Package provided by Kent Polk <kent@goathill.org> in personal email.
RPy is a very simple, yet robust, Python interface to the R
Programming Language. It can manage all kinds of R objects and can
execute arbitrary R functions (including the graphic functions).
All the errors from the R language are converted to Python exceptions.
Any modules that later were installed on the R system, can easily
be used from within Python, without introducing any changes.
Pkgsrc changes:
Now builds the libR.so and provides a buildlink2.mk for packages that want
to use it. From suggestions from Kent Polk.
Recommended library set is now included in the base package.
Changes:
CHANGES IN R VERSION 1.6.1
NEW FEATURES
o Added a few "trivial and obviously missing" functions to tcltk:
tkchooseDirectory, tkpopup, tkdialog, tkread
o barplot() has a new argument `axis.lty', which if set to 1
allows the pre-1.6.0 behaviour of plotting the axis and tick
marks for the categorical axis. (This was apparently not
intentional, but axis() used to ignore lty=0.)
The argument `border' is no longer ".NotYetUsed".
CHANGES IN R VERSION 1.6.0
USER-VISIBLE CHANGES
o The default colour palette now has "grey" instead of "white"
in location 8. See palette().
o grid(nx) behaves differently (but the same as in R versions <= 0.64).
NEW FEATURES
o Preparations for name space support:
o The objects created in the methods package to represent
classes, generic functions, method definitions, and
inheritance relations now themselves belong to true classes. In
particular, the "classRepresentation" objects follow the description
in "Programming with Data" (section 7.6).
o Other additions and changes to the methods package:
o New methods ([[, print, str) and extended plot() method
(incl. logical `horiz') for "dendrogram" class.
o sprintf() now checks the agreement between formats and object
types, and handles special values (NA, Inf, ...) correctly.
o chol() now uses a tolerance for non-positive-definiteness and
so should give more consistent results across platforms.
o New function agrep() for approximate (fuzzy) string matching.
o help.search() can now use both approximate (fuzzy) and regular
expression matching. By default, if the pattern to be matched
consists of only alphanumeric characters, whitespace or a dash,
approximate matching is used.
o axis() has three new optional arguments `col', `lty', and `lwd'
all for drawing the axis line and tick marks.
o Function vcov() (formerly in MASS), a generic function to
return the variance-covariance matrix of the parameter
estimates of a fitted model.
o duplicated() and unique() have methods for matrices and arrays
(based on ideas from Jens Oehlschl<E4>gel).
o Internally memory sizes and counts of cons cells are now stored
in unsigned longs. This allows memory limits to be set and
objects created in the range 2-4Gb on 32-bit platforms, and
allows 64-bit platforms to use much larger amounts of memory.
o Command-line flags to set memory can now use the suffix `G'
for gigabytes. The setting of maximum vsize is now only
limited by the platform's address space.
o All warning and error messages are truncated to a length set
by options(warning.length=), defaulting to 1000. (Previously
most (but not quite all) were truncated at 8192 characters.)
o [dpqr]gamma() check for shape parameter > 0.
o as.POSIX[cl]t can now convert logical NAs.
o All installed packages (even those shipped with R) are
given a `Built' field in the DESCRIPTION file.
o as.data.frame() now coerces logical matrices into logical
columns (rather than factors).
o [[<-.data.frame no longer coerces character replacement values
to factor. This is consistent with using $ to replace and
with S4.
o library() attempts to detect improperly installed packages, so
as from this version an installed package must have a
DESCRIPTION file and that file must have been stamped with a
`Built:' line (which was introduced in 1.2.0). Under
Unix-alikes, the platform is checked against that used for
installation.
o print.factor() has new arguments `max.levels' (with a smart default)
and `width'. print.ordered() is no longer needed.
o RNGkind() has an additional option for normal random generators:
"Inversion".
o data.frame() recycles factors and "AsIs" objects as well as
atomic vectors.
o rect() accepts additional graphics parameters through a ...
argument (in the same way as polygon).
o strwidth/strheight() now coerce their first argument in exactly
the same way text() does, so a wider range of inputs is allowed.
o prompt()'s default and data.frame methods have a new 3rd argument
`name' allowing them to used more easily in scripts and loops.
o rgb() has a new `maxColorValue' argument, allowing r,g,b in [0,M],
particularly in {0:255}, efficiently and non-error-prone.
o summaryRprof() provides the functionality of R CMD Rprof in R
code, though more slowly.
o pdf() now uses PDF not R code for clipping, which ensures that
partially visible text strings are (partially) shown.
o Each R session uses a per-session temporary directory which
is removed at normal termination. The directory name is given
by the tempdir() function, and filenames returned by
tempfile() will be within that directory.
o help.start() on Unix now uses a .R subdirectory of the
per-session temporary directory and not ~/.R. A side effect
is that ~/.R is now never deleted by R.
o cbind/rbind() used to ignore all zero-length vectors, an
undocumented quirk for S-compatibility. This caused problems
when combining zero-extent matrices and zero-length vectors, and
now zero-length vectors are ignored unless the result would
have zero rows/columns.
o plot.spec(x) now also works for other x than AR and Pgram results.
o New functions La.chol() and La.chol2inv() for Cholesky
decomposition and inverse of positive definite matrices using
Lapack.
o Changes to the tcltk package
o New function axTicks() returning tick mark locations like axis().
o grid() has a more sensible default behavior. Tick axis alignment
only happens when no numbers of grid cells are specified. New
arguments lwd and equilogs; nx/ny = NA for not drawing, see ?grid.
o installed.packages() has a new argument `priority'.
o termplot() uses factor levels rather than 1,2,3... for x-axis.
o The trace() function has been robustified and a new function
tracingState() added to turn tracing temporarily on and off.
o New cophenetic() in "mva" as utility for hierarchical clustering.
o p.adjust() has two new methods, 'Hommel' and 'FDR', contributed
by Gordon Smyth <smyth@wehi.edu.au>.
o stars() now has add and plot arguments.
and lots of bug fixes.
as math/eukleides.
A Euclidean drawing language compiler which allows one to typeset
geometry figures within a (La)TeX document. This program is also useful
to convert such figures into EPS format or into various other vector
graphic formats.
Supplied by ich (tsadowski at gmx dot net) in PR#19090. Thanks!
Fixed bugs:
[ #482603 ] Memory leak in MA/Numeric/Python
Reported by Reggie Dugard. Turned out to be
*two* memory leaks in one case in a routine in Numeric,
array_objectype. (Dubois)
[ none ] if vals was a null-array array([]) putmask and put would
crash. Fixed with check.
[ #469951 ] n = n1[0] gives array which shares dimension of n1 array.
This causes bugs if shape of n1 is changed (n didn't used
to have it's own dimensions array (Travis Oliphant)
[ #514588 ] MLab.cov(x,x) != MLab.cov(x) (Travis Oliphant)
[ #518702 ] segfault when invalid typecode for asarray (Travis Oliphant)
[ #497530 ] MA __getitem__ prevents 0 len arrays (Reggie Duggard)
[ #508363 ] outerproduct of noncontiguous arrays (Martin Wiechert)
[ #513010 ] memory leak in comparisons (Byran Nollett)
[ #512223 ] Character typecode not defined (Jochen Kupper)
[ #500784 ] MLab.py diff error (anonymous, fixed by Dubois)
[ #503741 ] accuracy of MLab.std(x) (Katsunori Waragai)
[ #507568 ] overlapping copy a[2:5] = a[3:6]
Change uses of memcpy to memmove which allows overlaps.
[ numpy-Patches-499722 ] size of buffer created from array is bad (Michel Sanner).
[ #502186 ] a BUG in RandomArray.normal (introduced by last bug fix in 20.3)
(Katsunori Waragai).
Fixed errors for Mac (Jack Jensen).
Make rpm's properly, better Windows installers. (Gerard Vermeulen)
Added files setup.cfg; setup calculates rpm_install.sh to use current Python.
New setup.py, eliminate setup_all.py. Use os.path.join everywhere. Revision
in b6 added file README.RPM, further improvements.
Implement true division operations for Python 2.2. (Bruce Sherwood)
Note: true division of all integer types results in an array of floats,
not doubles. This decision is arbitrary and there are arguments either way,
so users of this new feature should be aware that the decision may
change in the future.
New functions in Numeric; they work on any sequence a that can be converted to a
Numeric array. Similar change to average in MA. (Dubois)
def rank (a):
"Get the rank of a (the number of dimensions, not a matrix rank)"
def shape (a):
"Get the shape of a"
def size (a, axis=None):
"Get the number of elements in a, or along a certain axis."
def average (a, axis=0, weights=None, returned = 0):
Computes average along indicated axis.
Some applications, notably the numbering of points in outlines,
use a scheme that starts with the letter "a", goes to "z", and then
starts over with "aa" thru "az", then "ba", and so on. This module
provides functions that deal with that numbering system, converting
between it and integer values.
This C++ library is intended for scientists and engineers who need to
manipulate a variety of types of matrices using standard matrix operations.
Emphasis is on the kind of operations needed in statistical calculations such
as least squares, linear equation solve and eigenvalues.
It supports matrix types: Matrix (rectangular matrix); UpperTriangularMatrix;
LowerTriangularMatrix; DiagonalMatrix; SymmetricMatrix; BandMatrix;
UpperBandMatrix; LowerBandMatrix; SymmetricBandMatrix; IdentityMatrix;
RowVector; ColumnVector.
The library includes the operations *, +, -, *=, +=, -=, Kronecker product,
Schur product, concatenation, inverse, transpose, conversion between types,
submatrix, determinant, Cholesky decomposition, QR triangularisation, singular
value decomposition, eigenvalues of a symmetric matrix, sorting, fast Fourier
and trig. transforms, printing and an interface with Numerical Recipes in C.
It is intended for matrices in the range 10 x 10 to the maximum size your
machine will accommodate in a single array. The package works for very small
matrices but becomes rather inefficient. A lazy evaluation approach to
evaluating matrix expressions is used to improve efficiency and reduce use of
temporary storage.
* Fix valign=center in html exporter
* Fix the schema.
* Backport partial fix for named expressions.
* Export copy/paste data to primary and clipboard to communicate with 1.1.x.
* Add warning dialog when we can't activate guppi.
* Backport fix for sheet object ref count error.
* Allow format dialog to grow (debian 159949)
* Backport xls export fix to handle differing numbers of argument
* Backport fix for off by 1 error in repeated col/row printing
* Fix goal seek (and thus functions like XIRR.)
Corrections since bug fix level 1 include:
* A problem with the inversion routine for quaternions.
* A segmentation fault when appending to a length 0 compressed vector
over GF2.
* An error in the computation of inverses in quaternion algebras with
non-standard parameters.
* A problem in backtrack routines using `Suborbits' if the group has
fixed points in the range [1..max(Omega)].
* A problem with the linear algebra methods for Lie algebra cohomology.
* A Problem with inverting lists of compressed vectors over fields
of order greater than 2.
* An error in computing whether an element is in a Green's D equivalence
class or not.
* Problems with various functions (including GQuotient, IntScalarProduct,
NonnegIntScalarProducts, CharacterTableDirectProduct)
* Problems with various methods (including IsGreensLessThanOrEqual and
GroupHClassOfGreensDClass, AssociatedReesMatrixSemigroupOfDClass,
IsZeroSimpleSemigroup, IsomorphismReesMatrixSemigroup and
SandwichMatrixOfReesZeroMatrixSemigroup)
XXX A bug has been introduced into GAP which prevents the test suite
(zmodnz.tst) from working in this version. This will be fixed in
bug fix 4.
For full details, please see the "description3" file that comes with
this package in ${PREFIX}/lib/gap4.3.
