release notes:
https://puppet.com/docs/puppetserver/latest/release_notes.html#puppet-server-6120

With hat:	puppet
 2020-06-04 22:25:21 +00:00
Romain Tartière
79f3110975 Update to 6.16.0 
Release notes:
https://puppet.com/docs/puppet/latest/release_notes_puppet.html#puppet-release-notes-x.15.0

With hat:	puppet
 2020-06-04 22:24:50 +00:00
Romain Tartière
bf15af6215 Update to 3.14.11 
With hat:	puppet
 2020-06-04 22:24:04 +00:00
Bradley T. Hughes
54c15ccb38 www/node: Update 13.13.0_1 -> 13.14.0 
https://nodejs.org/en/blog/release/v13.14.0/

Refresh patches with `make makepatch`, and remove
patch-deps_v8_src_objects_js-number-format.cc which has been applied
upstream.

Sponsored by:	Miles AS
 2020-06-04 21:12:28 +00:00
Bradley T. Hughes
15c90a6e6e www/node12: Update 12.16.2_1 -> 12.16.3 
https://nodejs.org/en/blog/release/v12.16.3/

Refresh patches with `make makepatch`.

Sponsored by:	Miles AS
 2020-06-04 21:10:55 +00:00
Adriaan de Groot
273e40a293 Pre Qt 5.15 housekeeping: textproc/kreport 
This is probably a conflagration of CMake, Qt and other updates all
happening at once. In poudriere, build of databases/kexi fails with

ld: error: undefined symbol: KReportGroupTracker::qt_metacast(char const*)
>>> referenced by mocs_compilation.cpp
>>>               src/plugins/reports/CMakeFiles/kexi_reportplugin.dir/kexi_reportplugin_autogen/mocs_compilation.cpp.o:(KRScriptFunctions::qt_metacast(char const*))

The problem lies in textproc/kreport, which has a QObject-derived
class with no out-of-line virtual methods, and no clear path
to have moc called on it. This patch splits out the virtual
destructor, adds a .cpp file containing it, and causes automoc
to run normally on the class. This makes all the QObject machinery
appear in the shared library, and kexi can use it.
 2020-06-04 21:02:12 +00:00
Matthias Andree
f0711b4f79 Tools/scripts/mfh: revert accidental tab expansion 
Regression from r537876

Reported by:	tijl@
Approved by:	portmgr@ (implicit, whitespace-only edit to fix a regression)
 2020-06-04 21:01:37 +00:00
Matthias Fechner
53cdc91ced Make sure the installation message points to the current manual. 2020-06-04 20:37:34 +00:00
Lorenzo Salvadore
8ce442ff34 emulators/i386-wine-devel: Small simplification for distinfo-update 
Approved by:	gerald (mentor)
Differential Revision:	https://reviews.freebsd.org/D25042
 2020-06-04 20:14:44 +00:00
Romain Tartière
091fb8f723 Update to 2.12.0 
Release notes:
https://github.com/puppetlabs/bolt/blob/master/CHANGELOG.md#bolt-2120-2020-06-01

With hat:	puppet
 2020-06-04 20:14:35 +00:00
Romain Tartière
dc29751aee Update to 1.3.1 
With hat:	puppet
 2020-06-04 20:08:35 +00:00
Matthias Fechner
dffa6ca4c7 Update to gitlab-ce 13.0.5. 
Changelog:
https://about.gitlab.com/releases/2020/05/06/gitlab-com-13-0-breaking-changes/
https://about.gitlab.com/releases/2020/05/22/gitlab-13-0-released/
https://about.gitlab.com/releases/2020/05/27/security-release-13-0-1-released/
https://about.gitlab.com/releases/2020/05/29/gitlab-13-0-3-released/
https://about.gitlab.com/releases/2020/06/03/critical-security-release-13-0-4-released/

Make sure you read the upgrade manual very carefully, there is a manual change in file:
/usr/local/share/gitaly/config.toml
required that the diff does not show.
 2020-06-04 20:07:29 +00:00
Guido Falsi
8608013dc0 Update xfce4-stopwatch-plugin to 0.4.0 2020-06-04 20:04:54 +00:00
Matthias Fechner
4e5a424e44 Update depedency to point to required version devel/rubygem-request_store14. 2020-06-04 20:02:23 +00:00
Matthias Fechner
a382d749db Update to 8.31.1 which is required for gitlab-ce 13.0. 2020-06-04 20:01:15 +00:00
Matthias Fechner
66f6fc7289 Update to 1.18.0 which is required for gitlab-ce 13.0. 2020-06-04 20:00:39 +00:00
Matthias Fechner
8644d0f40b Update to 13.3.0 which is required for gitlab-ce 13.0. 2020-06-04 19:59:47 +00:00
Matthias Fechner
e4537bc3b3 Update to 13.0.5 which is required for gitlab-ce 13.0. 2020-06-04 19:59:04 +00:00
Matthias Fechner
554339327a Update to 5.5.5 which is required for gitlab-ce 13.0. 2020-06-04 19:57:53 +00:00
Matthias Fechner
11d3c6f5d4 Upgrade to 0.19.1 which is required for gitlab-ce 13.0. 2020-06-04 19:57:06 +00:00
Matthias Fechner
4b62c2061c Update to 6.3.1 which is required for gitlab-ce 13.0. 2020-06-04 19:56:15 +00:00
Matthias Fechner
1b497076b1 Update to 4.2.7.9 which is required for gitlab-ce 13.0. 2020-06-04 19:55:32 +00:00
Matthias Fechner
22fbc77173 Update to 7.9.0 which is required for gitlab-ce 13.0. 2020-06-04 19:54:43 +00:00
Matthias Fechner
eee181f88f update to 2.3.0 which is required for gitlab-ce 13.0. 2020-06-04 19:54:02 +00:00
Matthias Fechner
bf66ad1a95 Update to 6.0.2 which is required for gitlab-ce 13.0. 2020-06-04 19:53:21 +00:00
Matthias Fechner
36dad58328 Update to 5.0.3 which is required for gitlab-ce 13.0. 2020-06-04 19:52:33 +00:00
Matthias Fechner
8f5c5c9531 Update to 13.0.0.pre.rc1 which is required for gitlab-ce 13.0. 2020-06-04 19:51:54 +00:00
Matthias Fechner
d29276d69c New port required for gitlab-ce 13.0. 2020-06-04 19:51:11 +00:00
Matthias Fechner
786ac2a5da Update to 1.5.0 which is required for gitlab-ce 13.0. 2020-06-04 19:46:51 +00:00
Matthias Fechner
99cacde740 Update to 1.2.0 which is required for gitlab-ce 13.0. 2020-06-04 19:45:56 +00:00
Boris Samorodov
f2605465d5 java/intellij: Remove superfluous PYTHON_VER at the plist. 2020-06-04 19:36:47 +00:00
Gleb Popov
48e8d5ce03 lang/ghc: Depend on newer LLVM 7.0, for which upstream declares support. 
PR:		246988
Submitted by:	mikael
 2020-06-04 19:31:41 +00:00
Boris Samorodov
9093827413 java/intellij: Update to version 2020.1.2. 2020-06-04 19:20:58 +00:00
Boris Samorodov
268a41bd19 devel/pycharm-ce: Update to version 2020.1.2. 2020-06-04 19:17:05 +00:00
Stephen Montgomery-Smith
c1f3be27e2 - Fix build error caused by lack of py-pybind11 dependency. I decided to 
go this way instead of putting superbuild back on.
 2020-06-04 19:09:36 +00:00