ChangeLog:
* R: Along with a bug fix, edited utility functions for the
nbinomial family in the gssanova suite, eliminating unnecessary
subtractions to preserve numerical precision.
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 is optics.
to eliminate huge TeXLive dependency. Note that TeX terminal support is
still enabled by default because it works without them.
- Add Lua dependency to support TeX/Tikz terminal.
Approved by: glewis (maintainer)
- update to 0.6.1 and unbreak
- replace noegginfo with concurrent in USE_PYTHON
Differential Revision: https://reviews.freebsd.org/D1287
Approved by: swills (mentor)
the 32 ports that still use it. Bump PORTREVISION on their dependent
ports except the ones that depend on these:
audio/libogg
audio/libvorbis
devel/pcre
ftp/curl
graphics/jpeg
graphics/libart_lgpl
graphics/tiff
textproc/expat2
textproc/libxslt
In these cases the same trick as in the recent gettext update is used.
The ports install a symlink with the old library version. When enough
of their dependent ports have had regular updates the remaining ones can
get a PORTREVISION bump and the links can be removed.
Also remove the devel/pcre dependency from USE_GNOME=glib20. It causes
over 2200 packages to depend on devel/pcre while less than 200 actually
link with it. The glib20 package still depends on devel/pcre so this
should not make a difference for ports with USE_GNOME=glib20. Also,
libdata/pkgconfig/glib-2.0.pc lists pcre as a private library so
USE_GNOME=glib20 should not propagate it.
PR: 195724
Exp-run by: antoine
Approved by: portmgr (antoine)
Changes to Version 2.0-22
* corrected bug in 'terms' argument in residualPlots, and other graphic
functions with a 'terms' argument
* added residual curvature tests for glm.nb
* mcPlot and mcPlot draw 'marginal/conditional' plots for lm objects. The
marginal plot is of the centered response versus a centered regressor; the
conditional plot is the corresponding added-variable plot. The plots can be
overlaid or viewed side-by-side.
* added argument marginal.scale to avPlots to scale the added-variable plot for
Y on X|Z using the scale from the marginal plot of Y vs X ignoring X. The
default is FALSE, corresponding to using scaling to maximize resolution or
use xlim and ylim to set user scaling.
* Fixed bugs in Anova.survreg() that could affect types II, II tests, both Wald
and LR, and one similar bug in linearHypothesis.survreg().
* Replaced calls to require() with requireNamespace() where possible
(suggestion of Brian Ripley).
* The following functions now produce warnings rather than errors when there
are empty groups: scatterplot(), scatterplotMatrix(),scatter3d(),
densityPlot().
* Corrected name of "Blackmoor" dataset to "Blackmore".
* Added KosteckiDillon migraines dataset (contributed by Georges Monette).
* introduced linearHypothesis.rlm() for rlm models (suggestion of Matthieu
Stigler).
* Small bug fixes/improvements.
first contains runtime libraries such as libintl and the latter contains
developer tools such as msgfmt. Ports that use gettext will usually need
a LIB_DEPENDS on gettext-runtime and a BUILD_DEPENDS on gettext-tools.
USES=gettext-runtime can be used to set a LIB/BUILD/RUN_DEPENDS on
devel/gettext-runtime and USES=gettext-tools can be used to set a
BUILD/RUN_DEPENDS on devel/gettext-tools. USES=gettext is now the same
as "USES=gettext-runtime gettext-tools" meaning a LIB_DEPENDS on
devel/gettext-runtime and a BUILD_DEPENDS on devel/gettext-tools.
Update gettext to 0.19.3.
Remove :oldver from converters/libiconv and devel/gettext-runtime. Leave
symlinks with the old library versions to avoid the need to bump
PORTREVISION on a large number of dependent ports. When most of the
dependent ports have had normal version updates, PORTREVISION can be
bumped on the remaining ones (low number) and the links can be removed.
Fix some ports that installed files in lib/locale instead of share/locale.
PR: 194038
Reviewed by: bapt
Exp-run: antoine
Approved by: portmgr (antoine)
Before, we had:
site_perl : lib/perl5/site_perl/5.18
site_perl/perl_arch : lib/perl5/site_perl/5.18/mach
perl_man3 : lib/perl5/5.18/man/man3
Now we have:
site_perl : lib/perl5/site_perl
site_arch : lib/perl5/site_perl/mach/5.18
perl_man3 : lib/perl5/site_perl/man/man3
Modules without any .so will be installed at the same place regardless of the
Perl version, minimizing the upgrade when the major Perl version is changed.
It uses a version dependent directory for modules with compiled bits.
As PERL_ARCH is no longer needed in plists, it has been removed from
PLIST_SUB.
The USE_PERL5=fixpacklist keyword is removed, the .packlist file is now
always removed, as is perllocal.pod.
The old site_perl and site_perl/arch directories have been kept in the
default Perl @INC for all Perl ports, and will be phased out as these old
Perl versions expire.
PR: 194969
Differential Revision: https://reviews.freebsd.org/D1019
Exp-run by: antoine
Reviewed by: perl@
Approved by: portmgr
Gnome 3.14.1 and Cinnamon 2.2.16 are supported on FreeBSD 9.3-RELEASE and up.
This commit removes the old GNOME 2 desktop, bindings and some ports that
can't be compiled. A few ports where updated to more recent versions to
allow them to compile with this update.
Apart from updating ports to newer versions
GDM is more integrated with gnome-shell now, and handles several things for
the GNOME desktop such as screen locking. If you want to use GNOME 3 via
startx, you will have to add your own lock screen/screensaver. For example xscreensaver
can be used for sessions started without GDM.
Shell Extensions can be installed via https://extensions.gnome.org/ , we have
ported a few that can't be installed via this way.
The old gnome-utils and gnome-games ports where split up into single ports
and where converted to meta-ports.
gnome-terminal requires a UTF-8 locale to run, gdm handles this already, but
if you use startx you need to do this yourself.
Upgrade instructions:
Delete the old and conflicting packages:
# pkg delete clutter gnome-utils gnome-panel gnome-keyring vala-vapigen \
guile gcalctool gnome-media libgnomekbd
# pkg delete gnome-screensaver gnome-applets bug-buddy evolution-exchange \
evolution-webcal gnome-system-tools seahorse-plugins gnome-control-center
For package users the following lines will be enough:
# pkg upgrade
# pkg install gnome3
For ports users should do the following:
# portmaster -a
# portmaster x11/gnome3
We are currently aware of two issues. The first issue is a bug in the
file monitoring code in the glib20 port. This bug causes glib programs
to crash when files in a monitored directory are added or removed.
Upstream is aware of the problem, but since the problem is quite complex
there is no solution yet. This problem isn't restricted to BSD.
The second issue is that on certain video cards totem will display a
purple/pink overlay on the video. It not clear yet where the issues
comes from.
Major thanks goes to Gustau Perez for being a driving force behind getting
GNOME 3 up to speed again. Also thanks to Antoine Brodin for running the exp-runs.
This update was also made possible by:
Joe Maloney
Kris Moore
Beeblebrox
Ryan Lortie
Antoine Jacoutot
and everyone I missed
http://cpansearch.perl.org/src/SALVA/Math-Int64-0.34/Changes
- native_to_uint64 was broken when using native integers (bug report
by Aleksey Mashanov)
- add sv_seti64 and sv_setu64 macros (feature request by Graham Ollis)
PR: 194735
Approved by: sunpoet (maintainer timeout)
2014-11-07 math/elmer-umfpack: Obsoleted by cad/elmerfem
2014-11-07 science/elmer-eio: Obsoleted by cad/elmerfem
2014-11-07 science/elmer-matc: Obsoleted by cad/elmerfem
2014-11-07 science/elmer-meshgen2d: Obsoleted by cad/elmerfem
2014-11-07 science/elmergrid: Obsoleted by cad/elmerfem
py-fst:
In file included from fst/_fst.cpp:322:
In file included from /usr/local/include/fst/fstlib.h:49:
In file included from /usr/local/include/fst/fst.h:34:
In file included from /usr/local/include/fst/arc.h:31:
In file included from /usr/local/include/fst/power-weight.h:24:
/usr/local/include/fst/tuple-weight.h:179:14: error: call to 'isspace' is ambiguous
} while (isspace(c));
^~~~~~~
/usr/include/ctype.h:57:5: note: candidate function
int isspace(int);
^
/usr/include/c++/v1/cctype:125:38: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY int isspace(int __c) {return __libcpp_isspace(__c);}
/usr/include/ctype.h:57:5: note: candidate function
int isspace(int);
^
/usr/include/c++/v1/cctype:125:38: note: candidate function
inline _LIBCPP_INLINE_VISIBILITY int isspace(int __c) {return __libcpp_isspace(__c);}
pyfst provides a Python interface to the excellent OpenFst library.
Most of the essential functionality of the library is exposed through a
simplified API, allowing quick prototyping of algorithms using finite-state
methods and easy visual debugging of the results obtained by applying
FST operations.
WWW: http://pyfst.github.io
USE_KDE4=kdehier component has been deprecated, new components added:
baloo - Baloo core libraries
baloo-widgets - Baloo widgets library
kfilemetadata - KDE library for extracting file metadata
New ports:
graphics/kqtquickcharts - QtQuick plugin to render interactive charts
misc/artikulate - Pronunciation trainer for KDE
(not usable currently, links to both
GStreamer 1.x and 0.10.x via dependencies)
sysutils/baloo[-widgets] - KDE framework for searching and
managing user metadata
sysutils/kfilemetadata - Library for extracting file metadata
l10n ports:
- Farsi (Persian) and Indonesian translations has been readded
- Vietnamese didn't pass threshold for inclusion into release
astro/kstars:
- switch dependency from math/eigen2 to math/eigen3
- add PYKDE option for updating supernovae data
deskutils/kdepim4:
- update dependencies: add libkgapi and baloo,
remove now needless clucene, link-grammar, strigi
- add patch to fix build with gcc42
- update COMMENT and description for all KDE PIM ports
devel/ruby-krossruby:
- remove BROKEN, it builds with ruby 2.x now
editors/kate:
- add patch to disable memory-hungry build of the kate tests [1]
graphics/okular:
- add dependency on graphics/libkscreen
math/cantor:
- add optional dependency on lang/luajit for LuaJIT backend
- fix gfortran detection [2]
misc/kdehier4:
- adapt to new pkg world. Now the purpose of kdehier4 only
to link some stuff between KDE4_PREFIX and LOCALBASE.
science/kalzium:
- switch dependency from math/eigen2 to math/eigen3
- add dependence on science/chemical-mime-data
x11-themes/kdeartwork4
- switch dependency from math/eigen2 to math/eigen3
among other changes:
- drop deprecated USE_KDE4=kdehier
- drop @dirrm from plist
- clean up pkg-descr
- convert to options helpers
- other portlint fixes
The area51 repository features commits by alonso, rakuco and myself.
PR: 187150 [1]
Reported by: pe.freethread@live.com
Patch by: Tobias Berner <tcberner@gmail.com>
PR: 180674 [2]
Reported by: torsten.eichstaedt@web.de
PR: 194316
Exp-run: antoine
crazy with this
several things like this in the log + installing takes hours:
load-octave-pkg: octave is installing ltfat-2.0.0.tar.gz.
panic: Segmentation fault: 11 -- stopping myself...
With hat: portmgr
- Create a slave port to build a package with this option
- Switch to an external plist, because many files are added.
PR: ports/193810
Submitted by: /me
Approved by: bf (maintainer, by private mail)
With NO_WRKSUBDIR set, there's no need for a roll-your-own extraction
target, so remove it from this port.
While here:
- use <options> instead of <pre> + <post> includes
- Wrap the compound commands in parentheses and use "&&" conjunctions
instead of ";" for better multijob support
- Remove several command masks (@) that were suppressing log output
- Remove duplicate (and broken) softlink creation in lib target
- Fix second (also broken) softlink creation in do-install target
- Revbump for last
- Fix WWW whitespace
- Remove redundant @dirrm
- Patch libtool so it uses the same library version specification as on
Darwin, Linux and other systems. Given the version current:revision:age
a library will be given the extension .so.major.age.revision with major
equal to current-age. Before libtool would use .so.current on FreeBSD.
- Patch libtoolize to remove two cases of umask 0 that caused libltdl
files to be copied world writable (--ltdl option)
- Let USES=libtool patch this new version correctly
- Adjust all ports with USES=libtool:build and bump PORTREVISION on their
dependent ports if a library version changed
PR: 194068
Exp-run by: antoine
Approved by: portmgr (antoine)
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 is stk.
----------------------------------------------------------------------------
The STK is a (not so) Small Toolbox for Kriging. Its primary focus in on
the interpolation/regression technique known as kriging, which is very
closely related to Splines and Radial Basis Functions, and can be
interpreted as a non-parametric Bayesian method using a Gaussian Process
(GP) prior. The STK also provides tools for the sequential and
non-sequential design of experiments. Even though it is, currently, mostly
geared towards the Design and Analysis of Computer Experiments (DACE), the
STK can be useful for other applications areas (such as Geostatistics,
Machine Learning, Non-parametric Regression, etc.).
Move some python modules deps out of BUILD_DEPENDS (they seem to be
runtime only).
Thanks to Mikhail Tsatsenko <m.tsatsenko@gmail.com>,
Geoffrey Mainland <mainland@apeiron.net> (maintainer)
There were two issues with the previous commit.
- LDFLAGS wsa missing -L argument for libc++
- The libc++.so file is not actually a library, it's a linker script.
Specifying libc++.so in LIB_DEPENDS causes the port to fail when
it tries to install libc++ twice since it fails to recognize
libc++.so as a library.
This doesn't fix FreeBSD breakage because it seems that it's missing
the C99 math function symbols.
ImportError: /lib/libgcc_s.so.1: version GCC_4.6.0 required by /usr/local/lib/gcc48/libgfortran.so.3 not found
error when importing numpy module.
PR: 188114
Patch by Thierry Thomas <thierry@FreeBSD.org>
and libintl.so. This fixes a problem where DATADIRNAME gets an incorrect
value which causes locale files to be installed in the wrong place.
- The only configure checks that still need to be patched are related
to intltool so move DATADIRNAME patching from USES=pathfix to
USE_GNOME=intlhack.
- games/klavaro: remove excessive dependencies
- japanese/libskk: add INSTALL_TARGET=install-strip
- math/libqalculate: add INSTALL_TARGET=install-strip and remove pthread
patching
- multimedia/freetuxtv: remove excessive dependencies
- science/gramps: fix shared-mime-info use
Exp-run by: antoine
Approved by: portmgr (antoine)
The Fedora 10 infrastructure ports have been in use since June 2009 and, while
having served a great deed, have become unsupported upstream and hence affected
by unfixed security vulnerabilities. In addition to that, many recent Linux
binaries need newer libc / stdlibc++ versions.
This commit adds the linux-c6- userland as drop-in replacement for the -f10
infrastructure, as well as upgrading the linux_base-c6 port to CentOS 6.5.
If you want to switch to linux-c6 ports, please define at /etc/make.conf:
OVERRIDE_LINUX_BASE_PORT=c6
OVERRIDE_LINUX_NONBASE_PORTS=c6
Additionally, please add the following line to /etc/sysctl.conf:
compat.linux.osrelease=2.6.18
Upgrading procedures are shown in /usr/ports/UPDATING.
This work has been inspired by Artyom Mirgorodskiy's post to emulation@ in
November 2013, using and extending mav@'s work. It has been tested extensively
and most reported issues were already fixed. Please report any additional bug
or "features" to the emulation mailing list.
Many thanks to: mav@, rene@, allanjude@, netchild@, antoine@, everyone who's
filed Issues and Pull requests on GitHub,
PR: 186820
Differential Revision: https://reviews.freebsd.org/D793
Reviewed by: allanjude, antoine, bapt, rene
Approved by: portmgr (antoine, bapt)
Approved by: koobs (mentor)
Sponsored by: Perceivon Hosting Inc.
Also the compat NO_INSTALL_MANPAGES shim.
Differential Revision: https://reviews.freebsd.org/D730
Reviewed by: antoine
With hat: portmgr
Sponsored by: Absolight
specifically powerpc patch file.
Drop patch-ieee-utils-fp-freebsd.c alltogether and change the order
of #ifdefs in the setup to pull in fp-gnuc99.c instead of fp-freebsd.cc
Verified on redports for x86 builds and am bumping port revision.
Suggested by: nathanw
Phabric: https://reviews.freebsd.org/D787
Reviewed by: nathanw
Approved by: bdrewery (mentor)
prevent pkg-fallout errors
===> rpcalc-0.7.0 depends on package: py33-qt4-gui>=0 - not found
===> Verifying install for py33-qt4-gui>=0 in /usr/ports/x11-toolkits/py-qt4-gui
===> rpcalc-0.7.0 depends on package: /packages/All/py33-qt4-gui-4.11.1,1.txz - not found
===> USE_PACKAGE_DEPENDS_ONLY set - not building missing dependency from source
*** Error code 1
- Convert to USES=libtool and bump dependent ports
- Add INSTALL_TARGET=install-strip
- Remove patches that renamed include directories and libraries so they
didn't conflict with early development versions of glib/gtk 2.0
Remove patches and hacks that were used to work around the previous
situation
This allows to stage more ports as a regular user
Differential Revision: https://reviews.freebsd.org/D703
Reviewed by and discussed with: bapt
With hat: portmgr
- Update to 5.5.0
- Populate USES with desktop-file-utils, iconv, libtool, pathfix,
and shared-mime-info
- Add dependency on xdg-utils
- Remove needless USE_LDCONFIG
- Clean up CONFIGURE_ENV from stale stuff
- Update options:
. remove DOCS, FFTW, MATIO, UMFPACK (always build with them for simplicity)
. remove NLS (doesn't build without it)
. merge HELP with GUI
. PVM is not supported anymore
. Enable OCAML and TK by default
- Use options heplers
- Clean up post-patch section from stale fixes
- Convert to static pkg-plist
Moses is a statistical machine translation system that allows you to
automatically train translation models for any language pair. All you
need is a collection of translated texts (parallel corpus). Once you have a
trained model, an efficient search algorithm quickly finds the highest
probability translation among the exponential number of choices.
WWW: http://www.statmt.org/moses/
Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software
package for large-scale nonlinear optimization.
Ipopt is written in C++ and is released as open source code under the
Eclipse Public License (EPL). It is available from the COIN-OR
initiative. The code has been written by Carl Laird and Andreas Wächter,
who is the COIN project leader for Ipopt.
The Ipopt distribution can be used to generate a library that can be
linked to one's own C++, C, or Fortran code, as well as a solver
executable for the AMPL modeling environment. The package includes
interfaces to CUTEr optimization testing environment, as well as the
MATLAB and R programming environments. IPOPT can be used on Linux/UNIX,
Mac OS X and Windows platforms.
An excellent reference for this library can be found in:
Wächter and L. T. Biegler, On the Implementation of a Primal-Dual Interior
Point Filter Line Search Algorithm for Large-Scale Nonlinear Programming,
Mathematical Programming 106(1), pp. 25-57, 2006
WWW: https://projects.coin-or.org/Ipopt
PR: 168290
Submitted by: Pedro F. Giffuni <pfg@FreeBSD.org>
- Use options helpers
- take back in perl@
Also, don't add OPENGL to the default options when PACKAGE_BUILDING because
graphics/p5-OpenGL needs a *real* display to build, and that doesn't happen in
poudriere.
Sponsored by: Absolight
- Remove from devel/Makefile
- Add to math/Makefile
- Update CATEGORIES for both ports
- Add MOVED entries
While I'm here, sort MOVED entries causing MOVEDlint.awk error [1]
after r365599 [2]
[1] 6470: date going backwards from 2014-08-20 to 2014-08-15
[2] https://svnweb.freebsd.org/changeset/ports/365599
Suggested by: vsevolod
ChangeLog:
* residualPlot error when using 'type="rstudent" has been fixed.
* Minor change to "recode" documentation; improved error checking in
recode().
* Fixed a bug in gamLine with non-canonical links. (Thanks to Hani Christoph)
* Added has.intercept.multinom() to make Anova() work with multinom objects
fit to a dichotomous response (after bug report by Kristian Hovde Liland).
* Replaced vif.lm() with vif.default() to cover wider variety of models
(after question by Laura Rigg about gls models).
* Diagonal panels in scatterplotMatrix() (except for histograms) show
groups separately when plotted by groups (suggestion by Erich Neuwirth).
* Added vcov. argument to Anova.lm().
Add an option to the menu to control whether the tuning info and build
logs are installed. install these files uncompressed plain text instead
of compressed tarballs
PR: 192823
Submitted by: Don Lewis
rubyforge.org shutdown on May 15, 2014. This commit accounts for that by doing
several things:
- Deprecate ruby that had only rubyforge.org as MASTER_SITES (and so are now
only fetchable via our cache)
- Deprecate ports that depend on those
- Update the WWW pkg-descr line that points to rubyforge.org for rubygem ports
(which are still fetchable from rubygems.org)
The next step will be to remove rubyforge.org from bsd.sites.mk, after these
deprecated ports are deleted.
Phabric: D591
With hat: ruby
Approved by: portmgr (because of committing to unstaged graphics/mingplot port)
