- Hide the regression-test under a MAINTAINER_MODE since skipped checks appear as failures
PR: 128447
Submitted by: "Pedro F. Giffuni" <giffunip at tutopia dot com> (maintainer)
- This is in order to prepare for the update (which currently fails some regression tests).
- No functional change.
PR: ports/127099
Submitted by: Pedro F. Giffuni <giffunip@tutopia.com> (maintainer)
agglomerative clustering. Its features include
* generating hierarchical clusters from distance matrices
* computing distance matrices from observation vectors
* computing statistics on clusters
* cutting linkages to generate flat clusters
* and visualizing clusters with dendrograms.
The interface is very similar to MATLAB's Statistics
Toolbox API to make code easier to port from MATLAB to
Python/Numpy. The core implementation of this library
is in C for efficiency.
WWW: http://code.google.com/p/scipy-cluster/
PR: ports/127515
Submitted by: Wen Heping <wenheping at gmail.com>
- Remove BROKEN for Metis option: it builds fine
- Remove BROKENness for 4.x, we don't check that anymore.
PR: 126696
Submitted by: Pedro Giffuni <pfgshield-freebsd at yahoo dot com>
Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.
To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.
To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.
Changes to Mk/*:
- Add runtime detection magic in bsd.port.mk
- Remove CONFIGURE_TARGET hack in various bsd.*.mk
- USE_GNOME=gnometarget is now an no-op
Changes to individual ports, other than removing the CONFIGURE_TARGET hack:
= pkg-plist changed (due to the ugly CONFIGURE_TARGET prefix in * executables)
- comms/gnuradio
- science/abinit
- science/elmer-fem
- science/elmer-matc
- science/elmer-meshgen2d
- science/elmerfront
- science/elmerpost
= use x86_64 as ARCH
- devel/g-wrap
= other changes
- print/magicfilter
GNU_CONFIGURE -> HAS_CONFIGURE since it's not generated by autoconf
Total # of ports modified: 1,027
Total # of ports affected: ~7,000 (set GNU_CONFIGURE to yes)
PR: 126524 (obsoletes 52917)
Submitted by: rafan
Tested on: two pointyhat 7-amd64 exp runs (by pav)
Approved by: portmgr (pav)
- This port is unrelated with x11/silo so I suppose
NO_LATEST_LINK is relevant.
- While here, remove the unnecessary $LOCALBASE includes
in CPPFLAGS/LDFLAGS for the configure environment.
PR: ports/126614
Submitted by: "Pedro F. Giffuni" <giffunip@tutopia.com>
- It's off by default as it doesn't seem to be required by any port.
- No functional change.
PR: ports/125915
Submitted by: Pedro F. Giffuni <pfgshield-freebsd@yahoo.com>
Approved by: maintainer timeout (>2 Weeks)
- While here, rename the BROWSER option to SILEXB to avoid confusion.
- No version bump since no package has been built.
PR: ports/125846
Submitted by: Pedro F. Giffuni <giffunip@tutopia.com> (maintainer)
Reported by: pointyhat via erwin
A mesh and field I/O library and scientific database
Silo is a library for reading and writing a wide variety of scientific
data to binary, disk files. The files Silo produces and the data within
them can be easily shared and exchanged between wholly independently
developed applications running on disparate computing platforms.
Consequently, Silo facilitates the development of general purpose tools
for processing scientific data. One of the more popular tools that process
Silo data files is the VisIt visualization tool.
Silo supports gridless (point) meshes, structured meshes, unstructured-zoo
and unstructured-arbitrary-polyhedral meshes, block structured AMR meshes,
constructive solid geometry (CSG) meshes, piecewise-constant (e.g.
zone-centered) and piecewise-linear (e.g. node-centered) variables defined
on the node, edge, face or volume elements of meshes as well as the
decomposition of meshes into arbitrary subset hierarchies including
materials and mixing materials. In addition, Silo supports a wide variety
of other useful objects to address various scientific computing
application needs.Although the Silo library is a serial library, it has
some key features which enable it to be applied quite effectively and
scalably in parallel.
PR: ports/125725
Submitted by: Pedro F. Giffuni <giffunip at tutopia.com>
The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).
PR: ports/124340
Submitted by: edwin@
Approved by: portmgr (pav)
almost complete coverage of the netCDF C API, wrapping it inside easy to
use python classes.
WWW: http://pysclint.sourceforge.net/pycdf/
PR: ports/123303
Submitted by: wenheping at gmail.com
2d-rewriter is fractals generator based on pattern matching
and rewriting. The program takes input containing initial
object placement and rewriting rules and keeps applying
rules to the data field until it reaches an arrangement
where no rules can be applied.
PR: ports/118906
Submitted by: Igor Serikov <bt@turtle.freedns.us>
three-dimensional chemical structures.
Features include reading a variety
of file types and output from quantum
chemistry programs, and animation of
multi-frame files and computed normal
modes from quantum programs.
WWW: http://sourceforge.net/projects/jmol/
PR: ports/123631
Submitted by: Wen heping <wenheping at gmail.com>
consists of several free Java libraries, for user convenience bundled under one
single uniform umbrella. Namely the Colt library, the Jet library, the CoreJava
library, and the Concurrent library.
The Colt library provides fundamental general-purpose data structures optimized
for numerical data, such as resizable arrays, dense and sparse matrices
(multi-dimensional arrays), linear algebra, associative containers and buffer
management.
WWW: http://dsd.lbl.gov/~hoschek/colt/
PR: 122913
Submitted by: Wen heping <wenheping@gmail.com>
Code_Saturne 1.3.2 contains important corrections in the extended
neighbourhood (used for gradient calculation with options IMRGRA=2 and 3
and for the LES dynamic model), in the steady-state algorithm and for
rotation periodicity. Therefore it is strongly advised to upgrade to
version 1.3.2. Earlier releases of version 1.3 (especially versions 1.3.f
and 1.3.1) are considered obsolete and have been removed from the website.
Note: the pdf handbooks don't build at the moment, but they are
available from the Code_Saturne's main site.
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Remove X11BASE support in favor of LOCALBASE or PREFIX
- Use USE_LDCONFIG instead of INSTALLS_SHLIB
- Remove unneeded USE_GCC 3.4+
Thanks to all Helpers:
Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr,
ehaupt, nox, itetcu, flz, pav
PR: 116263
Tested on: pointyhat
Approved by: portmgr (pav)
- Pass maintainership to submitter
- Enable 64-bit support (experimental per stated by the project web page)
PR: ports/122337
Submitted by: Wen heping <wenheping at gmail.com>
