Changes:
* Use explicit pkg-plist instead of autoplist. Using an explicit pkg-plist
is more robust against "silent" errors or changes.
ChangeLog:
- influencePlot now returns Cook's distance, not its square root.
- Anova() now supports "coxme" objects (produced by coxme() in coxme package)
(request of Philipp Sprenger).
- Anova() now works via its default method with "vglm" objects produced by
functions in the VGAM package; and the default method of linearHypothesis()
again works with these objects (problem reported by Michael Friendly).
- Fixed Anova.coxph() so that it takes account of method (ties) argument (bug
reported by Karl Ove Hufthammer).
- Improvements to Anova.default() so that a wider variety of model classes are
accommodated (following request of Liviu Andronic.)
- dataEllipse() now throws an error if there are too few colors for the number
of groups (fixing bug reported by Ottorino Pantani).
- spreadLevelPlot.lm() now includes an optional smoother in addition to the
fitted straight line (suggestion of Michael Friendly).
- No longer import methods (as opposed to generics) directly from pbkrtest.
- Added axis.ticks argument to scatter3d() (code contributed by
David Winsemius).
while here:
* simplify TARGET_SDIR so inclusion not required
* add --build configure argument (from dports, no effect on fbsd)
approved by: infrastructure blanket
There are numerous graphviz related packages in PyPI, including:
graphviz, graphviz-python and pygraphviz.
This port, py-graphviz, is not and does not provide the same package
as the 'graphviz' package on PyPI (CHEESESHOP).
Further, it blocks the creation of a correctly named py-graphviz port,
is a POLA violation in terms of users expecting to find and recieve
the package they expect based on a standard search, and is likely to
create confusion among other ports if they depend on a python graphviz
package, which could result in incorrect packages/dependencies.
This is why among other reasons, Python packages should be named
exactly what they are called in PyPI, or inside install_requires,
setup_requires or tests_requires as dependencies in other packages.
This change moves py-graphviz to py-pygraphviz to correct the above
incorrect naming.
While I'm here:
- Remove backup (http) MASTER_SITES, CHEESESHOP is highly-available
and provides a Geo-aware CDN by Fastly.
- Remove {BUILD,RUN}_DEPENDS in favour of the actual LIB_DEPENDS
- Use PYDISTUTILS_* framework variables to customise the build instead
of hack patching setup.py
- Enable autoplist, fixing builds on Python 3.x [1]
- Enable concurrent (Python version) installation
- Hack patch setup.py to preclude docs installation, as it adds a
directory to --record and breaks pkg-plist output [2]
- Remove DOCSDIR override (no longer necessary)
- Assign MAINTAINER'ship to python@
- Add TEST_DEPENDS and test target
- pkg-descr: Match WWW URL to setup.py:homepage field
- pkg-descr: Improve package description text (matching upstream)
While I'm sweeping dependencies:
- Fix a typo in science/gramps: s|>-|>=
[2] https://wiki.freebsd.org/Python (Open task for install_data bug)
Reported by: Ben Woods (via IRC) [1]
In file included from fst/_fst.cpp:322:
In file included from /usr/local/include/fst/fstlib.h:93:
/usr/local/include/fst/shortest-path.h:75:52: error: a space is required between consecutive right angle brackets (use '> >')
const vector<pair<typename Arc::StateId, size_t>>& parent,
^~
> >
/usr/local/include/fst/shortest-path.h:91:26: error: a space is required between consecutive right angle brackets (use '> >')
ArcIterator<Fst<Arc>> aiter(ifst, s);
^~
> >
Reported by: pkg-fallout
- Fix build with new GCC and remove BROKEN
- Regenerate patches to make portlint(1) happy
- Add fortran to USES
- Bump PORTREVISION
PR: 205241
Submitted by: Carlos J. Puga Medina <cpm@fbsd.es>
Approved by: junovitch (mentor)
conflicts with the new one, it was impossible to install together
math/plplot and math/qhull;
- fix PKG_CONFIG_DIR.
PR: ports/205937
Submitted by: /me
Approved by: maintainer
The OPTIONS_DEFINE line was placed after <bsd.ports.pre.mk> meaning the
<bsd.ports.option.mk> file was imported before the options were defined.
This is revealed by SELECTED_OPTIONS showing up blank rather than as
"DOCS". Move the line before the includes to fix.
Approved by: just-fix-it
The octave-forge package is the result of The GNU Octave Repositry project,
which is intended to be a central location for custom scripts, functions and
extensions for GNU Octave. contains the source for all the functions plus
build and install scripts.
The octave-forge package is the result of The GNU Octave Repositry project,
which is intended to be a central location for custom scripts, functions and
extensions for GNU Octave. contains the source for all the functions plus
build and install scripts.
This port uses math/librsb, which is quite difficult to install. Therefore
this port will not be installed as part of the math/octave-forge meta-port.
LICENSE= PD
Note that although Public Domain is not technically a license, it's
handled in the same way as licenses here, which is a common practice
(Arch, Gentoo, Fedora, Debian, even FOSSology do the same).
Convert all ports which redefine Public Domain LICENSE to LICENSE=PD.
Approved by: portmgr (bapt)
Differential Revision: D4149
and make makeplist is doing the same job just fine
- Remove DOCS option, only DOCSDIR directory was installed,
bump PORTREVISION - plist changed for default configuration
- Use options helper for EXAMPLES option
Drop the python version limit, by asking user to uncheck some options,
that will not work with python3 for now.
PR: 204594
Submitted by: John W. O'Brien <john@saltant.com>
Approved by: dikshie@sfc.wide.ad.jp (maintainer)
- Reintroduce DOCVERSION variable, PDF documentation is not synchronized with
release
- Add missing dependency [1] for NETLIB option
PR: 203638 [1]
Submitted by: John Hein [1]
Switch to fetching the source tarball from the website indicated in WWW. It
is slightly different from the previous tarball: some build system files
were generated by a more recent version of autotools, the documentation
contains a typo fix and its ChangeLog mentions this fix.
2015-12-30 www/ocsigen: Broken for more than 6 months
2015-12-30 devel/monodevelop-database: Broken for more than 6 months
2015-12-30 lang/cduce: Broken for more than 6 months
2015-12-30 science/hdf-java: Broken for more than 6 months
2015-12-30 math/p5-Math-Geometry-Planar-GPC-Polygon: Broken for more than 6 months
2015-12-30 www/eliom: Depends on broken and expiring www/ocsigen
2015-12-30 audio/py-fastaudio: Broken for more than 6 months
2015-12-30 devel/jgoodies-common: Broken for more than 6 months
2015-12-30 graphics/pinta: Broken for more than 6 months
2015-12-30 games/kanatest: Broken for more than 6 months
2015-12-30 editors/bless: Broken for more than 6 months
2015-12-30 security/burpsuite: Broken for more than 6 months
gnuplot completely removed support for the gnugraph and unixplot terminal
drivers in 2011. From the one of the ChangeLog files:
> 2011-05-31 Ethan A Merritt <merritt@u.washington.edu>
> [...]
> Remove obsolete terminal drivers gnugraph and unixplot. The underlying
> gnu plotutils library is itself more than 10 years out of date (last
> release July 2000) and the terminal drivers haven't been upgraded for
> longer than that. In any event, current gnuplot has better native
> terminal drivers for the devices supported by unixplot/gnugraph.
In practice, this means the PLOT option is a no-op and the dependency on
graphics/plotutils is unnecessary. Indeed, if one looks at the port's build
logs in the cluster the following can be seen:
configure: WARNING: unrecognized options: --without-lisp-files, --with-plot,
--disable-thin-splines, --with-wx-config
PR: 205488
Approved by: glewis (maintainer)
- Use other distfile naming scheme again
- Correct usage of wx-config for SAGA GIS module io_virtual
- Adjust naming scheme of patches via 'make makepatch'
- Update pkg-plist
PR: 205491
Submitted by: maintainer
control groups with similar covariate distributions - can be used
to match exactly on covariates, to match on propensity scores, or
perform a variety of other matching procedures.
WWW: http://gking.harvard.edu/matchit
mean, scale, and correlation structures, through mean link,
scale link, and correlation link. Can also handle clustered
categorical responses.
WWW: https://cran.r-project.org/web/packages/geepack/
${PERL5} points to a specific version of perl, say, perl5.22.1, it is
fine to use it in a ports Makefile to do Perly things, but ports using
it must use ${PERL}, that points to /usr/local/bin/perl so that if the
minor version is updated, the shebang keep working.
While there, make some ports use shebangfix, regen a few patches, and
bump PORTREVISION where a shebang went from PERL5 to PERL.
PR: 205367
With hat: portmgr
Sponsored by: Absolight
declare the pre and post conditions that you code should satisfy,
while also producing friendly error messages so that your users
know what they've done wrong.
WWW: https://cran.r-project.org/web/packages/assertthat/
(such as a survey), from a time series (like variables collected for
each year in a country), or from a time-series-cross-sectional data set
(such as collected by years for each of several countries).
WWW: http://gking.harvard.edu/amelia
Bring in some long overdue updates, some of which are required for us to
later land the PyQt5 ports.
One big change with this update is that the PyQt4 ports now install their
.sip files into share/py-sip/PyQt4 instead of share/py-sip. This way we do
not end up with directories like share/py-sip/QtCore, which are especially
confusing once PyQt5 lands and starts installing files with the same names.
Other noteworthy items:
- PORTREVISION has been bumped on ports depending on devel/qscintilla2
because libqscintilla2.so's SOVERSION has changed.
- graphics/seexpr has been converted to USE_PYQT, as the file it used to
define a build-time dependency on x11-toolkits/py-qt4-gui has moved.
Once again, big thanks to Tobias Berner <tcberner@gmail.com> and Guido Falsi
(madpilot@) for their initial work on these ports as part of the effort to
land PyQt5 into the tree (see D2910 in Phabricator for an earlier version of
the PyQt5 patch set).
PR: 205143
There are two reasons to rename this port.
1) Upstream never liked it and requested -spark be the suffix instead
2) An ongoing attempt to fix lang/spark may result in a number of slave
ports with a -spark suffix, so this keeps up consistency as all of
these ports only exist to support that port.
This is the first major release of FreePascal in nearly four years.
There are a ton of new features, way more to list here. see:
http://wiki.freepascal.org/FPC_New_Features_3.0
Several new unit ports were added, some were contracted. Most of
those were absorbed into the main FPC packages, but two units are
no longer supported: sndfile and matroshka.
All 99 remaining ports (including Lazarus ports) were build tested
on FreeBSD i386 and amd64 Release 10.2
- Changes:
http://www.gnuplot.info/ReleaseNotes_5_0_1.html
- The "gnuplot mode" elisp and TeX files for use with emacs are now
maintained as a separate project
PR: 204886
Submitted by: pi
Approved by: glewis (maintainer), via mail
optimization, and related tools. It includes a unified way to
call different optimizers, and classes and methods to handle the
results from the ML viewpoint. It also includes a number of
convenience tools for testing and developing your own models.
WWW: http://www.maxlik.org/
Changes:
- Remove port's broken and depreciated status
- Add two dependencies
- Add GPLv3 as dual license
- Update website URL
Change Log:
- New power family called skewPower has been added that can be used with the
Box Cox method with a few negative responses (joint work with Doug Hawkins).
Several functions modified to accomodate two-parameter power families.
- Fixed bug in Anova() for coxph models with clusters (reported by Jesus
Humberto Gomez ), due apparently to a change in coxph().
- Anova() F-tests for binomial and Poisson GLMs now changes
error.estimate="dispersion" to "pearson" as advertized (bug reported by
Will Petry).
- Improved behavior of above-plot legends in scatterplot().
- Fixed sp() (bug reported by Cesar Rabak).
- Conforms to new CRAN requirements for package imports.
Reported by: tota@
PR: 203418
PR: 204587
models.At the heart of it are the vector generalized linear and
additive model (VGLM/VGAM) classes, and the book "Vector Generalized
Linear and Additive Models: With an Implementation in R" (Yee, 2015)
gives details of the statistical framework and VGAM package. Currently
only fixed-effects models are implemented, i.e., no random-effects models.
WWW: https://www.stat.auckland.ac.nz/~yee/VGAM
- Set LICENSE_FILE.
- Depend on devel/yasm instead of building a bundled yasm.
- Remove post-install target, the build system takes care of creating the
proper soversion symlinks.
- Bump PORTREVISION in dependent ports due to a change in the soversion
number.
- update to 1.10
- add YAML option (on by default)
- remove gratuitous word from option descriptions
- USE_PYTHON=concurrent instead of setting EXAMPLESDIR
- alphabetize USE_PYTHON
- discard pkg-message given all options are enabled by default
While here limit python version to 2.x, because it's dependencies
graphics/py-graphviz and math/py-matplotlib failed to configure
with python3.
PR: 204594
Submitted by: John W. O'Brien <john@saltant.com>
Approved by: dikshie@sfc.wide.ad.jp (maintainer)
Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation
penalized) models for conditional quantiles of a univariate response
and several methods for handling censored survival data. Portfolio
selection methods based on expected shortfall risk are also included.
WWW: https://cran.r-project.org/web/packages/quantreg/
Some basic linear algebra functionality for sparse matrices is
provided: including Cholesky decomposition and backsolving as well
as standard R subsetting and Kronecker products.
WWW: https://cran.r-project.org/web/packages/SparseM/
Test in linear mixed effects models. Attention is on linear mixed
effects models as implemented in the lme4 package. The package
implements a parametric bootstrap test. The package implements a
Kenward-Roger modification of F-tests.
WWW: https://cran.r-project.org/web/packages/pbkrtest/
Fit linear and generalized linear mixed-effects models. The models
and their components are represented using S4 classes and methods.
The core computational algorithms are implemented using the Eigen
C++ library for numerical linear algebra and RcppEigen "glue".
WWW: https://github.com/lme4/lme4/
R and Eigen integration using Rcpp. Eigen is a C++ template library
for linear algebra: matrices, vectors, numerical solvers and related
algorithms. It supports dense and sparse matrices on integer,
floating point and complex numbers, decompositions of such matrices,
and solutions of linear systems. Its performance on many algorithms
is comparable with some of the best implementations based on Lapack
and level-3 BLAS. The RcppEigen package includes the header files
from the Eigen C++ template library (currently version 3.2.2). Thus
users do not need to install Eigen itself in order to use RcppEigen.
Since version 3.1.1, Eigen is licensed under the Mozilla Public
License (version 2); earlier version were licensed under the GNU
LGPL version 3 or later. RcppEigen (the Rcpp bindings/bridge to
Eigen) is licensed under the GNU GPL version 2 or later, as is the
rest of Rcpp.
WWW: https://cran.r-project.org/web/packages/RcppEigen/
nloptr is an R interface to NLopt. NLopt is a free/open-source
library for nonlinear optimization, providing a common interface
for a number of different free optimization routines available
online as well as original implementations of various other algorithms.
WWW: https://cran.r-project.org/web/packages/nloptr/
