and expected value function for the truncated normal distribution
with mean equal to 'mean' and standard deviation equal to 'sd'.
WWW: http://cran.r-project.org/web/packages/truncnorm/
PR: 213091
Submitted by: pfg@
- Clean up the Makefile.
- Follow some upstream recommendations (--with-data-packaging=archive,
--disable-renaming, -DICU_NO_USER_DATA_OVERRIDE).
- Patch makefiles to install static libraries with INSTALL_DATA so they
aren't stripped.
- Patch config/mh-bsd-gcc to sync with config/mh-linux-gcc.
- Fix endianness detection in ICU. The code wanted to use BYTE_ORDER
defined in machine/endian.h, but this isn't visible because ICU is
compiled with _XOPEN_SOURCE. Patch the code to use _BYTE_ORDER instead.
- Compile ICU with C++11 compiler to enable move constructors.
- Patch ICU to fix a problem with atomics in the case of a C++11 compiler
without C++11 header <atomic> (like Clang on FreeBSD 9).
- Bump all ports that depend on it due to library version change.
- Add USES=compiler:c++0x to some ports that pick up -std=c++0x from ICU
pkgconfig files.
- Add USES=compiler:c++11-lib to graphics/libcdr01 because it also needs
a C++11 runtime library now. Add this to all ports that depend on it
so their executables load the right libstdc++.so on FreeBSD 9.
PR: 205120
Exp-run by: antoine
Approved by: portmgr (antoine)
- Update LICENSE
- Take maintainer'ship
Changelog:
1.0.5
- Fix bug in stats_stat_binomial_coef which causes segfault in some
environments
- Fix bug in stats_stat_factorial which leads infinite loop in some
cases
- stats_stat_factorial returns immediately when the value are reached
to +INF
- Change supported version to PHP 5.3 or higher
1.0.4
- Fixed bugs (see tests for details)
PR: 212504
Submitted by: dbaio@bsd.com.br
- If a port has another upstream, remove GOOGLE_CODE
- If a port only has GOOGLE_CODE mark it BROKEN
Some ports have a local mirror configured but for security reasons, it
is not considered upstream.
Sponsored by: Absolight
*_DEPENDS. Helper variables derived from the loop variable aren't
expanded causing *_DEPENDS to be incorrect.
- Bump all ports with more than one value in USE_LINUX.
PR: 211645
Reported by: jkim
- Follow upstream move from SF to GitHub, and new website hosting
- Add USES=autoreconf libtool as GH tarball only comes with configure.ac
- Add OPTIONS to select GTK3 or GTK2 (GTK3 by default as per upstream)
- Add USE_GNOME=cairo und GTK2_LIB_DEPENDS undeclared dependencies
Changes this release:
https://github.com/galculator/galculator/blob/v2.1.4/ChangeLog
Reviewed by: adamw (mentor)
Approved by: naddy (maintainer), mat (mentor)
Differential Revision: https://reviews.freebsd.org/D7789
Mk/Uses/linux.mk.
- Replace USE_LINUX=yes with USES+=linux and USE_LINUX=(.*) with
USES+=linux:\1 in all ports.
- Replace USE_LINUX_APPS with USE_LINUX in all ports.
- Use INSTALL_SCRIPT instead of INSTALL_PROGRAM to install scripts in some
ports.
- When USE_LINUX_RPM is defined, simplify the way DISTFILES and EXTRACT_ONLY
are defined.
- Remove BRANDELF_DIRS and BRANDELF_FILES handling. In the very rare cases
that it is still necessary ports can run ${BRANDELF} from post-patch.
- Remove AUTOMATIC_PLIST handling. Only one port used it.
- Fix Linux MASTER_SITES.
- Replace OVERRIDE_LINUX_BASE_PORT and OVERRIDE_LINUX_NONBASE_PORTS with
default versions framework.
- bsd.port.mk:
- Move Linux related bits to Uses/linux.mk, except USE_LINUX_PREFIX.
- Put USE_LINUX_PREFIX handling after USES processing.
- Define DOCSDIR, DATADIR, etc. after handling USE_LINUX_PREFIX so it can
give these variables a different default value.
- When a package needs to run Linux ldconfig check before installation if
Linux support is enabled.
- emulators/linux_base-*:
- Use USES=linux and remove duplication.
- Remove files/lp. FreeBSD or CUPS lp(1) should work.
- Remove files/yp.conf. No longer seems to be used.
- Remove pkg-deinstall and move pkg-install into pkg-plist.
- Update pkg-descr and pkg-message.
- Fix handling of ldconfig cache in pkg-plist.
- devel/fb-adb: Use a Linux shell to run a Linux script but patch the script
to use FreeBSD mkdir so mkdir -p $path creates $path and not
/compat/linux/$path.
PR: 211645
Exp-run by: antoine
Approved by: portmgr (antoine)
Plasma5 ports
At the moment KDE ports use bsd.kde4.mk to handle their dependencies. When
working on the ports for KDE Frameworks and Plasma5 it seemed to be more
reasonable to create a new kde.mk instead of adding an bsd.kde5.mk.
The kde.mk in this review is a stripped down version of the one we are using in
the KDE Test repositories plasma5 branch [1] to only contain the parts relevant
to the current KDE4 ports in the portstree [2].
Changes to the KDE Ports needed by this:
Replace USE_KDE4 by USE_KDE [3]
Add USES=kde:4 [4]
[1] http://src.mouf.net/area51/view/branches/plasma5/KDE/Mk/Uses/kde.mk
[2] The version in the plasma5 branch also handles frameworks/plasma5 and
handles MASTER_SITES via a KDE_DIST variable similar to bsd.qt.mk for Qt
Ports -- I chose to leave this out for now, as the diff is already large
enough.
[3] I chose USE_KDE instead of USE_KDE4, USE_KDE5, USE_KDEX as the version we
want is already specified as argument to kde:<arg>
[4] For KDE Frameworks and Plasma5 ports this would be kde:5
PR: 210667
Approved by: portmgr, mat (mentor), rakuco (mentor)
Reviewed by: mat, rakuco
Differential Revision: https://reviews.freebsd.org/D6961
The --build configure argument is a re-invention of CONFIGURE_TARGET
except that platform is hardcoded to freebsd rather than the value
of OPSYS:tl. Use CONFIGURE_TARGET instead. It's a no-op for FreeBSD
but is a fix for DragonFly.
Approved by: non-invasive DF support blanket
- Add EXAMPLES option [1]
- Fix COMMENT declaration, use ?= so that slave can overide it
- Add LICENSE_FILE
- Convert to options helpers, test framework
- Remove MPI option and move it's all functionality to slave port
This allows removal of setting PKGNAMESUFFIX in master port depending
on options selected which is deprecated. Move LIB_DEPENDS on mpich2
to slave, declare CONFLICTS_INSTALL, MPICH_ARG in such way that can
be overidden by the slave.
PR: 211454 [1]
Submitted by: Iblis Lin [1]
- Corrected documentation for mcPlots
- added id.location argument to showLabels to vary location of labels
- added fix for compatiblity with Rcmdr with missing data in several plotting
functions.
- deltaMethod() now reports confidence intervals.
- print.summary.Anova.mlm() has new SSP and SSPE arguments to determine
whether the corresponding matrices are printed (suggestion of Michael
Friendly).
- summary() and print() methods for Anova.mlm() can now report univariate
ANOVAs (suggestion and some code by Michael Friendly).
- added "value" and "vcov" attributes to objects returned by
linearHypothesis() (after suggestions by Liviu Andronic and Steven Yen).
- compareCoefs() now checks classes of models.
- small fixes/changes.
The upcoming KDE Frameworks ports need grantlee5
* Add devel/grantlee5 and move installed headers into a subdirectory include/grantlee5
* Move header files from devel/grantlee into a subdirectory
include/grantlee4
to make sure ports do not pick up the wrong headers
* Add Uses/grantlee.mk to handle the PLIST_SUB and LIB_DEEPENDS needed
by ports using grantlee (before we set the PLIST_SUB manual in very
of the depending ports, which now should not be needed anymore).
* The ports depending on devel/grantlee have been modified from
LIB_DEPENDS=libgrantlee_gui.so:devel/grantlee
to
USES=grantlee:4
as this does not affect the package no version bumped was made.
Reviewed by: mat, rakuco
Approved by: rakuco (mentor)
Differential Revision: https://reviews.freebsd.org/D7434
See PR for signficant changes to math/R port including options,
build defaults, and patch updates.
PR: 211393
Submitted by: Joseph Mingrone (maintainer)
I made a mistake; some of the post-patch target does apply to DragonFly
as well as the pre-configure target. Tighten up which code is designated
as FreeBSD only. (again, a No-Op for FreeBSD)
Approved by: OSVERSION/OPSYS blanket
There are several OSVERSION checks but everything is specific to FreeBSD
so the entire block is wrapped with a single OPSYS check to minimize
changes to the makefile.
Approved by: OSVERSION/OPSYS blanket
file, so the order remains the same.
Every PHP (or Zend) extension now installs its own .ini file in
/usr/local/etc/php. A PHP extension will be automatically activated
when installed. The order into which extensions are loaded is
automatically guessed. In some very rare cases, the guess will be
wrong, and PHP_MOD_PRIO will need to be set. Refer to the USES=php
section of the Porter's Handbook for more information.
Convert ports touching etc/php/extensions.ini manually, or telling the
OP to do it.
And finally, bump PORTREVISION for all php extensions.
PR: 210697
Submitted by: mat
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D7022
- Convert to USES=localbase
- Move OPTIONS block to proper place, use helpers
- Argument --disable-dl for MYSQL=off was dropped because
it made configure script fail when IODBC=on
PR: 203448
Submitted by: pfg [1]
2. updated to version 4.0.3
deleted obsolete patch 'patch-libinterp-octave-value-ov-classdef'
Java and GUI are now optional
plist is now generated automatically
revised dependencies
PR: 211291
Submitted by: bsam (1), Alexander Sherikov (2)
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
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2016-07-04 x11-wm/e-module-penguins: Broken for more than 6 months
2016-07-04 ftp/fget: Broken for more than 6 months
2016-07-04 net-mgmt/netmond: Broken for more than 6 months
2016-07-04 net-mgmt/ipfm: Broken for more than 6 months
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
