influenceR: Software Tools to Quantify Structural Importance of
Nodes in a Network
Provides functionality to compute various node centrality measures
on networks. Included are functions to compute betweenness centrality
(by utilizing Madduri and Bader's SNAP library), implementations
of Burt's constraint and effective network size (ENS) metrics,
Borgatti's algorithm to identify key players, and Valente's bridging
metric. On Unix systems, the betweenness, Key Players, and bridging
implementations are parallelized with OpenMP, which may run faster
on systems which have OpenMP configured.
WWW: https://cran.r-project.org/web/packages/influenceR/
everything at once. Sometime, rename post-install into a options helper
target.
I did not fix ports that were such a mess that I could not figure out
what they really wanted to do. I also did not change ports that had
some version of an auto-plist code in post-install, for the same reason.
With hat: portmgr
Sponsored by: Absolight
Detailed maintainer log:
- Explicitly rely on required perl for the build
- math/R cannot be built in poudriere when math/atlas is chosen for the
BLAS implementation. It's not the default, so handle gracefully with
an IGNORE (could also have set MANUAL_PACKAGE_BUILD with
ATLAS_VARS= MANUAL_PACKAGE_BUILD=...)
- fix a type: DOC_BUILD_DEPEND -> DOCS_BUILD_DEPEND
PR: 210983
Submitted by: jrm@ftfl.ca (maintainer)
Simulates continuous distributions of random vectors using Markov
chain Monte Carlo (MCMC). Users specify the distribution by an R
function that evaluates the log unnormalized density. Algorithms
are random walk Metropolis algorithm (function metrop), simulated
tempering (function temper), and morphometric random walk Metropolis
(Johnson and Geyer, Annals of Statistics, 2012, function morph.metrop),
which achieves geometric ergodicity by change of variable.
WWW: https://cran.r-project.org/web/packages/mcmc/
Cadabra is a symbolic computer algebra system (CAS) designed
specifically for the solution of problems encountered in field
theory. It has extensive functionality for tensor computer algebra,
tensor polynomial simplification including multi-term symmetries,
fermions and anti-commuting variables, Clifford algebras and Fierz
transformations, component computations, implicit coordinate
dependence, multiple index types and many more. The input format
is a subset of TeX.
WWW: http://cadabra.science/
PR: 210476
Submitted by: Yuri Victorovich <yuri@rawbw.com>
PR: 210595
Submitted by: yuri@rawbw.com
PySparse extends the Python interpreter by a set of sparse matrix
types holding double precision values. PySparse also includes modules
that implement:
- iterative methods for solving linear systems of equations
- a set of standard preconditioners
- an interface to a direct solver for sparse linear systems of
equations (SuperLU)
- a Jacobi-Davidson eigenvalue solver for the symmetric, generalised
matrix eigenvalue problem (JDSYM)
https://github.com/PythonOptimizers/pysparse
2016-07-04 security/openpgpsdk: Broken for more than 6 months
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The last change submitted or approved by Horia in Bugzilla dates back to
September 2015. Since then, all commits to his ports were landed by others
after the maintainer timeout period expired (see r383744, r405055, r405057,
r400461 and r414655, for example).
Horia did show interest in coming back after I sent a private email a few
months ago, but since nothing has changed it is better to reassign his ports
back to the heap.
Differential Revision: https://reviews.freebsd.org/D5980
- Adjust dependencies, 'numpy/core/multiarray.so' is also linked to
math/openblas (reported by QA script)
- Add patches in order to detect 'sys/endian.h' header
* Update DISTVERSION and distinfo checksum (965)
* Add CONFIGURE_SCRIPT (filename change to .sh extension)
* Add DEBUG option
* Use --trace, --stats (and --logs) with DEBUG, rather than in the
default (non-debug) build.
* Specify --static explicitly even though its built to avoid possible
future footshooting.
http://fmv.jku.at/picosat/NEWS
There are a couple of enhancements that can be made to math/R
regarding optimization: one would be to enable LTO and OpenMP
whenever the compiler supports it, another one would be to allow
linking to OpenBLAS besides ATLAS or R's internal BLAS implementation.
The patch was inspired by math/octave's handling of BLAS.
PR: 207425
Submitted by: elferdo@gmail.com
Approved by: bf (maintainer timeout)
This only affects "Created by" lines with one exception: devel/uclcmd. There the maintainer is changed. This was overlooked in r416918.
Approved by: junovitch (mentor)
p5-Term-ReadLine-(Gnu,Perl,TTYtter).
I can't find any reason for p5-ReadLine-Gnu to have been added as
ReadLine-Gnu instead of Term-ReadLine-Gnu twenty years ago.
devel/p5-Term-ReadLine-Perl was added as a dupplicate a few years back
where it should not have, so change its maintainer to be perl@ like
devel/p5-ReadLine-Perl had.
Sponsored by: Absolight
From experience, OCAML simply is not guaranteed to build concurrently.
Like many other ports that require OCAML to build, Scilab is not jobs
safe. While confirmed this, I discovered the pkg-plist was missing
four files, so I've added those while marking the port jobs unsafe.
[1] Add "compiles" argument to cran to allow R-cran ports need to compile
code to bring in the correct compiler dependencies. Also, ensure
consistency between the compiler selected by the R port and the R-cran ports.
[2] Migrate R-cran ports that manually specify the compiler to
USES=cran,compiles.
PR: 210343
Approved by: wen (1), portmgr (2, blanket)
In addition to supporting GMP or MPIR for multiple-precision integer and
rational arithmetic, gmpy2 adds support for the MPFR (correctly rounded real
floating-point arithmetic) and MPC (correctly rounded complex floating-point
arithmetic) libraries.
WWW: https://pypi.python.org/pypi/gmpy2
WWW: https://github.com/aleaxit/gmpy/releases
PR: 210127
Submitted by: yuri@rawbw.com
checking for pcre_fullinfo in -lpcre... no
checking whether PCRE support suffices... configure: error: pcre >= 8.10 library and headers are required
===> Script "configure" failed unexpectedly.
Reported by: pkg-fallout
- Use the version tag instead of commit hash when they're the same.
- Remove unnneeded variables.
- Simplify go- ports when possible.
- Various fixes.
Sponsored by: Absolight
longer. This is a no-op because KDE4_PREFIX is equal to LOCALBASE
Fix up properties for misc/kde4-l10n/files/bsd.l10n.mk to make svn happy.
PR: 209014 (partial)
Submitted by: myself
Approved by: portmgr (bapt)
Differential Revision: https://reviews.freebsd.org/D6542
- Introduce new ports for the sqlalchemy 0.9 and 1.0 release branches.
- Deprecate the ports for the 0.6 and 0.7 release branches, as these
have been declared EoL and are no longer supported by upstream.
- Update to the latest available version in each branch.
In detail:
Port Version Maintainer
----------------------------------------------
py-sqlalchemy06 0.6.9 nivit@FreeBSD.org (Deprecate 2016-08-20) [1]
py-sqlalchemy07 0.7.10 nivit@FreeBSD.org (renamed py-sqlalchemy, Deprecate 2016-08-20) [1]
py-sqlalchemy08 0.8.7 nivit@FreeBSD.org (renamed py-sqlalchemy-devel) [1]
py-sqlalchemy09 0.9.10 m.tsatsenko@gmail.com (new, repocopy from py-sqlalchemy-devel) [2]
py-sqlalchemy10 1.0.13 m.tsatsenko@gmail.com (new, repocopy from py-sqlalchemy-devel) [2]
- Use options-helpers and option dependent make targets.
- Use autoplist for documents as well as python code
- Add all the docments to the packages: previously an arbitrary
subset was added in a way that excluded CSS, images and other HTML
assets.
- Use TEST_DEPENDS and add a TEST_TARGET instead of having a 'TEST'
option.
- Use py-pytest for 0.9.x and later, rather than py-nose.
- Add CONFLICTS_INSTALL between all of the py-sqlalchemyXY ports.
PR: 191442
Submitted by: robak
Reviewed by: robak
Reviewed by: pi
Approved by: nivit (maintainer timeout, ~300days) [1]
Approved by: m.tsatsenko@gmail.com (maintainer) [2]
Sponsored by: https://reviews.freebsd.org/D908
- Added Python 3 support (thanks to Thomas Kluyver).
- Maintain the package (thanks to Thomas Kluyver and David Froger).
- Development is moved under Github.
PR: 209646
Submitted by: Yuri Victorovich <yuri@rawbw.com> (maintainer)
Sets can be created from and displayed as integer spans such as
1-3,14,29,92-97 rather than exhaustive member listings.
WWW: https://pypi.python.org/pypi/intspan/
Changes:
http://pandas.pydata.org/pandas-docs/version/0.18.1/
- Add optional dependencies on devel/py-Jinja2 and textproc/py-xlsxwriter
PR: 209521
Submitted by: John W. O'Brien <john@saltant.com> (maintainer)
- This new version also allows octave-forge-video to build successfully once
multimedia/ffmpeg is updated to 3.0.x. Note that multimedia/ffmpeg is
currently still on the 2.8.x branch, however this update is backwards
compatible with ffmpeg 2.8.x.
- Add CPPFLAGS+=-I${LOCALBASE}/include to allow build to find ffmpeg headers.
PR: ports/209380
Submitted by: Ben Woods <woodsb02@gmail.com>
use the version 1.8 API.
Fix the build when the GUI option is disabled.
Since this port installs icons, add INSTALLS_ICONS=yes to Makefile.
PR: 209244
Approved by: makc (maintainer)
SAGA GIS version 2.2.7 [r2893] is a bug fix release, because a
serious bug in the command line interpreter saga_cmd prevents correct
setting of floating point value parameters.
Some more fixes and features are:
- taking respect for future use of new date parameter
- bug fixes for flip method in grid operation and orientation
- overworked grid system
- bug fix for atan2, which did not work before
- bug fixes for some tool parameter ids
- updated dictionaries and tool interfaces
PR: 209175
Submitted by: Rainer Hurling <rhurlin@gwdg.de> (maintainer)
GCC 6.1 was released this week. The Ada Framework in FreeBSD ports has
been based on GCC 5.3 GNAT although GCC 6.x has been supported for awhile
via the ADA_DEFAULT option in make.conf.
Now that GCC 6 has been officially released, switch to it by default.
People can maintain the old foundation by putting "ADA_DEFAULT=5" in
/etc/make.conf.
Libraries built by one GNAT are unusable by another, so almost every Ada
port has been bumped as a result. Noticable exceptions are dns/ironsides
which fails to build on gcc6 (thus USES=ada:5 is set) and cad/ghdl which
needs additional testing as it may require gcc5 on FreeBSD (DragonFly
uses the LLVM backend only).
