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11697 Commits

Author SHA1 Message Date
Sunpoet Po-Chuan Hsieh
30ba624a30 Update to 2.16
Changes:	http://search.cpan.org/dist/Math-GMP/Changes
2017-12-19 18:20:37 +00:00
Jochen Neumeister
503e12abad math/dynare: Update from 4.5.1 to 4.5.3
This release is compatible with MATLAB versions 7.3 (R2006b) to 9.3 (R2017b)
and with GNU Octave versions 4.2.

Here is a list of the problems identified in version 4.5.1 and that have been
fixed in version 4.5.2:

 - Fixed bug in perfect foresight solver:

   + If expected shocks were declared after the terminal period, as specified
   by the `periods` option, Dynare was crashing.

   + Models declared with the `linear` option were crashing if exogenous
   variables were present with a lead or lag.

 - After ML or Bayesian estimation when the smoother option or `mh_replic=0`
   were not specified, not all smoothed measurement errors were displayed.

 - Fixed error in reference manual about the `conditional_forecasts` command.

 - Fixed smoother behaviour, provide informative error instead of crashing when
   model cannot be solved.

 - The `nopathchange` preprocessor option was always triggered, regardless of
   whether it was passed or not.

 - When `ramsey_policy` is used, allow state variables to be set in `histval`
   block.

 - `histval` erroneously accepted leads, leading to cryptic crashes.

 - The prior MC draws from previous runs were not deleted, potentially
   resulting in loading stale files.

 - `estim_params_` was being declared `global` more than once.

 - Fixed crashes happening when simulating linear models with order>1.

 - Make empirical moments independent of `simul_replic`, as stated in the
   reference manual, by outputting moments computed with the first simulated
   sample.

 - The `prior_function` required a preceding `estimation`-command to properly
   set up the prior.

 - If the mode for a parameter was at exactly 0, `mode_check` was crashing.

 - Fixed `get_posterior_parameters`-routine which should not do more than
   getting parameters. As a consequence, the `shock_decomposition`-command
   did not correctly set the `parameter_set` for use in subsequent function
   calls if shocks are correlated or measurement error is present.

 - Fixed bug in Ramsey problem with constraints both on a policy instrument and
   another variable. Note that the constraint on a variable that is not an
   instrument of the Ramsey problem must be written with an equation tag in the
   model block.

 - Fixed bug in Ramsey problem with constraints on policy instrument.

 - Fixed crash with optimizer 5 when not used with DSGE model at order 1.

 - Fixed mex file used for third order approximation (was crashing on
   Matlab/Windows 7).

 - `isfile` routine was failing with MATLAB older than R2016b. This bug
did not affect Octave.

PR:		223430
Submitted by:	fernando.apesteguia@gmail.com (maintainer)
Approved by:	tcberner (mentor)
MFH:	2017Q4
Differential Revision:	https://reviews.freebsd.org/D13058
2017-12-19 18:01:43 +00:00
Mathieu Arnold
bf406b4d24 Enhance USES=uniquefiles to be more generic.
This allows to have more complex renaming schemes.  Until now, it could
only add a prefix or a suffix, but this was not working at all for man
pages, because it would give man/man1/pyfoo.1.gz-2.7 or
man/man1/pyfoo-1-2.7.gz.  With this change, a man page will be correctly
renamed to man/man1/pyfoo-2.7.1.gz.

Unfix ports that were already handling man pages.

PR:		220214
Submitted by:	Fukang Chen (previous patch)
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D13444
2017-12-19 16:23:48 +00:00
Dmitry Marakasov
03a998408f Bring back mistakenly removed PORTEPOCH
Reported by:	Tamas TEVESZ <ice@extreme.hu>
2017-12-18 12:34:51 +00:00
David Naylor
6769568054 math/R-cran-car: updated to version 2.1-6
- remove unused test dependencies:
   - math/R-cran-nloptr
 - changelog:
   - Made several functions compatible with vcov() in R-devel (3.5.0).

Generated by:	portcran (0.1.6)
2017-12-18 07:32:48 +00:00
Baptiste Daroussin
1994117e17 Update to 0.7.0
Register ncurses dependency
2017-12-15 10:53:54 +00:00
Torsten Zuehlsdorff
1d7e0541a4 Add missing IGNORE_WITH_PHP for various pecl-ports.
After testing every pecl-* port with PHP 5.6, 7.0, 7.1 and 7.2
i set the IGNORE_WITH_PHP accordingly to the fallout.

PR:          222165
Reported by: brnd
Approved by: portmgr (blanket)
Differential Revision: https://reviews.freebsd.org/D13476
2017-12-14 13:57:28 +00:00
Greg Lewis
a202998baa Add a -lite version for gnuplot which has minimal dependencies.
This has been requested particularly by those running it in a headless
environment.
2017-12-13 07:23:10 +00:00
Greg Lewis
43bdbadbf9 Fix packing list substitutions for the lite port. 2017-12-13 07:14:56 +00:00
Greg Lewis
926d6221f6 Prepare for gnuplot-lite by splitting up the configure options, the
dependencies and adding some packing list substitution and hiding some
of it based on the definition of "LITE".
2017-12-13 07:11:07 +00:00
Dmitry Marakasov
58612140c7 - Switch to options helpers
- Switch to new test framework

Approved by:	portmgr blanket
2017-12-12 15:51:45 +00:00
Johannes M Dieterich
9514042786 math/blis: update to the first snapshot working on FreeBSD to support runtime kernel selection. For amd64, this will now select, if available, an assembly optimized kernel for the CPU architecture blis is running on. The other architectures continue to only use what is now called the generic kernel but in theory arm and power7 assembly optimizations are available.
Due to this, remove the old explicit kernel selection. Also switch to use devel/llvm50 as a compiler to actually support all the architectures (and upstream compile flags) properly. This hopefully will also help with getting blis to work on other architectures out of the box.

Reviewed by:	swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D13264
2017-12-12 02:49:56 +00:00
Dmitry Marakasov
51d66dd104 - Update to 5.41.0 [1]
- Add LICENSE_FILE
- Whitespace fixes
- Switch to new test framework

PR:		223316 [1]
Submitted by:	satosi.kimura@nifty.ne.jp [1]
2017-12-11 16:52:56 +00:00
Bradley T. Hughes
9b69f56c5e math/saga: Update 4.1.0 -> 6.1.0
PR:		223890
Submitted by:	Rainer Hurling <rhurlin@gwdg.de> (maintainer)
Approved by:	robak (mentor)
Differential Revision:	https://reviews.freebsd.org/D13436
2017-12-11 13:02:58 +00:00
Sunpoet Po-Chuan Hsieh
970d13f495 Fix build
PR:		223043
Submitted by:	Markus Mann <freebsd-public@it64.de>
MFH:		2017Q4
2017-12-11 10:40:51 +00:00
Antoine Brodin
a021c1b8c0 - Those ports fail to build with python3
- Add some explicit FLAVOR to dependencies where needed
2017-12-10 20:48:45 +00:00
Antoine Brodin
2744dfd2f4 ogdf fails to build with python3 2017-12-09 10:09:04 +00:00
Kurt Jaeger
9afab9fe40 math/nfft: update 3.3.2 -> 3.4.0
PR:		224163
Relnotes:	https://github.com/NFFT/nfft/releases
Submitted by:	Michael Danilov <mike.d.ft402@gmail.com> (maintainer)
2017-12-08 06:34:39 +00:00
Steve Wills
2d9bfab980 math/py-keras: Update to 2.1.2
PR:		224154
Submitted by:	Neel Chauhan <neel@neelc.org> (maintainer)
2017-12-07 18:11:08 +00:00
Tobias Kortkamp
1aaf849b21 math/py-matplotlib: Allow build for Python 3.x
- x11-toolkits/{py-gtk2,py-wxPython28} do not support Python 3.x, so
  exclude the GTKBACKEND, GTKAGGBACKEND, and WXAGGBACKEND in that case.

PR:		213636
Reported by:	lbartoletti@tuxfamily.org
Submitted by:	rsmith@xs4all.nl (based on)
Reviewed by:	mat
Approved by:	maintainer timeout
Differential Revision:	https://reviews.freebsd.org/D13377
2017-12-06 19:46:53 +00:00
Wen Heping
bac49068f3 - Update to 5.1.5 2017-12-06 02:28:55 +00:00
Antoine Brodin
8b36d27d2e clarence doesn't run with python3 2017-12-04 21:00:33 +00:00
Kurt Jaeger
4a70d839f9 math/glpk: update 4.63 -> 4.64, submitter becomes maintainer
PR:		224082
Changes: https://lists.gnu.org/archive/html/help-glpk/2017-12/msg00000.html
Submitted by:	Dmitri Goutnik <dg@syrec.org>
2017-12-04 18:11:52 +00:00
Dmitry Marakasov
1ae3c1cb27 - Update to 0.9.8.5 2017-12-04 11:32:28 +00:00
Rodrigo Osorio
646a05f6f8 Add new port math/nfft
NFFT is a software library, written in C, for computing non-equispaced fast
Fourier transforms and related variations. It implements the following
transforms:

1. Non-equispaced fast Fourier transform (NFFT)
 - forward transform (NFFT), i.e. frequency to time/space domain
 - adjoint transform (adjoint NFFT), i.e. time/space to frequency domain

2. Generalisations
 - to arbitrary nodes in time and frequency domain (NNFFT)
 - to real-valued data, i.e. (co)sine transforms, (NFCT, NFST)
 - to the sphere S^2 (NFSFT)
 - to the rotation group (NFSOFT)
 - to the hyperbolic cross (NSFFT)
3. Generalised inverse transformations based on iterative methods, e.g.
   CGNR/CGNE

PR:		223429
Submitted by:	Michael Danilov <mike.d.ft402@gmail.com>
2017-12-03 23:12:34 +00:00
Sunpoet Po-Chuan Hsieh
a001f466b0 Update to 0.15
- Update WWW

Changes:	https://bitbucket.org/ronaldoussoren/altgraph/src/default/doc/changelog.rst
2017-12-03 20:37:58 +00:00
David Chisnall
f9197640d9 Fix configure options for gnustep-make
We were not setting the flag to select the GNUstep ABI, so were defaulting to
using the GCC-compatible version, which was likely to trigger a lot of subtle
bugs.  This was noticed when C++ exceptions thrown through Objective-C stack
frames caused segfaults.
2017-12-03 12:23:53 +00:00
Joseph Mingrone
de876a285d math/libRmath: Update to version 3.4.3 and add armv[67] to ONLY_FOR_ARCHS 2017-12-03 03:46:11 +00:00
Antoine Brodin
b9ae2ff4d2 Explicitely pass ipython FLAVOR in a few ports 2017-12-02 09:22:02 +00:00
Jochen Neumeister
e9a9a7cb34 math/octave: Set correct USE_LDCONFIG=
PR:		223690
Reported by:	joneum
Approved by:	maintainer timeout (2 weeks) rene (mentor)
Differential Revision:	https://reviews.freebsd.org/D13245
2017-12-01 17:43:21 +00:00
Joseph Mingrone
c27670d577 math/R: Rename files/extra-patch-src_main_Makefile.in to
files/patch-src_main_Makefile.in, so that the SONAME for libR is included.
This was intended for r455296.
2017-12-01 15:28:01 +00:00
Joseph Mingrone
220ae6f41e math/R: Update to version 3.4.3
Other port changes:
- Add armv6 and armv7 to ONLY_FOR_ARCHS; armv6 and armv7 were tested by mmel@
  and working on 11.
- Remove LIBR option and always build the shared library.  This was requested by
  yuri@ and a RFC was posted on ports@ with no response.
- Exclude OPENMP option for everything except amd64 and i386.
- Turn on OPENMP option by default to match upstream.
- Turn off TCLTK option by default.
- LLVM, which gets pulled in with FLANG, provides libomp, so only depend on
  devel/openmp, when GFORTRAN and OPENMP are on.
2017-12-01 14:59:51 +00:00
Antoine Brodin
07faea058d Cleanup LIB_DEPENDS on libpng 2017-12-01 07:19:53 +00:00
Danilo G. Baio
d19df08a56 math/py-keras: Update to 2.1.1
PR:		223978
Submitted by:	Neel Chauhan <neel@neelc.org> (maintainer)
2017-12-01 00:35:42 +00:00
Dmitry Marakasov
12c90e659d - Add LICENSE
- Switch to USES=localbase
2017-11-30 17:06:14 +00:00
Mathieu Arnold
551be3c723 Convert Python ports to FLAVORS.
Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
  current python flavor.  It can be used in dependency lines when the
  port itself is not python flavored.  For example, deskutils/calibre.

  By default, all the flavors are generated.  To only generate flavors
  for the versions in PYTHON2_DEFAULT and PYTHON3_DEFAULT, define
  BUILD_DEFAULT_PYTHON_FLAVORS in your make.conf.

  In all the ports with Python dependencies, the *_DEPENDS entries MUST
  end with the flavor so that the framework knows which to build/use.
  This is done by appending '@${PY_FLAVOR}' after the origin (or
  @${FLAVOR} if in a Python module with Python flavors, as the content
  will be the same).  For example:

    RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR}

PR:		223071
Reviewed by:	portmgr, python
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D12464
2017-11-30 15:50:30 +00:00
Mark Linimon
3082a020e0 NO_ASM is also needed on armv7.
Approved by:	portmgr (tier-2 blanket)
2017-11-30 08:22:47 +00:00
Mark Linimon
bf43557044 For ports that are marked BROKEN on armv6, and also fail to build on
armv7, mark them so.

This is part two of a multipart commit to bring armv7 ports to parity
with armv6.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run
2017-11-30 06:13:34 +00:00
Dmitry Marakasov
984534fd14 - Switch to new test framework
- Take maintainership
- Update WWW
2017-11-28 11:46:54 +00:00
Yuri Victorovich
dd615f00c6 math/glpk: Update to 4.63
PR:		223884
Submitted by:	Dmitri Goutnik <dg@syrec.org>
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13261
2017-11-28 03:03:52 +00:00
Antoine Brodin
165a4093ee Fix depends, clang38 is provided by devel/llvm38 2017-11-27 15:56:06 +00:00
Dmitry Marakasov
0585612f2a - Update WWW
Approved by:	portmgr blanket
2017-11-27 09:00:17 +00:00
Tobias C. Berner
dd0658d1b5 Update math/py-pandas to 0.21.0
PR:		223849
Submitted by:	John W. O'Brien <john@saltant.com> (maintainer)
2017-11-25 18:39:42 +00:00
Mathieu Arnold
d9033160f4 Don't use MASTER_SITE_SUBDIR when it is not needed.
Sponsored by:	Absolight
2017-11-24 17:53:11 +00:00
Greg Lewis
dc8d7d2256 . Update to 5.2.2.
. Remove most options and configure unconditional support for them.
  This is now a full featured port of gnuplot.  If there is enough
  interest then I'll creating a 'gnuplot-lite' port for a minimalist
  version.
2017-11-24 00:05:20 +00:00
Yuri Victorovich
7c95d801ab math/pari: Fixed install without threads; Removed MAKE_JOBS_UNSAFE; Added LICENSE_FILE
PR:		222041
Submitted by:	Anton Yuzhaninov <citrin+pr@citrin.ru>
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13174
2017-11-22 18:55:30 +00:00
Steve Wills
c296805691 math/mprime: Fix some issues from the previous commit
Put back original creator and whitespace
Fix patching
Greatly simplify the Makefile
Make it LOCALBASE safe

Reported by:	danfe
Pointyhat to:	swills
2017-11-22 17:40:24 +00:00
Steve Wills
18af141cc0 math/mprime: Update to 28.10
While here:

* Set maintainer to submitter
* Add License file
* Appease portlint by tweaking comment and moving ONLY_FOR_ARCHES

PR:		219432
Submitted by:	rozhuk.im@gmail.com
2017-11-21 22:43:06 +00:00
Sunpoet Po-Chuan Hsieh
423c9db218 Update IGNORE_WITH_PHP 2017-11-20 04:32:36 +00:00
Yuri Victorovich
91d97411ae New port: math/eprover : Theorem prover for full first-order logic with equality
PR:		211903
Submitted by:	Greg V <greg@unrelenting.technology>
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13150
2017-11-19 21:59:32 +00:00