Commit graph

4574 commits

Author SHA1 Message Date
Yuri Victorovich
9e9b750538 science/py-ase: Update 3.17.0 -> 3.18.0 2019-07-20 23:20:19 +00:00
Yuri Victorovich
1a2f33a253 science/ncnn: Fix grammar and spelling in pkg-descr 2019-07-20 22:13:56 +00:00
Yuri Victorovich
b244f3c977 New port: science/ncnn: High-performance neural network inference framework 2019-07-20 21:57:30 +00:00
Yuri Victorovich
69e6e7aa5a science/agrum: Update 0.15.0 -> 0.15.2 2019-07-20 20:56:16 +00:00
Yuri Victorovich
82b9326ffe New port: science/wwplot: Plotting tool for experimental physics classes 2019-07-20 16:51:13 +00:00
Piotr Kubaj
d20914ecc3 science/paraview: fix build on GCC architectures
Needs newer GCC than what is in base:
CMake Error at VTK/CMake/vtkCompilerChecks.cmake:4 (message):
  GCC 4.8 or later is required.

Approved by:	mentors (implicit approval)
2019-07-19 20:34:28 +00:00
Yuri Victorovich
747697260d New port: science/kim-api: Framework for reliable, reproducible, portable molecular simulations 2019-07-19 17:51:08 +00:00
Sunpoet Po-Chuan Hsieh
9b37e33325 Update to 2.13.0
Changes:	https://confluence.ecmwf.int/display/ECC/Latest+news
2019-07-19 17:02:43 +00:00
Piotr Kubaj
362b75e38d science/kalzium: fix build on GCC architectures
Needs C++11 compiler:
  The compiler feature "cxx_decltype" is not known to CXX compiler

Approved by:	mentors (implicit approval)
2019-07-19 09:35:46 +00:00
Piotr Kubaj
436840879c science/py-veusz: fix build on GCC architectures
This port uses C++11:
cc1plus: error: unrecognized command line option "-std=c++11"

Approved by:	mentors (implicit approval)
2019-07-18 11:26:50 +00:00
Danilo Egea Gondolfo
7f6316b9d8 - Update math/armadillo to 9.600.4
Reported by:	Nina Santi
2019-07-17 20:00:42 +00:00
Yuri Victorovich
98ca4ad5a5 science/tinker: Update 8.6.1 -> 8.7.1
Reported by:	portscout
2019-07-14 00:34:53 +00:00
Tobias C. Berner
61ee61d083 science/massxpert: prepare for Qt 5.13
PR:		238782
2019-07-13 12:50:04 +00:00
Mark Linimon
4603257363 Simplify architecture tests for 64-bit. Listing each ARCH is fragile; e.g.,
misses some 64-bit mips variants.

While here, further collapse tests for multiple variants of arm, mips, powerpc.

Approved by:	portmgr (tier-2 blanket)
2019-07-12 15:41:37 +00:00
Tobias C. Berner
37e8575738 KDE Applications: update to 19.04.3
July 11, 2019.
Today KDE released the third stability update for KDE Applications 19.04. This
release contains only bugfixes and translation updates, providing a safe and
pleasant update for everyone.

Over sixty recorded bugfixes include improvements to Kontact, Ark, Cantor, JuK,
K3b, Kdenlive, KTouch, Okular, Umbrello, among others.

Improvements include:

  *  Konqueror and Kontact no longer crash on exit with QtWebEngine 5.13
  *  Cutting groups with compositions no longer crashes the Kdenlive video editor
  *  The Python importer in Umbrello UML designer now handles parameters with default arguments

Changelog:
	https://kde.org/announcements/fulllog_applications-aether.php?version=19.04.3
2019-07-12 05:32:09 +00:00
Mark Linimon
7bfae932f7 Prepare for powerpc-on-clang by deleting hard-coded tests for libstdc++.so
as a stand-in for "are we running on gcc".

For people already testing powerpc on clang, it is possible that they
already have both compilers in base.  Thus, the assumption that "gcc is
in base" (e.g.  libstdc++.so exists) always means "force use of GCC" is
already broken.  It will be for everyone on -CURRENT once the switch is
made.

While here, standardize on compiler:c++11-lang instead of -lib (they are
equivalent these days), pet portlint, and do some other cleanup.

Approved by:	portmgr (tier-2 blanket)
2019-07-12 02:25:07 +00:00
Kai Knoblich
a3706632aa New port: science/py-ruffus
The Ruffus module is a lightweight way to add support for running
computational pipelines.

Computational pipelines are often conceptually quite simple, especially if
we breakdown the process into simple stages, or separate tasks.

Each stage or task in a computational pipeline is represented by a Python
function. Each Python function can be called in parallel to run multiple
jobs.

Ruffus was originally designed for use in bioinformatics to analyse multiple
genome data sets.

WWW: http://www.ruffus.org.uk
2019-07-11 16:50:44 +00:00
Sunpoet Po-Chuan Hsieh
1db36ba705 Update to 0.9.2
Changes:	https://github.com/ecmwf/eccodes-python/blob/master/CHANGELOG.rst
2019-07-10 17:00:42 +00:00
Sunpoet Po-Chuan Hsieh
5912a04893 Update to 1.2.2
Changes:	https://github.com/scipy/scipy/releases
PR:		238965
Exp-run by:	antoine
2019-07-07 19:14:54 +00:00
TAKATSU Tomonari
92e50689c1 - Update to 1.0.5 2019-07-07 13:57:22 +00:00
TAKATSU Tomonari
830251e179 - Update to 1.7-2 2019-07-07 12:51:23 +00:00
TAKATSU Tomonari
337325103e - Update to 2.37 2019-07-07 12:34:59 +00:00
TAKATSU Tomonari
58ebf300c4 - Update to 2.2-8
- Fix LICENSE section
2019-07-07 12:32:58 +00:00
Yuri Victorovich
0e630246b2 science/py-spglib: Update 1.12.2 -> 1.13.0
Reported by:	portscout
2019-07-06 03:01:12 +00:00
Sunpoet Po-Chuan Hsieh
70ffc9c0fd Update devel/protobuf to 3.8.0
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/protocolbuffers/protobuf/releases
PR:		238808
Exp-run by:	antoine
2019-07-05 19:08:49 +00:00
Stephen Montgomery-Smith
5d14d686f0 - Update to 3.2.0. 2019-07-03 23:55:47 +00:00
Tobias Kortkamp
f8bce16669 science/dftbplus: Unbreak build with GCC 9
/usr/local/bin/ld: coulomb.o: in function `__coulomb_MOD_invrstress._omp_fn.0':
coulomb.f90:(.text+0x42): undefined reference to `GOMP_loop_maybe_nonmonotonic_runtime_start'
/usr/local/bin/ld: coulomb.f90:(.text+0x176): undefined reference to `GOMP_loop_maybe_nonmonotonic_runtime_next'
/usr/local/bin/ld: coulomb.o: in function `__coulomb_MOD_invrstress._omp_fn.1':
coulomb.f90:(.text+0xfbc): undefined reference to `GOMP_loop_maybe_nonmonotonic_runtime_start'
/usr/local/bin/ld: coulomb.f90:(.text+0x1172): undefined reference to `GOMP_loop_maybe_nonmonotonic_runtime_next'
[...]

PR:		238666
Submitted by:	jbeich
Reported by:	antoine (via exp-run in PR 238330)
Approved by:	yuri (maintainer timeout, 2 weeks)
2019-07-03 10:05:47 +00:00
Piotr Kubaj
d61e14362a science/PETSc: fix typo
s/CONFIGURE_ARG_/CONFIGURE_ARGS_/
2019-07-01 19:52:04 +00:00
Piotr Kubaj
991f4493fa science/PETSc: fix build with non-x86
Only i386 and amd64 have SSE, don't use it on other platforms.

It probably also builds on ARM platforms with this patch, but someone would have to test it.

PR:		238631
Approved by:	yuri (maintainer timeout), mat (mentor)
Differential Revision:	https://reviews.freebsd.org/D20821
2019-07-01 19:47:39 +00:00
Yuri Victorovich
c517ce256e science/h5z-zfp: Update 0.9.0 -> 1.0.1
Reported by:	portscout
2019-06-30 08:34:58 +00:00
Piotr Kubaj
f5f826f007 science/py-MDAnalysis: fix build
Add USES=compiler:c++11-lang to fix:
cc1plus: error: unrecognized command line option "-std=c++11"

Approved by:	mentors (implicit approval)
2019-06-29 10:28:48 +00:00
Tobias Kortkamp
3726f94254 Convert all Go ports to USES=go
This allows for port testing with lang/go-devel via GO_PORT, setting
up the Go build environment in a single place, and is step one in
simplifying Go ports that often define too complicated do-build
targets themselves.

USES=go gains new arguments 'run' to add lang/go to RUN_DEPENDS and
'no_targets' for ports with composite builds that call 'go' themselves
and do not need the do-build/do-install targets of USES=go.

PR:		238849
Submitted by:	dg@syrec.org (also D20745)
Reviewed by:	mat, tobik
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20746
2019-06-29 03:51:13 +00:00
Yuri Victorovich
6fd3cb6c9a science/nest: Update 2.16.0 -> 2.18.0
Reported by:	portscout
2019-06-28 09:10:18 +00:00
Mathieu Arnold
08bc95f4c0 Remove dupplicate port.
Pointy hat:	yuri
2019-06-28 06:57:09 +00:00
Yuri Victorovich
0d19872a61 science/py-phonopy: Update 2.1.3 -> 2.1.4
Reported by:	portscout
2019-06-28 05:04:05 +00:00
Yuri Victorovich
8bc4dee0ff science/atompaw: Update 4.1.0.5 -> 4.1.0.6
Reported by:	portscout
2019-06-28 04:52:35 +00:00
Yuri Victorovich
8e5eb0b6f8 New port: science/molden: Program for molecular and electronic structure visualization 2019-06-28 03:51:26 +00:00
Sunpoet Po-Chuan Hsieh
b98ac213c1 Cosmetic change 2019-06-27 20:03:54 +00:00
Sunpoet Po-Chuan Hsieh
1b91103fe7 Update graphics/libgeotiff to 1.5.1
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/OSGeo/libgeotiff/blob/master/libgeotiff/NEWS
		https://lists.osgeo.org/pipermail/geotiff/2019-March/000861.html
		https://lists.osgeo.org/pipermail/geotiff/2019-March/000862.html
2019-06-27 19:57:33 +00:00
Alexey Dokuchaev
3186e08e7c Update Guile to version 2.2.5, modern stable version, and fix dependent
ports to build against it.  Most changes are rather minor and mechanical
except for the devel/gdb (obtained via their bugtracker [1], courtesy of
Doug Evans).  One port (science/meep) I had to mark BROKEN after fixing
it proved to be very tedious and actually unreliable.  It is very old,
there are newer versions available so it should be fixed by updating.

One port (devel/libruin) had revealed a bug in the new Guile code (an
auxiliary script, really) that had to be worked-round; reference to the
problematic upstream commit is provided in the patch.

PR:		229613
Exp-run by:	antoine

[1] https://sourceware.org/bugzilla/show_bug.cgi?id=21104#c8
2019-06-27 09:02:56 +00:00
Wen Heping
3d23ba68ab - Update to 6.1.0 and fix some ports
- Add missing DEPENDS
- Add TEST_TARGET
- Take maintainership

PR:		237932, 238795
Submitted by:	wenheping2000@hotmail.com,rhurlin@gwdg.de
Approved by:	maintainer(timeout, > 30 days), portmgr@(implicit, fix build)
Exp-run by:	antoine@
Thanks to:	antoine@, sunpoet@, rhurlin@gwdg.de
2019-06-27 03:37:10 +00:00
Sunpoet Po-Chuan Hsieh
4f1d0ee1ec Update to 1.5.3
Changes:	https://github.com/Try2Code/cdo-bindings/blob/master/README.md#changelog
		https://github.com/Try2Code/cdo-bindings/commits/master
2019-06-25 20:52:05 +00:00
Tobias C. Berner
4196590fa5 KDE Applications: complete dependency lists
This has been on the TODO list for forever...

PR:		238764
Reported by:	yuri
2019-06-23 15:39:32 +00:00
Sunpoet Po-Chuan Hsieh
d12f07dc24 Update to 0.113
Changes:	https://metacpan.org/changes/distribution/Geo-WebService-Elevation-USGS
2019-06-22 21:50:07 +00:00
Yuri Victorovich
5204c782ce science/qbox: Update 1.67.2 -> 1.67.4 2019-06-20 22:06:56 +00:00
Guido Falsi
ad1ecbc81b - Simplify XFCE MASTER_SITES usage
- Update XFCE Master sites list

Submitted by:		olivierd
Reviewed by:		mat
Approved by:		portmgr (mat)
Differential Revision:	https://reviews.freebsd.org/D8416
2019-06-19 16:14:27 +00:00
Yuri Victorovich
e77c7663ca science/py-qcengine: Update 0.6.4 -> 0.7.1
Reported by:	portscout
2019-06-19 08:15:53 +00:00
Yuri Victorovich
4de4161b08 science/py-qcelemental: Update 0.4.1 -> 0.4.2
Reported by:	portscout
2019-06-19 08:14:24 +00:00
Jason W. Bacon
6be8fa3bb2 science/afni: Upgrade to 19.1.20
Upstreamed FreeBSD patches, other minor fixes and enhancements

Reported by:    portscout, Rick Reynolds (NIH)
2019-06-18 19:00:55 +00:00
Mark Linimon
4b97875495 Add compiler:c++11-lang to USES to fix the following on GCC-based systems:
/usr/local/lib/libgraphite2.so.3: undefined reference to `__cxa_throw_bad_array_new_length@CXXABI_1.3.8'

Approved by:	portmgr (tier-2 blanket)
2019-06-17 11:39:30 +00:00