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Eigen 2 is a C++ template library for linear algebra: vectors, matrices, and
related algorithms. It is:
* Versatile. Eigen handles, without code duplication, and in a completely
integrated way:
o both fixed-size and dynamic-size matrices and vectors.
o both dense and sparse (the latter is still experimental) matrices and
vectors.
o both plain matrices/vectors and abstract expressions.
o both column-major (the default) and row-major matrix storage.
o both basic matrix/vector manipulation and many more advanced, specialized
modules providing algorithms for linear algebra, geometry, quaternions,
or advanced array manipulation.
* Fast.
o Expression templates allow to intelligently remove temporaries and enable
lazy evaluation, when that is appropriate -- Eigen takes care of this
automatically and handles aliasing too in most cases.
o Explicit vectorization is performed for the SSE (2 and later) and AltiVec
instruction sets, with graceful fallback to non-vectorized code.
Expression templates allow to perform these optimizations globally for
whole expressions.
o With fixed-size objects, dynamic memory allocation is avoided, and the
loops are unrolled when that makes sense.
o For large matrices, special attention is paid to cache-friendliness.
* Elegant. The API is extremely clean and expressive, thanks to expression
templates. Implementing an algorithm on top of Eigen feels like just copying
pseudocode. You can use complex expressions and still rely on Eigen to
produce optimized code: there is no need for you to manually decompose
expressions into small steps.
* Compiler-friendy. Eigen has very reasonable compilation times at least with
GCC, compared to other C++ libraries based on expression templates and heavy
metaprogramming. Eigen is also standard C++ and supports various compilers.
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Discussed with tnn@.
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Upstream changes:
0.42 1 January 2009
+ Fix for world writeable files in distro to allow PAUSE indexing.
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scrollkeeper is nowadays included in rarian, so the omf.mk file should
be there as well.
Adapt all references.
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and tested by Aleksej Saushev and Stathis Kamperis.
Major changes:
- Expand code for special functions
- quad_qagi accepts upper and lower limits instead of flags for limits
- Cut out solve_inconsistent_error
- new, alternate implementation of vector operations
- colorterm: simple output color-coding
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Numerous improvements since 14.0.5. See
http://mathomatic.orgserve.de/changes.txt for the complete list of changes.
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No longer identical.
Don't say Linux since this is for other platforms too.
Don't mention GUI interface in the description for the console package.
By the way, the gtk version is really GNOME, but upstreams calls it gtk.
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This is a maintenance release, which fixes reported bugs and upgrades
the build system to the latest libtool, autoconf and automake.
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SciPy is an open source library of scientific tools for Python. SciPy
supplements the popular Numeric module, gathering a variety of high level
science and engineering modules together as a single package.
SciPy includes modules for graphics and plotting, optimization, integration,
special functions, signal and image processing, genetic algorithms, ODE
solvers, and others.
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NumPy is a general-purpose array-processing package designed to
efficiently manipulate large multi-dimensional arrays of arbitrary
records without sacrificing too much speed for small multi-dimensional
arrays. NumPy is built on the Numeric code base and adds features
introduced by numarray as well as an extended C-API and the ability to
create arrays of arbitrary type.
There are also basic facilities for discrete fourier transform,
basic linear algebra and random number generation.
Pkgsrc issue: if the package build happens to find a fortran it prefers
over the one pkgsrc is using it will try to use it and the wrong thing
will happen.
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* The GNU MathProg modeling language was supplemented with three
new built-in functions:
gmtime obtaining current calendar time
str2time converting character string to calendar time
time2str converting calendar time to character string
* For detailed description of these functions see Appendix A in
the document "Modeling Language GNU MathProg", a new edition of
which was included in the distribution.
* A bug was fixed in the MIP solver.
* A new makefile was added to build the GLPK DLL with Microsoft
Visual Studio Express 2008 for 64-bit Windows.
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Version 4.3.6 (February 22, 2004)
* Fixed a label handling error in the `set' function that was
introduced in version 4.3.1. Also cleaned up and documented
Label handling in `complement', `intersection', and `union'.
Version 4.3.5 (February 11, 2004)
* Added support for short int endian conversions in `fread'. This
was a quick fix -- we really need to go through that code (and
`fwrite') to clean it up and support a variety of missing cases.
Version 4.3.4 (December 16, 2003)
* Fixed disassemble bug causing wipeout on `veil' statement.
* Now use --enable-debug instead of --with-debug in configure.
(It was and has been broken since version 4.3.0.)
Version 4.3.3 (December 9, 2003)
* By default, use Doug Lea's dlmalloc package in place of the
C library's malloc. On some systems, dlmalloc is far superior.
For example, Algae's timing suite runs 2.5 times faster with
dlmalloc than with the AIX 5.1 malloc routines. (On Linux,
dlmalloc is the default anyway.)
* Replaced code for `magic' with faster code from Octave.
* Supplied some missing prototypes that caused trouble.
* Quit installing header files. Not sure how or why that got
started, but if you have installed previous versions of Algae,
you may have junk left around in /usr/src/algae.
Version 4.3.2 (November 29, 2003)
* Ouch! Fixed a nasty bug in `filter'.
Version 4.3.1 (November 24, 2003)
* Several efficiency improvements, some pretty dramatic.
* Short ints supported in `fread' and `fwrite'.
* New functions `erf', `erfc', `gcd', `lcm', `primef', `primes', and
`trapz'.
Version 4.3.0 (October 4, 2003)
* Enable linking to fftw (http://www.fftw.org/) for high-performance
Fourier transforms.
* The `fft' and `ifft' functions now handle matrices. By default
they transform each column, but that can be changed with an option.
* The `max' and `min' (and `imax' and `imin') functions now handle
matrix and table arguments. Note: The old versions converted
matrix arguments to vectors, if possible; the new versions may
give different results in those cases.
* The new `circshift' function performs circular shifts of arrays.
* Minor code changes to support Mac OS X.
* Fixed several potential buffer overrun problems.
* Included latest (3 June 2003) SuperLU updates.
* Included current ARPACK patches.
Version 4.2.1 (August 6, 2003)
* Added the `$digits' global variable.
Version 4.2.0 (August 5, 2003)
* New `veil' statement allows temporary changes to global variables.
Version 4.1.4 (August 2, 2003)
* Improved configuration for floating point exception handling.
* Added numerous "volatile" qualifiers, to protect against longjmp
problems with optimized gcc.
* Fix `select' function for zero-length vectors.
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texdrive is an emacs minor-mode for adding mathematical equations
to html-pages; things like Euler's identity, Pythagoras theorem
and so on.
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Overview of changes in gcalctool 5.24.2
* Re-enable trigonometric types which have been disabled since 2.24.0 (Robert Ancell, Bug #559575)
* Remember setting to ignore change mode warning between instances (Robert Ancell, Bug #556407)
* Always read configuration from /apps/gcalctool not /apps/(appname) as
the application name is different when symlinked (Matt Keenan, Bug #559260).
* Open help with gtk_show_uri() (Thomas Andersen, Bug #556207).
* Removed double conversion in boolean and 32 bit and 16 bit mask operations so
they can handle larger numbers (Robert Ancell, Bug #509988)
* Updated translations: et (Ivar Smolin), pt_BR (Leonardo Ferreira Fontenelle), uk (Maxim Dziumanenko).
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* Worked around apparent glibc bug that leads to rare hangs when freeing
semaphores.
* Fixed segfault due to unaligned access in certain obscure problems
that use SSE and multiple threads.
* MPI transforms not included, as they are still in alpha; the alpha
versions of the MPI transforms have been moved to FFTW 3.3alpha1.
* Performance improvements for sizes with factors of 5 and 10.
* Documented FFTW_WISDOM_ONLY flag, at the suggestion of Mario
Emmenlauer and Phil Dumont.
* Port Cell code to SDK2.1 (libspe2), as opposed to the old libspe1 code.
* Performance improvements in Cell code for N < 32k, thanks to Jan Wagner
for the suggestions.
* Cycle counter for Sun x86_64 compiler, and compilation fix in cycle
counter for AIX/xlc (thanks to Jeff Haferman for the bug report).
* Fixed incorrect type prefix in MPI code that prevented wisdom routines
from working in single precision (thanks to Eric A. Borisch for the report).
* Added 'make check' for MPI code (which still fails in a couple corner
cases, but should be much better than in alpha2).
* Many other small fixes.
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Upstream changes:
2.25 September 9 - Minor
+ Fix for set_properties() bug due to 5.10/5.8 UTF-8 differences.
+ Fix for failing tests due to localtime() issues.
2.24 September 6 - Minor
+ Added set_properties() method to set document properties.
Added test suite and example.
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Pkgsrc changes:
o Update to use Module::Build
o Adjust MASTER_SITES, dist not present in common directory
(reported upstream)
Upstream changes:
0.41 24 October 2008
+ Changed maintainership to John McNamara.
! Fixed bug when parsing RK numbers (generally ints or small floats).
http://rt.cpan.org/Public/Bug/Display.html?id=39892
! Changed margin units to inches to (cleanly) avoid undef warning in
SaveParser.
0.33 2008.09.07
- Default format for formatted dates changed from 'm-d-yy' to 'yyyy-mm-dd'
- Numeric fields with date-formats now promote to Date
- Added docs about date type 14 problem
- skip another test when prereq is missing
- split Spreadsheet::ParseExcel::SaveParser into packages
- split Spreadsheet::ParseExcel into packages
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Pkgsrc changes:
o Add a patch to make ExtUtils::MakeMaker emit use of the gmp
library. Actual use will be handled by bulidlink / wrapper.
o Added commented-out extra modules which can be optionally
used during "make test" if various TEST_* environment variables
are set.
Upstream changes:
2.05 2008-10-06 Greg
- New maintainer: Greg Sabino Mullane
- Allow tests to work on 64-bit platforms. Patch from Flo.
(CPAN bugs #5960, #30327, #27641, #12751, #15459)
- Add support for probab_prime function. Patch by shlomif@iglu.org.il.
(CPAN bug #6184)
- Get smarter about detecting lack of GMP libraries.
(CPAN bug #18709)
- Add META.yml and some more tests.
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NO_IMPORT_PYGOBJECT in plugins/python-loader to avoid link
errors
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http://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2008-4983
Bump pkgrev.
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* New API routines
* A crude implementation of CPLEX-like interface to GLPK API was
added to the package. Currently it allows using GLPK as a core
LP solver for Concorde, a well known computer code for solving
the symmetric TSP.
* Some bugs were fixed in the SQL table driver.
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substantially less current than the current octave.
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tweaks. See bundled changelog for full details.
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BaseCnv provides a few simple functions for converting between
arbitrary number bases. It is as fast as I currently know how to
make it (of course relying only on the lovely Perl). If you would
rather utilize an object syntax for number-base conversion, please
see Ken Williams's <Ken@Forum.Swarthmore.Edu> fine Math::BaseCalc
module.
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* Bug fixes
* Improvements
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Overview of changes in gcalctool 5.24.1
* Fixed GtkSpinButton warning (Robin Sonefors, Bug #553965)
* Only update bit panel when display contains a solved number (Bug #548690).
* gcalctool/gtk.c: Remove inline declaration so can compile in C89 (Jens Granseuer, Bug #553307).
* Updated translations: ar (Anas Afif Emad), bg (Alexander Shopov), pt_BR (Vladimir Melo).
Overview of changes in gcalctool 5.24.0
* Updated translations: af (Friedel Wolff), ar (Anas Afif Emad, Khaled Hosny),
bn_IN (Sankarshan Mukhopadhyay), da (Kenneth Nielsen),
dz (Pema Geyleg), gu (Sweta Kothari),
hr (Robert Sedak), hu (Gabor Kelemen),
it (Luca Ferretti), kn (Shankar Prasad),
ko (Changwoo Ryu), lt (Gintautas Miliauskas),
ml (Sreejith K incorporated, Praveen Arimbrathodiyil),
mr (Sandeep Shedmake), ro (Mişu Moldovan),
sq (Laurent Dhima), ta (Tirumurthi Vasudevan),
te (Krishnababu K), tr (Baris Cicek),
zh_CN (Funda Wang)
* Updated help: es (Jorge Gonzalez)
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Overview of changes in gcalctool 5.23.92
* Updated translations: en_GB (Philip Withnall), ca (Gil Forcada),
bg (Alexander Shopov)
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Overview of changes in gcalctool 5.23.91
* Fix packing for modulus button (Bug #548880)
* Change from OnlyShowIn=GNOME;XFCE; to NotShowIn=KDE; so
other desktops can use GCalctool (bug #518862).
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Overview of changes in gcalctool 5.23.90
* Fix some small memory leaks (Felix Riemann, Bug #547942)
* More work tidying up MP code (Klaus Niederkrueger, Robert Ancell, Bug #524091)
* Updated translations: ar (Khaled Hosny), fi (Ilkka Tuohela), he (Yair Hershkovitz), ja (Takeshi Aihana), pt (Duarte Loreto), sk (Marcel Telka)
* Updated documentation: ru (Yuriy Penkin)
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Overview of changes in gcalctool 5.23.6
* Deprecated left-to-right mode (Bug #500994).
* Updated remaining documentation (bg, zh_CN, zh_HK, zh_TW) to gnome-doc-utils (Robert Ancell, Bug #336104)
* Changed icon from deprecated 'gnome-calculator' to 'accessories-calculator') (Matthias Clasen, Bug #545074)
* Updated translations: ar (Djihed Afifi), fr (Claude Paroz), pt_BG (Fabrício Godoy)
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Overview of changes in gcalctool 5.23.5
* Fix regression in factorial operation (Klaus Niederkrueger)
* Made trigonometric button text translatable (Yuri Penkin, Bug #540196)
* More work tidying up MP code (Klaus Niederkrueger, Robert Ancell, Bug #524091)
* Updated Japanese documentation to gnome-doc-utils (Claude Paroz, Takeshi Aihana, Bug #336104)
* Updated translations: ca (Joan Duran), oc (Yannig Marchegay), ru (Yuriy Penkin), sv (Daniel Nylander), th (Theppitak Karoonboonyanan)
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Overview of changes in gcalctool 5.23.4
* Added workaround to stop display disappearing when editing large displays (Bug #524602)
* Applied second mp math tidy up patch from Klaus Niederkrueger (Bug #524091)
* Updated translations: ar (Djihed Afifi)
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Overview of changes in gcalctool 5.23.3
* Default to no thousands separator not ',' for locales that do not require one (Bug #527669)
* Updated translations: ar (Djihed Afifi), et (Ivar Smolin), vi (Clytie Siddall)
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Overview of changes in gcalctool 5.23.2
* Fixes the cursor from moving around when editing numbers with thousands separators (Bug #527669)
* Structural changes in preperation for full unicode support (Bug #530532)
* Updated translations: es (Jorge González), gl (Ignacio Casal Quinteiro), nb (Kjartan Maraas),
nl (Tino Meinen), pt_BR (Leonardo Ferreira Fontenelle), sl (Matej Urbančič)
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Overview of changes in gcalctool 5.23.1
* Fixes a number of compiler warnings (Bugs #526976, #526702, #527318)
* Fixes incorrect negation precedence (Bug #526094)
* Fixes issues with thousands seperators and radix in non-english
locales (Bug #527669)
* Fixes regression in constant and function menus (Bug #527545)
* Fixes problem where display is invisible after solving equation
(Bug #524602)
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This module is an extension of the Excel::Template module, which
allows the user to use various "engines" from which you can create
Excel files through Excel::Template.
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This is a module used for templating Excel files. Its genesis came
from the need to use the same datastructure as HTML::Template, but
provide Excel files instead. The existing modules don't do the
trick, as they require replication of logic that's already been
done within HTML::Template.
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to trigger/signal a rebuild for the transition 5.8.8 -> 5.10.0.
The list of packages is computed by finding all packages which end
up having either of PERL5_USE_PACKLIST, BUILDLINK_API_DEPENDS.perl,
or PERL5_PACKLIST defined in their make setup (tested via
"make show-vars VARNAMES=...").
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many bug fixes
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Changes unknown
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A package that provides classes and methods for spatial data. The classes document
where the spatial location information resides, for 2D or 3D data. Utility functions
are provided, e.g. for plotting data as maps, spatial selection, as well as methods
for retrieving coordinates, for subsetting, print, summary, etc.
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Changes unknown
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genetics 1.3.4 - 2008-08-20
---------------------------
- Fix bug in makeGenotypes that caused it to ignore the 'sep' argument
when determining which columns contain genotypes & add a corresponing
regression test
genetics 1.3.3 - 2007-04-29
---------------------------
- Correct 'obsolete' use of '$'. R no longer permits '$' to be used
to extract named elements from vectors (just lists).
- Remove the power.casectl() function, which was based on invalid
assumpations. It has been marked depreciated. Please use the
functions in the Bioconductor package 'GeneticsDesign' instead.
genetics 1.3.2 - 2007-11-20
---------------------------
- Fix bug in handling of assignment of NA value(s) to elements of an
existing genotype object.
- Fix warning messages from R CMD CHECK
- Correct documentation error by swapping definitions of kp and alpha
arguments of power.casectl().
genetics 1.3.1
--------------
- fixes in genotypeOrder to ensure all genotype/haplotype combinations
are used.
- genotypeOrder<- is now exported
genetics 1.3.0
--------------
- A note is now displayed on startup:
The R-Genetics project has developed an set of enhanced genetics
packages that will shortly replace 'genetics'. Please visit the
project homepage at http://rgenetics.org for more information.
- binsearch() has been moved to the gtools package
- New function groupGenotype to create groups/levels based on genotype
names
- Added some internal utility functions
(.genotype2Haplotype, .genotype2Allele, and .matchGenotype)
- Genotype class gets additional slot genotypeOrder (and genotype()
function gets additional argument with the same name) in order to enable
predefined order of genotypes in other functions e.g. summary
- Added order, sort and %in% methods for genotype and haplotype classes.
- Fixed genotype() with allow.partial.missing=FALSE when 'alleles' argument
is passed
- There is no more warning in genotype() if 'a1' or 'a2' have NA value(s)
and 'alleles'' argument is specified, since NA is NA anyway
- Fixed documentation of power.casectrl()
- added gtools to Depends as needed by expectedGenotypes(); the latter now
gives sorted genotypes according to order of given alleles
- print.HWE.test() wasn't displaying the observed vs expected genotype
frequency table. Fixed.
genetics 1.2.1
--------------
- Update Greg's email address
- Fixed a bug in function allele.number, as pointed out by Chris
Wallace
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