Commit graph

11738 commits

Author SHA1 Message Date
Jan Beich
d45773d7cc math/coinmp: unbreak build with Clang 6 (C++14 by default)
ClpModel.cpp:3848:24: error: reinterpret_cast from 'nullptr_t' to 'const char *' is not allowed
                       reinterpret_cast<const char*> (NULL) /*integrality*/,
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
OsiClpSolverInterface.cpp:1451:50: error: reinterpret_cast from 'nullptr_t' to 'int *' is not allowed
    messagesPointer->setDetailMessages(100,10000,reinterpret_cast<int *> (NULL));
                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from CglLandPSimplex.cpp:11:
In file included from ./CglLandPSimplex.hpp:31:
./CglLandPUtils.hpp:88:25: error: reinterpret_cast from 'nullptr_t' to 'OsiRowCut *' is not allowed
        cuts_.resize(i, reinterpret_cast<OsiRowCut *> (NULL));
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CbcModel.cpp:5322:41: error: reinterpret_cast from 'nullptr_t' to 'double *' is not allowed
            clpSolver->setFakeObjective(reinterpret_cast<double *> (NULL));
                                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Reported by:	antoine (via bug 224669)
2018-01-05 12:37:45 +00:00
Dmitry Marakasov
5ab85d28ec - Mark MAKE_JOBS_SAFE, this fixes build on mips and mips64
Approved by:	portmgr blanket
2018-01-04 08:38:19 +00:00
Wen Heping
e4264478dd - Update to 1.10
Changes: http://search.cpan.org/src/MARKOV/Math-Polygon-1.10/ChangeLog
2018-01-04 00:46:11 +00:00
Wen Heping
8a8b5ec070 - Update to 4.10.1
PR:		222339
Submitted by:	lbartoletti@tuxfamily.org
2018-01-03 23:43:28 +00:00
Wen Heping
be8f85bd0d - Update to 1.08
Changes: http://cpansearch.perl.org/src/MARKOV/Math-Polygon-1.08/ChangeLog
2018-01-03 03:22:30 +00:00
Tobias C. Berner
51d04637cb New USES=eigen
Usage:
    USES=eigen:<version>[,<type>]

    version: 2 or 3 (required)
    type:    build (default), run

  For example:
    USES=eigen:2,build,run
  will add a BUILD- and RUN_DEPENDS on math/eigen2, and
    USES=eigen:3
  will add a BUILD_DEPENDS on math/eigen3.

* Convert the existing ports to use it
  - biology/iqtree: remove run time dependency (seemed not to be needed)
  - graphics/movit: remove run time dependency (seemed not to be needed)
  - science/avogadro: add run time dependeny (installed cmake file requires it to be present)

Reviewed by:	rakuco, mat
Differential Revision:	https://reviews.freebsd.org/D13702
2018-01-02 16:49:24 +00:00
Raphael Kubo da Costa
b5b351761b Add a patch to fix the build with newer versions of SIP.
We're currently testing an update to SIP 4.19.6, but it breaks qtiplot's build.

This patch, obtained via Debian and Gentoo, allows the port to build with both
SIP 4.19.2 (currently in the tree) as well as 4.19.6.

In the future, we might look into disabling Python scripting support: it tends
to break with almost every SIP update, and upstream has stopped releasing the
source code for newer qtiplot releases.

PR:		224739
Obtained from:	https://anonscm.debian.org/git/debian-science/packages/qtiplot.git/tree/debian/patches/20_fix_FTBFS_sip4.19.patch
Obtained from:	https://bugs.gentoo.org/641514#c2
2018-01-02 12:52:21 +00:00
Mark Linimon
a931122c7a Fix up Makefiles for ports that used to fetch from www.sourcefiles.org.
It is gone.

While here, chase other mastersites, pet portlint, and set DEPRECATED
for ports that do not fetch from alternative sites.

Note: most of these ports are ancient and unmaintained.
2018-01-02 01:51:11 +00:00
Yuri Victorovich
4280dcf14b New port: math/symmetrica: Collection of routines for combinatorial mathematics
Submitted by:	myself
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13711
2018-01-01 17:11:44 +00:00
Jan Beich
9d1dc2407c Improve CMake style in my ports
- Convert to CMAKE_{ON,OFF} helpers
- Convert to _CMAKE_BOOL option helpers
- android-file-transfer: Share _CMAKE_BOOL via _IMPLIES
- Annotate types
2018-01-01 13:42:54 +00:00
Yuri Victorovich
f483577155 math/eigen3: Added NO_ARCH=yes
PR:		224630
Submitted by:	myself
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13698
2017-12-31 01:28:28 +00:00
Yuri Victorovich
936f63cf4a New port: math/flann: Library for fast nearest neighbor searches in high dimensional spaces
Submitted by:	myself
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13692
2017-12-30 19:45:33 +00:00
Yuri Victorovich
aa62378ce0 math/sundials: Changed to using <opt>_IMPLIES for HYPRE and PETSC options, and removed the .include clause
Submitted by:	myself
Reported by:	jbeich
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13653
2017-12-30 08:15:36 +00:00
Sunpoet Po-Chuan Hsieh
960a7599f3 Fix WWW
Approved by:	portmgr (blanket)
2017-12-30 00:15:20 +00:00
Sunpoet Po-Chuan Hsieh
4333960470 Fix WWW
Approved by:	portmgr (blanket)
2017-12-30 00:15:15 +00:00
Sunpoet Po-Chuan Hsieh
f7e2942391 Fix WWW
Approved by:	portmgr (blanket)
2017-12-30 00:15:10 +00:00
Sunpoet Po-Chuan Hsieh
4d45ea289a Update to 1.07
Changes:	http://search.cpan.org/dist/Math-Polygon/ChangeLog
2017-12-28 13:41:34 +00:00
Ed Maste
3d47bbff06 math/p5-Math-Pari: set LLD_UNSAFE to avoid linking with lld
lld defaults to disallowing relocations in readonly segments (e.g., the
one containing .text).  For now just fall back to linking with ld.bfd if
the system ld is lld.

PR:		214864
Approved by:	portmgr (LLD_UNSAFE blanket)
Sponsored by:	The FreeBSD Foundation
2017-12-27 15:23:24 +00:00
Wen Heping
44f4ca605b - Upgrade to 0.21.1
- Remove stale testing bits

PR:		224598
Submitted by:	john@saltant.com(maintainer)
2017-12-27 12:29:16 +00:00
Antoine Brodin
3a678350fb Deprecate ports broken for more than 6 months 2017-12-27 09:30:47 +00:00
Yuri Victorovich
2a3f43cb6b New port: math/sundials: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
This port was originally created by Pedro Giffuni. He offered me to take over it.
I updated it to 3.1.0, added many options, etc.

The option FCMIX is broken upstream, so it is not present in the port.

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13647
2017-12-27 07:47:30 +00:00
Danilo Egea Gondolfo
3218d7a203 - Update to 8.300.2 2017-12-27 02:21:44 +00:00
Li-Wen Hsu
675f13b32d - Update to 2.3.0 2017-12-26 19:30:17 +00:00
Yuri Victorovich
b14897a777 math/adept: Replaced DOCS option with PDFTEXDOCS option because the LaTeX dependency is huge.
Reported by:	adamw
Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13643
2017-12-26 19:28:08 +00:00
Yuri Victorovich
e4eaee25c7 New port: math/adept: Combined array and automatic differentiation library in C++
This library implements a very unusual and interesting approach. It takes a function
of several arguments supplied by the caller, deconstructs its analytic structure
using C++ type substitution for all values, and computes gradients (Jacobians) of
the function while ony calling the function once. A very innovative approach.

Submitted by:	myself
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13635
2017-12-26 17:43:40 +00:00
Yuri Victorovich
6ff500470b New port: math/zimpl: Language to translate the LP models into .lp or .mps
Submitted by:	myself
Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13623
2017-12-25 21:31:55 +00:00
Tijl Coosemans
3196152243 Remove USE_AUTOTOOLS. There's already USES=autoreconf. 2017-12-25 20:00:04 +00:00
Tijl Coosemans
75fec94b7f Remove unneeded USE_AUTOTOOLS. 2017-12-25 19:58:10 +00:00
Yuri Victorovich
f9279ba0bc New port: math/SCIP: Solver for mixed integer, mixed integer nonlinear programming
Submitted by:	myself
Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13614
2017-12-25 19:03:30 +00:00
Yuri Victorovich
71268705bb New port: math/SoPlex: Optimization package for solving linear programming problems (LPs)
Submitted by:	myself
Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13613
2017-12-25 18:47:47 +00:00
Alexey Dokuchaev
1b92122f42 Remove BROKEN_sparc64 statement which was originally added in r224062 by
linimon@ 9 years ago, for version 0.10.  It now builds and packages fine
on 10.4-STABLE running under QEMU 2.9.0.
2017-12-24 15:41:58 +00:00
Joseph Mingrone
ff2bee6b2a math/z3: Add missing dependency on devel/py-setuptools
PR:		224438
Reported by:	cem
Reviewed by:	mat
Approved by:	6yearold@gmail.com (maintainer)
Differential Revision:	https://reviews.freebsd.org/D13542
2017-12-24 13:01:36 +00:00
Antoine Brodin
8c313cfaa8 Remove flavors from vtk6, it's not useful with PY_FLAVOR (initial
implementation of python flavors didn't have PY_FLAVOR)
2017-12-24 12:17:40 +00:00
Adriaan de Groot
74c0e748b9 Update CMake to 3.10.1
- https://blog.kitware.com/cmake-3-10-1-available-for-download/
   - flang support
   - changes to automoc policies
   - support for FreeBSD package generation with CPack

Necessary fixes to other ports:
 - cad/openvsp make search for libxml explicit
 - math/scalapack force C compiler to be compatible with mpi
 - deskutils/kdepim4 fix incorrect sources list
 - www/qt5-webkit fix incorrect sources list

Thanks to Antoine for the multiple exp-runs.

PR:		223872
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D13210
2017-12-23 10:44:23 +00:00
Stephen Montgomery-Smith
37e563c614 - Update to 3.1.0. 2017-12-22 04:55:14 +00:00
Sunpoet Po-Chuan Hsieh
702724f863 Update to 0.48
Changes:	http://search.cpan.org/dist/Math-GMPz/CHANGES
2017-12-21 17:41:01 +00:00
Wen Heping
bd7fbe41bb - Update to 0.7.4 2017-12-21 10:55:13 +00:00
Yuri Victorovich
435512ec91 New port: math/libmesh: Numerical simulation of partial differential equations
Submitted by:	myself
Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D13524
2017-12-20 20:36:19 +00:00
Baptiste Daroussin
2e9911f602 Switch from swig 2.0 to swig 3.0 2017-12-20 19:34:11 +00:00
Baptiste Daroussin
9c08d60a3f Use swig 3.0 2017-12-20 15:16:30 +00:00
Sunpoet Po-Chuan Hsieh
04e4780b30 Update to 0.47
Changes:	http://search.cpan.org/dist/Math-GMPz/CHANGES
2017-12-20 14:37:47 +00:00
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