### 0.9.2 / 11.11.2013
commit e70dc0dbbc966ce312b45b0d44d0c3b1dc10aad6
Author: Malcolm Blyth <trashbat@co.ck>
Date: Mon Nov 11 15:53:58 2013 +0000
*Corrected compressed string formatting - *U (UTF-8) should have been *S (16-bit
string)
*Completed addition of notes hash to worksheet
*Bumped revision
*Updated reader and note
Note class no longer extends string for simplicity and debug of class (pp now
works a bit more easily)
Reader has had loads of changes (still WIP) to allow objects of class
Note and NoteObject to be created and combined in the postread_worksheet function
*Adding noteObject to deal with the Object (and ultimately text comment field)
created by excel's madness
SciPy 0.12.1 is a bug-fix release with no new features compared to
0.12.0. The single issue fixed by this release is a security issue in
``scipy.weave``, which was previously using temporary directories in
an insecure manner under certain circumstances.
Changes since 3.1.3:
Bug 620: Fix robustness and performance issues in JacobiSVD::solve.
Bug 613: Fix accuracy of SSE sqrt for very small numbers.
Bug 608: Fix sign computation in LDLT.
Fix write access to CwiseUnaryView expressions.
Fix compilation of transposeInPlace() for Array expressions.
Fix non const data() member in Array and Matrix wrappers.
Fix a few warnings and compilation issues with recent compiler versions.
Documentation fixes.
o The vignette hwde.Rnw has been modified to add missing text and to
conform to current Sweave markup conventions
o Code for the functions hwde() and make.contrasts() has been modified
so that R CMD check no longer reports "No visible binding for global
variable 'oset'."
=== 0.8.9 / 24.08.2013
Author: Doug Renn <renn@nestegg.com>
Date: Fri Aug 23 17:10:24 2013 -0600
* Work around to handle number formats that are being mistaken time formats
Add missing BUILD_DEPENDS
Upstream changes:
1.07 Thu Jan 19 2012
- synchronised the autoseeding mechanism with that of Math::Random::MT
1.08 Mon May 28 2012
- synchronised the autoseeding mechanism with that of Math::Random::MT that
is more elegant and portable
1.09 Mon Jun 4 2012
- added the irand() function to draw random integers, as in Math::Random::MT
1.10 Mon Aug 6 2012
- made set_seed() return the seed, as does Math::Random::MT
- migrated test suite to Test::More and Test::Number::Delta
1.11
- Improvement of unit tests
Upstream changes:
6.22 Tue Sep 4 14:06:20 2012
- Enhancement to shuffle() to return an array
6.21 Mon Aug 6 17:27:37 2012
- Haiku does not support non-blocking IO
6.19 Fri Jul 27 00:48:20 2012
- Prevent use of incompatible state vectors
6.18 Thu Jan 26 14:58:57 2012
- Ignore warnings from other modules during tests
6.17 Wed Jan 11 05:55:09 2012
- Require OIO 3.85 to fix some 'used only once' warnings
Upstream changes:
0.31 2013-08-07
- Change proof certificate documentation to reflect the new text format.
- Some platforms were using __int128 when it wasn't supported. Only
x86_64 and Power64 use it now.
- Small speedup for ranged totient internals.
- Patch MPU::GMP 0.13 giving us not quite what we expected from a small
certificate. Fixed in MPU::GMP 0.14, worked around here regardless.
0.30 2013-08-06
[API Changes]
- Primality proofs now use the new "MPU Certificate" format, which is
text rather than a nested Perl data structure. This is much better
for external interaction, especially with non-Perl tools. It is
not quite as convenient for all-Perl manipulation.
[Functions Added]
- is_frobenius_underwood_pseudoprime
- is_almost_extra_strong_lucas_pseudoprime
- lucas_sequence
- pplus1_factor
[Enhancements]
- Documentation and PP is_prime changed to use extra strong Lucas test
from the strong test. This matches what the newest MPU::GMP does.
This has no effect at all for numbers < 2^64. No counter-example is
known for the standard, strong, extra strong, or almost extra strong
(increment 1 or 2) tests. The extra strong test is faster than the
strong test and produces fewer pseudoprimes. It retains the residue
class properties of the strong Lucas test (where the SPSP-2
pseudoprimes favor residue class 1 and the Lucas pseudoprimes favor
residue class -1), hence should retain the BPSW test strength.
- XS code for all 4 Lucas tests.
- Clean up is_prob_prime, also ~10% faster for n >= 885594169.
- Small mulmod speedup for non-gcc/x86_64 platforms, and for any platform
with gcc 4.4 or newer.
[Bug Fixes]
- Fixed a rare refcount / bignum / callback issue in next_prime.
========
The cdecimal package is a fast drop-in replacement for the decimal module
in Python's standard library. Both modules provide complete implementations
of Mike Cowlishaw/IBM's General Decimal Arithmetic Specification.
This archive is identical to the mpdecimal package, except that library
tests and documentation have been removed.
For documentation, visit:
http://www.bytereef.org/mpdecimal/index.htmlhttp://www.bytereef.org/mpdecimal/doc/index.html
Contact: Stefan Krah <skrah@bytereef.org>
Upstream changes:
Changes in version 1.6-1
write.matrix.csr() now accepts a fac argument similar to read.matrix.csr(), writing factor levels instead of the numeric codes.
naiveBayes() uses a numerically more stable formula for calculating the a-posterior probabilities.
predict.naiveBayes() now accepts data with predictors in an order different from the training data, and also ignores variables not in the model (especially the response variable).
svm() checks whether parameters which are passed to the C-code are set to NULL to avoid segfaults.
plyr is a set of tools that solves a common set of problems: you
need to break a big problem down into manageable pieces, operate
on each pieces and then put all the pieces back together. For example,
you might want to fit a model to each spatial location or time point
in your study, summarise data by panels or collapse high-dimensional
arrays to simpler summary statistics. The development of plyr has
been generously supported by BD (Becton Dickinson).
Upstream changes:
Version 0.2-7
* Trivial changes (updated package fields, daj)
Version 0.2-6
* Removed deprecated \synopsis in some Rd files (thanks to Prof. Ripley)
Upstream changes:
Changes to Version 2.0-18
o Bug fix to boot with type="residual"
o Added densityPlot() function.
Changes to Version 2.0-17
o Add a variable to AMSsurvey.
o Fix to residualPlots to compute lack of fit tests with missing values and glms.
o Fix to residualPlots with a 0/1 variable not declared a factor.
o Boxplot() now works properly with at argument passed to boxplot() via ... (contribution of Steve Ellison).
o qqPlot.lm() now works with "aov" objects (fixing problem reported by Thomas Burk).
o Small fixes to code and docs.
Changes to Version 2.0-16
o Fixed bug in printing of hypotheses by linearHypothesis(), where numeric
constants of the form 1.* or -1.* were printed incorrectly (reported by Johannes Kutsam).
o Fixed a bug in showLabels() with multiple groups in the scatterplot() and scatterplotMatrix() function.
o linearHypothesisTest() now tolerates newlines and tabs in hypotheses (suggestion of David Hugh-Jones).
o two bugs fixed in Boot() (found by David Pain) changed argument f to f. in bootCase().
o summary.Boot(), confint.Boot() and hist.Boot() handle aliases correctly.
o Boxplot.formula() now accepts more than one conditioning variable (suggestion of Christina Yassouridis).
O Boxplot() now properly handles at argument passed through via ... to boxplot() (contribution of Steve Ellison).
o Small fixes.
Changes to Version 2.0-15
o Added an argument coef. to linearHypothesis so tests of the linear hypohtesis form can be computed without reference to a fitted model
o Added a linearHypothesis.nlsList method
o Added an nls method for Boot
o Recode() introduced as alias for recode() to avoid name clash with Hmisc.
o residualPlots for glms now ignore starting values for the computing algorithm when computing lack of fit tests; starting values previously caused an error.
o Marginal Model Plots now allow conditioning on a categorical variable.
Changes to Version 2.0-14
o Smoothers now given as arguments to scatterplot(), scatterplotMatrix(), residualPlots() and other functions; gamLine(), loessLine() (default), and quantregLine() smoothers provided.
o linearHypothesis.mer() and Anova.mer() now consistent with pbkrtest version 0.3-2.
o Small changes and fixes.
Changes to Version 2.0-13
o Added point marking (id.n, etc.) to dataEllipse
o Changed the default for id.method with the invTranPlot to "x".
o The ncvTest has been rewritten for stability, and unneeded 'data', 'subset' and 'na.action' argument have been removed
o Added new function 'Boot' that is a simple front-end to boot::boot that will be useful when bootstrapping regression models. Implemented for lm and glm, but this is likely to work for many other S3 regression models with and 'update' method, 'subset' argument.
o Fixed bug in 'compareCoefs' with non-full rank models
o Modified 'bootCase' to return a matrix of class c("bootCase", "matrix") so generic functions can be written to summarize these objects.
o Minor changes to the returned value of showLabels to give both the label and the corresponding row number. showLabels documentation tweaked.
o Improved handling of center.pch argument to ellipse() (suggestion of Rob Kushler).
o New test argument for linearHypothesis.mer() and test.statistic argument for Anova.mer() for F-tests with Kenward/Roger df, provided by pbkrtest package.
o Anova.mlm() now will do univariate repeated-measures ANOVA even if the error SSP matrix is singular.
o hccm() will now accept a weighted linear models (suggestion of Stefan Holst Bache).
o deltaMethod.default() now applies coef() and vcov() to a model for which these are supported (generalizing a suggestion by Scott Kostyshak).
o Fixed handling of labels argument in scatterplot.formula() and scatterplotMatrix.formula().
o Fixed qqPlot.default() so that it honors line="none" (bug reported by Rob Kushler).
o Added new default method for confidenceEllipse(), which now can construct confidence ellipses for linear functions of coefficients.
o globalVariables() called for R 2.15.1 or later.
o Fixed bug in logit() when percents=TRUE and largest percent is 1 (reported by Eric Goodwin).
o Added radius argument to scatter3d() (suggestion of Antonino Messina).
o Fixed spurious errors message in scatter3d() when groups present but surface=FALSE (reported by David L. Carlson).
=== 0.8.8 / 02.08.2013
Author: Nathan Colgate <nathancolgate@gmail.com>
Date: Thu Aug 1 15:01:57 2013 -0500
* Update excel/internals.rb to reference a valid Encoding type
* Encoding.find("MACINTOSH") was throwing an error. Encoding.find("MACROMAN") does not.
=== 0.8.7 / 24.07.2013
Author: Yasuhiro Asaka <yasaka@ywesee.com>
Date: Wed Jul 24 11:31:12 2013 +0900
* Remove warnings for test suite
* warning: mismatched indentations at 'end' with 'class' at xxx
* warning: method redefined; discarding old xxx
* warning: assigned but unused variable xxx
* warning: previous definition of xxx was here
* The source :rubygems is deprecated because HTTP
* requests are insecure. (Gemfile)
This is a bug-fix release.
A version information bug in Makefile.am was fixed. Thanks to
Sebastien Villemot <sebastien@debian.org> for bug report.
GLPK 4.52 (release date: Jul 18, 2013)
The clique cut generator was essentially reimplemented, and now
it is able to process very large and/or dense conflict graphs.
A simple rounding heuristic was added to the MIP optimizer.
Some bugs were fixed in the proximity search heuristic routine.
Thanks to Giorgio Sartor <0gioker0@gmail.com>.
New command-line option '--proxy [nnn]' was added to glpsol to
enable using the proximity search heuristic.
A bug (incorrect processing of LI column indicator) was fixed
in the mps format reading routine. Thanks to Charles Brixko for
bug report.
changes:
-Plotting uses cairo (and is antialised) by using updated GtkExtra
-Improvements to line plots including autoscaling the y axis by default
-PDF export
-Lots of of fixes and other minor improvements all over
* What is new in gsl-1.16:
** fixed error in gsl_rng_fwrite where uninitialized padding
bytes were being written (bug #39104)
** fixed error in gsl_block_alloc where padding bytes were not
properly initialized (bugs #39101,#39102,#39103)
** fixed error in ntuple/test.c where padding bytes were not
properly initialized (bug #39105)
** fixed triangle selection bug in gsl_sf_coupling_6j_e and
gsl_sf_coupling_9j_e (bugs #39466 and #29606) (Håkan Johansson and
Alexey Illarionov)
** added higher level wrapper routine gsl_multifit_fdfsolver_driver
** converted gsl_multifit_linear_residuals to use dgemv to improve
efficiency (bug #39153)
** added functions gsl_stats_spearman and gsl_sort_vector2 to compute
Spearman rank correlation
** added function gsl_poly_dd_hermite_init for Hermite interpolation
** Added support for robust linear least squares
** Added function gsl_linalg_SV_leverage for computing statistical
leverages from SVD decomposition
** Added support for approximating the Jacobian of nonlinear least
squares fits using forward finite differences
** Extended gsl_sf_coupling_3j to allow larger range and to handle
the special case (ja jb jc; 0 0 0)=0 when ja+jb+jc is odd
** Fixed gsl_sf_mathieu_se_array to return zero when the order is zero
[bug #33679].
** Fixed overflow in gsl_sf_lncosh for large negative x (x<-354).
** Improved gsl_ran_negative_binomial_pdf to avoid underflow/overflow
for large arguments.
** Multisets now allow k strictly greater than n.
** Fixed gsl_matrix_complex_fwrite/fread failure for noncontiguous
matrices (Matthias Sitte).
are replaced with .include "../../devel/readline/buildlink3.mk", and
USE_GNU_READLINE are removed,
* .include "../../devel/readline/buildlink3.mk" without USE_GNU_READLINE
are replaced with .include "../../mk/readline.buildlink3.mk".
Add missing DEPENDS
Upstream changes:
0.29 30 May 2013
- Fix a signed vs. unsigned char issue in ranged moebius. Thanks to the
Debian testers for finding this.
- XS is_prob_prime / is_prime now use a BPSW-style test (SPRP2 plus
extra strong Lucas test) for values over 2^32. This results in up
to 2.5x faster performance for large 64-bit values on most machines.
All PSP2s have been verified with Jan Feitsma's database.
- forprimes now uses a segmented sieve. This (1) allows arbitrary 64-bit
ranges with good memory use, and (2) allows nesting on threaded perls.
- prime_count_approx for very large values (> 10^36) was very slow without
Math::MPFR. Switch to Li+correction for large values if Math::MPFR is
not available.
- Workaround for MSVC compiler.
- Added:
is_pseudoprime (Fermat probable prime test)
is_lucas_pseudoprime (standard Lucas-Selfridge test)
is_extra_strong_lucas_pseudoprime (Mo/Jones/Grantham E.S. Lucas test)
0.28 23 May 2013
- An optimization to nth_prime caused occasional threaded Win32 faults.
Adjust so this is avoided.
- Yet another XS micro-speedup (PERL_NO_GET_CONTEXT)
- forprimes { block } [begin,]end. e.g.
forprimes { say } 100;
$sum = 0; forprimes { $sum += $_ } 1000,50000; say $sum;
forprimes { say if is_prime($_+2) } 10000; # print twin primes
- my $it = prime_iterator(10000); say $it->();
This is experimental (that is, the interface may change).
0.27 20 May 2013
- is_prime, is_prob_prime, next_prime, and prev_prime now all go straight
to XS if possible. This makes them much faster for small inputs without
having to use the -nobigint flag.
- XS simple number validation to lower function call overhead. Still a
lot more overhead compared to directly calling the XS functions, but
it shaves a little bit of time off every call.
- Speedup pure Perl factoring of small numbers.
- is_prob_prime / is_prime about 10% faster for composites.
- Allow '+N' as the second parameter to primes.pl. This allows:
primes.pl 100 +30
to return the primes between 100 and 130. Or:
primes.pl 'nth_prime(1000000000)' +2**8
- Use EXTENDED_TESTING to turn on extra tests.
0.26 21 April 2013
- Pure Perl factoring:
- real p-1 -- much faster and more effective
- Fermat (no better than HOLF)
- speedup for pbrent
- simple ECM
- redo factoring mix
- New functions:
prime_certificate produces a certificate of primality.
verify_prime checks a primality certificate.
- Pure perl primality proof now uses BLS75 instead of Lucas, so some
numbers will be much faster [n-1 only needs factoring to (n/2)^1/3].
- Math::Prime::Util::ECAffinePoint and ECProjectivePoint modules for
dealing with elliptic curves.
0.25 19 March 2013
- Speed up p-1 stage 2 factoring. Combined with some minor changes to the
general factoring combination, ~20% faster for 19 digit semiprimes.
- New internal macro to loop over primary sieve starting at 2. Simplifies
code in quite a few places.
- Forgot to skip one of the tests with broken 5.6.2.
0.24 10 March 2013
- Fix compilation with old pre-C99 strict compilers (decl after statement).
- euler_phi on a range wasn't working right with some ranges.
- More XS prime count improvements to speed and space. Add some tables
to the sieve count so it runs a bit faster. Transition from sieve later.
- PP prime count for 10^9 and larger is ~2x faster and uses much less
memory. Similar impact for nth_prime 10^8 or larger.
- Let factor.pl accept expressions just like primes.pl.
0.23 5 March 2013
- Replace XS Zeta for x > 5 with series from Cephes. It is 1 eps more
accurate for a small fraction of inputs. More importantly, it is much
faster in range 5 < x < 10. This only affects non-integer inputs.
- PP Zeta code replaced (for no-MPFR, non-bignums) with new series. The
new code is much more accurate for small values, and *much* faster.
- Add consecutive_integer_lcm function, just like MPU::GMP's (though we
define ci_lcm(0) = 0, which should get propogated).
- Implement binary search on RiemannR for XS nth_prime when n > 2e11.
Runs ~2x faster for 1e12, 3x faster for 1e13. Thanks to Programming
Praxis for the idea and motivation.
- Add the first and second Chebyshev functions (theta and psi).
- put isqrt(n) in util.h, use it everywhere.
put icbrt(n) in lehmer.h, use it there.
- Start on Lagarias-Miller-Odlyzko prime count.
- A new data structure for the phi(x,a) function used by all the fast
prime count routines. Quite a bit faster and most importantly, uses
half the memory of the old structure.
- Performance:
- Divisor sum with no sub is ~10x faster.
- Speed up PP version of exp_mangoldt, create XS version.
- Zeta much faster as mentioned above.
- faster nth_prime as mentioned above.
- AKS about 10% faster.
- Unroll a little more in sieve inner loop. A couple percent faster.
- Faster prime_count and nth_prime due to new phi(x,a) (about 1.25x).
0.22 26 February 2013
- Move main factor loop out of xs and into factor.c.
- Totient and Moebius now have complete XS implementations.
- Ranged totient uses less memory when segmented.
- Switch thread locking to pthreads condition variables.
0.21 22 February 2013
- Switch to using Bytes::Random::Secure for random primes. This is a
big change in that it is the first non-CORE module used. However, it
gets rid of lots of possible stupidness from system rand.
- Spelling fixes in documentation.
- primes.pl: Add circular and Panaitopol primes.
- euler_phi and moebius now will compute over a range.
- Add mertens function: 1000+ times faster than summing moebius($_).
- Add exp_mangoldt function: exponential of von Mangoldt's function.
- divisor_sum defaults to sigma if no sub is given (i.e. it sums).
- Performance:
- Speedup factoring small numbers. With -nobigint factoring from
1 to 10M, it's 1.2x faster. 1.5x faster than Math::Factor::XS.
- Totient and M枚bius over a range are much faster than separate calls.
- divisor_sum is 2x faster.
- primes.pl is much faster with Pillai primes.
- Reduce overhead in euler_phi -- about 2x faster for individual calls.
0.20 3 February 2013
- Speedup for PP AKS, and turn off test on 32-bit machines.
- Replaced fast sqrt detection in PP.pm with a slightly slower version.
The bloom filter doesn't work right in 32-bit Perl. Having a non-working
detector led to really bad performance. Hence this and the AKS change
should speed up testing on some 32-bit machines by a huge amount.
- Fix is_perfect_power in XS AKS.
0.19 1 February 2013
- Update MR bases with newest from http://miller-rabin.appspot.com/.
- Fixed some issues when using bignum and Calc BigInt backend, and bignum
and Perl 5.6.
- Added tests for bigint is_provable_prime.
- Added a few tests to give better coverage.
- Adjust some validation subroutines to cut down on overhead.
0.18 14 January 2013
- Add random_strong_prime.
- Fix builds with Solaris 9 and older.
- Add some debug info to perhaps find out why old ActiveState Perls are
dying in Math::BigInt::Calc, as if they were using really old versions
that run out of memory trying to calculate '2 ** 66'.
http://code.activestate.com/ppm/Math-Prime-Util/
0.17 20 December 2012
- Perl 5.8.1 - 5.8.7 miscalculates 12345 ** 4, which I used in a test.
- Fix (hopefully) for MSC compilation.
- Unroll sieve loop for another 20% or so speedup. It won't have much
practical application now that we use Lehmer's method for counts, but
there are some cases that can still show speedups.
- Changed the rand functionality yet again. Sorry. This should give
better support for plugging in crypto RNG's when used from other
modules.
0.16 11 December 2012
- randbits >= 32 on some 32-bit systems was messing us up. Restrict our
internal randbits to wordsize-1.
Upstream changes:
Version 3.98-1
* Compilation error with clang. Simple declaration of a routine.
Version 3.98-0
* Update for libxml2-2.9.1 and reading from a connection for xmlEventParse().
* xmlIncludes() is a hierarchical version of getXIncludes()
* Modifications to xmlSource(), e.g. verbose = TRUE as default.
Version 3.97-0
* Fix for xmlValue(node) = text. Identified by Lawrence Edwards.
Uses xmlNodeSetContent() now and leaves freeing the original content to that routine.
* Updates for xmlSource()
Version 3.96-1
* readHTMLTable() ignores headers that are over 999 characters.
* Fix a problem in readHTMLTable() with some table headers not having
the correct number of elements to match the columns.
Version 3.96-0
* Introduced readHTMLList(), getHTMLLinks(), getHTMLExternalFiles(), getXIncludes().
* When serializing XMLNode objects, i.e. R representations of nodes, ensure " and <, etc. in attributes
are serialized correctly.
Version 3.95-1
* Allow htmlParse(), xmlParse(), etc. ?
Version 3.95-0
* Moved development version of the source code for the package to github -
https://github.com/omegahat/XML.git
* Changes to the structure of the package to allow installation directly rather than
via a one-step staging into the R package structure.
* Sample XML documents moved from data/ to exampleData, and examples updated.
* getDefaultNamespace() and matchNamespaces() use simplify = TRUE to call
xmlNamespaceDefinitions() to get the namespaces as a character vector rather than
list.
* Documentation updates
Version 3.94-0
* getNodeLocation() now reports the actual line number for text nodes rather than 0,
using the sibling nodes' or parent node's line number.
* xpathApply() and related functions work with builtin type "functions",
e.g. class.
* xpathApply() and related functions (getNodeSet, xpathSApply) allow
the caller to specify multiple queries as a character vector
and these are pasted together as compound location paths by
separating them with a '|'. This makes it easier for the
caller to manage the different queries.
* assigning to a child of a node works, e.g. node[["abc"]] = text/node
and node[[index]] = text/node. We replace a matching name. If the
replacement value is text, we use the name to
* getChildrenStrings() is a function that implements the equivalent of
xmlApply(node, xmlValue) but faster because we avoid the function call
for each element.
* options parameter for xmlParse() and htmlParse() for controlling the parser.
(Currently only used when encoding is explicitly specified.)
* encoding parameter for xmlParse() and xmlTreeParse() now works for XML documents,
not just HTML documents.
* Update for readHTMLTable() method so that we look at just the final <tr> node
in a <thead>.
Version 3.93-1
* Fixed bug in findXInclude() that sometimes got the wrong XMLXIncludeStartNode.
Hence getNodeLocation() might report the wrong file, but correct line number!
* findXInclude() now has a recursive parameter that resolves the chain of XIncludes.
This returns the full path to the file, relative to the base/top-level document,
not just the parent document.
* Change to the default value of the error parameter in htmlParse() and htmlTreeParse()
which will generate a structured R error if there is an IO error.
The set of issues that will raise an error will be broadened in the future.
Version 3.93-0
* Enabled the fixing of <dummy> namespaces by finding the definition o
for that prefix in the ancestor nodes.
Version 3.92-2
* Synchronized compilation flags for Windows with those on OSX & Linux.
Version 3.92-1
* Restore original error handler function for htmlParse() and htmlTreeParse()
* Fixed a reference counting problem caused by not adding a finalizer in the
as() method for coercing an XMLInternalNode to an XMLInternalDocument.
Example from Janko Thyson.
* Fixed up some partial argument names found by R CMD check!
Version 3.92-0
* Added --enable-xml-debug option for the configure script and this activates
the debugging diagnostic reporting, mainly for the garbage collection and node
reference counts.
* Work-around for HTML documents not being freed (but XML documents are!)
* Added an isHTML parameter for xmlTreeParse.
* Merge htmlTreeParse/htmlParse with xmlTreeParse.
* Implemented some diagnostic facilities to determine if an external pointer
is in R's weak references list. This needs support within R. (Ask for code if
you want.)
Version 3.91-0
* Start of implementation to allow nested calls to newXMLNode() to use namespace prefixes
defined in ancestor nodes. Disabled at present.
Update LICENSE
Upstream changes:
2013-02-28 Albrecht Gebhardt <agebhard@uni-klu.ac.at>
* DESCRIPTION, LICENSE: final version of license desription done.
Upstream changes:
Changes in Version 1.7-10
o All methods that had previously been fully exported (merge.zoo,
MATCH.default, ..., and many more) in order to be accessible to
_all_ conceivable generics are now additionally registered as
S3method()s for the standard generics. Exception: as.Date.* are
still only fully exported.
o Added a new mean() method for "zoo" objects that simply does
mean(coredata(obj), ...).
o Added yearmon_trans, scale_x_yearmon and scale_y_yearmon and
yearqtr_trans, scale_x_yearqtr and scale_y_yearqtr to ggplot2 interface.
o Removed the use of the shape and linetype aesthetic by default
in autoplot() method.
o Bug fix in na.fill for univariate series based on 1-column matrices
(provided by Josh Ulrich).
o Added [[ methods for "yearmon" and "yearqtr".
o Constructs like time(obj)[ORDER(time(obj))] are now split up into
two steps in the package code. If zoo is only imported but not
loaded, R can otherwise have problems correctly dispatching to
the new generics ORDER and MATCH.
o as.Date() now also works for yearqtr/yearmon that are all NA
(especially needed for format() and print() method).
This package lets you create and manipulate complex numbers. By default, Perl
limits itself to real numbers, but an extra use statement brings full complex
support, along with a full set of mathematical functions typically associated
with and/or extended to complex numbers.
Gnumeric 1.12.3
Andreas:
* Fix border handling for merged cells in LaTeX export.
* Fix 'Go to First'. [#699631]
* Fix data merges. [#699897]
* Fix editing of hyperlinks. [#700732]
* Fix conditional formatting crash. [#700969]
* Do not include hidden cells in automatic print range. [#700994]
* Make buttons 1 and 2 behave similarly when selecting cells. [#700792]
* Warn when encountering extLst in xlsx import. [#700018]
* Use ctrl-a only to select the whole sheet, if the sheet
has focus. [#699746]
* Add a keyboard shortcut to jump to the current cell indicator.
[#699710]
* Fix placement of hyperlink tooltip. [#701436]
* Adjust cell comment display. [#698519]
* Make reference display in paste/define names dialog consistent with
sheet preferences. [Debian #699054]
* Write/read pagesetup settings to/from xlsx. [#701834]
* Fix in-cell-combos attached to merged cells. [#702146]
* Use the pagesetup setting to determine the landscape option in LaTeX
export [#702169]
* Fix ODF crash. [#702197]
* In ODF import ignored mentioned but not included sheets. [#698388]
* Fix crash on corrupted files. [#702205] [#702219] [#702285]
[#702288] [#702364] [#702409] [#702486] [#702485] [#702498] [#702322]
[#702689]
* Some documentation improvements. [Debian #621735] [Debian #530462]
* Fix crash on xlsx import due to external references. [#702407]
* Fix reading of conditional formats from xls files. [#702612]
* Fix reading of solid fill conditional formats from xlsx files.
[#702615]
* Improve xlsx import of new stat function names.
* Fix export of FLOOR(x) to xlsx. [Debian #464732]
* Fix clipboard related crash. [#702868]
Darrell Tangman:
* Update documentation for Edit and Insert menus. [#700596]
* Update documentation for comments and hyperlinks. [#700797]
* Consolidate comment, hyperlinks, names documentation.
* Update documentation for Manage Sheets, R1C1 notation,
sheet ranges. 1.12 updates, typo corrections, misc. cleanup.
Dmitry Smirnov:
* Fixes to the gnumeric and ssconvert manual pages.
Jean:
* Adjust labels vertical alignment in document properties
dialog. [#700156]
* Don't crash when exchanging missing axes. [#702126]
* Don't accept GNM_SHEET_PATTERNS as a valid pattern. [#702833]
Morten:
* Improve xlsx import of style-only cells.
* Don't write empty cells to .gnumeric.
* Add MPSEUDOINVERSE function.
* Add ctrl-shift-z as extra accelerator for redo. [#699579]
* Fix conditional format problem. [#699647]
* Remove gobject property strings from translation corpus.
* Improve LINEST. [#551457]
* Improve statfuns tests. [#700294]
* Improve mathfuns tests. [#700295]
* Add new R.PTUKEY function. [#700132]
* Add new Q.PTUKEY function. [#700132]
* Fix missing translation of certain function examples.
* Add new SNORM.DIST.RANGE function.
* Fix critical when last row deleted.
* Fix criticals in about dialog.
* Introspection fixes.
* Fix xls/biff5 link export. [#701604]
* Workaround problems with automake 1.13.
* Fix crashes on corrupted files. [#702101] [#702182] [#702218]
[#702267] [#702277] [#702379] [#702658] [#703006]
* Improve xls import of new stat function names.
* Plug leaks.
math/p5-Math-Random-ISAAC.
As with other Pseudo-Random Number Generator (PRNG) algorithms like the
Mersenne Twister (see Math::Random::MT), this algorithm is designed to
take some seed information and produce seemingly random results as output.
However, ISAAC (Indirection, Shift, Accumulate, Add, and Count) has
different goals than these commonly used algorithms. In particular, it's
really fast - on average, it requires only 18.75 machine cycles to generate
a 32-bit value. This makes it suitable for applications where a significant
amount of random data needs to be produced quickly, such solving using the
Monte Carlo method or for games.
The results are uniformly distributed, unbiased, and unpredictable unless
you know the seed. The algorithm was published by Bob Jenkins in the late
90s and despite the best efforts of many security researchers, no feasible
attacks have been found to date.
math/Math-Random-ISAAC-XS.
This module implements the same interface as Math::Random::ISAAC and can
be used as a drop-in replacement. This is the recommended implementation
of the module, based on Bob Jenkins' reference implementation in C.
Selecting the backend to use manually really only has two uses:
* If you are trying to avoid the small overhead incurred with
dispatching method calls to the appropriate backend modules.
* If you are testing the module for performance and wish to
explicitly decide which module you would like to use.
devel/p5-Algorithm-Cluster.
This module is an interface to the C Clustering Library, a general purpose
library implementing functions for hierarchical clustering (pairwise simple,
complete, average, and centroid linkage), along with k-means and k-medians
clustering, and 2D self-organizing maps. This library was developed at the
Human Genome Center of the University of Tokyo. The C Clustering Library
is distributed along with Cluster 3.0, an enhanced version of the famous
Cluster program originally written by Michael Eisen while at Stanford
University.
math/p5-Number-Tolerant.
Number::Tolerant creates a number-like object whose value refers to a
range of possible values, each equally acceptable. It overloads
comparison operations to reflect this.
I use this module to simplify the comparison of measurement results to
specified tolerances.
reject $product unless $measurement == $specification;
Singleton and dense phases were implemented on computing
LU-factorization with Gaussian elimination. The singleton phase
is a feature that allows processing row and column singletons
on initial elimination steps more efficiently. The dense phase
is a feature used on final elimination steps when the active
submatrix becomes relatively dense. It significantly reduces
the time needed, especially if the active submatrix fits in CPU
cache, and improves numerical accuracy due to full pivoting.
The API routine glp_adv_basis that constructs advanced initial
LP basis was replaced by an improved version, which (unlike the
old version) takes into account numerical values of constraint
coefficients.
The proximity search heuristic for MIP was included in the GLPK
integer optimizer glp_intopt. On API level the heuristic can be
enabled by setting the parameter ps_heur in glp_iocp to GLP_ON.
This feature is also available in the solver glpsol through
command-line option '--proxy'.
A bug was fixed that caused numerical instability in the FPUMP
heuristic.
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.
This package is legacy version.
This commit makes no semantic change; it merely splits
USE_LANGUAGES=c fortran77
into two lines, reorders, and adds comments.
However, one can then easily turn off
USE_LANGUAGES+= fortran77
and turn on
CONFIGURE_ARGS+= --disable-fortran
and build, without a fortran dependency, and observe that there are no
PLIST problems.
to address issues with NetBSD-6(and earlier)'s fontconfig not being
new enough for pango.
While doing that, also bump freetype2 dependency to current pkgsrc
version.
Suggested by tron in PR 47882
a) refer 'perl' in their Makefile, or
b) have a directory name of p5-*, or
c) have any dependency on any p5-* package
Like last time, where this caused no complaints.
Changes since 3.1.2:
Bug 526 - Fix linear vectorized transversal in linspace.
Bug 551 - Fix compilation issue when using EIGEN_DEFAULT_DENSE_INDEX_TYPE.
Bug 533 - Fix some missing const qualifiers in Transpose
Fix a compilation with CGAL::Gmpq by adding explicit internal:: namespace when calling abs().
Fix computation of outer-stride when calling .real() or .imag().
Fix handmade_aligned_realloc (affected conservativeResize()).
Fix sparse vector assignment from a sparse matrix.
Fix log(0) with SSE.
Fix bug in aligned_free with windows CE.
Fix traits of Map<Quaternion.
Fix a few warnings (507, 535, 581).
Enable SSE with ICC even when it mimics a gcc version lower than 4.2
Workaround gcc-4.7 bug #53900 (too aggressive optimization in our alignment check)
A new version of LU-factorization routines were added.
Currently this version provides the same functionality as the
old one, however, the new version allows further improving.
Old routines for FHV-factorization used to update the basis
factorization were replaced by a new version conforming to the
new version of LU-factorization.
Some clarifications about using the name index routines were
added.
Some typos were corrected in the MathProg language reference.
A serious bug (out-of-range indexing error) was *tentatively*
fixed in the routine glp_relax4. Unfortunatly, this bug is
inherited from the original Fortran version of the RELAX-IV
code (for details please see ChangeLog), and since the code is
very intricate, the bug is still under investigation.
Update to version 2.77
Fix RPM spec file to not install tutorial twice
By default, the tutorial gets stuck in /usr/share/doc/nickle, while
rpm wants it in /usr/shar/doc/nickle-<version>. Ignore the one in /usr/share/doc/nickle.
doc: Expand tabs to spaces in .sgml files
Makes code examples readable.
Build tutorial when docbook2pdf is available
And build it on debian
tutorial: Use sgml entities instead of < and >
Tutorial: twixt doesn't have an optional 'else' block
This was a proposed feature that was removed
Rename nickle tutorial to nickle-tutorial
Makes any built files include 'nickle' by default
corrected some Nickle Tour nits
Handle OpFarJump in CompileReachable
A FarJump within a catch block references instructions one or more
frames outside of the instruction context. When checking for reachable
code, look down inside the catch blocks to see if any of the FarJumps
within them touch the target instruction.
Fixes this example:
void foo() {
for (;;)
try {
} catch uninitialized_value(string x) {
break;
}
}
Without this fix, the 'break' will not get noticed and no ReturnVoid
will be appended to the object code for 'foo', leaving the break
dangling in space.
New instructions IsType and HasMember need entries in OpNames
Otherwise, the array no longer matches the enum
Fix VALIDATE_EXECUTION test code
Needed ObjType defined.
Update to 2.76
Don't erase twixt pointer during JumpContinue until after stack copy
Otherwise, if MemCollect occurs during the stack copy, the twixt's
stack copy can get collected.
Check for lost stack chunks
If a stack chunk gets collected, the 'type' field will get
cleared. Check to see if this has happened and abort.
Add debug code to check thread validity during execution
If something gets corrupted, it's useful to have this code to help
track it down.
Handle initializers with undefined types.
Emit an error instead of crashing.
Handle systems which don't define PATH_MAX (Hurd)
This is a hack; a correct fix would involve actually allocating the
correct length object.
Version 2.75
Delete ancient .cvsignore files
Not exactly useful anymore
Examples shouldn't be executable
Fix Source URL in nickle.spec file
Point at nickle.org, as appropriate.
Make 'G' format limit array and struct recursion
This makes stack traces tractable.
Switch to dh for debian builds
Vastly simplifies debian/rules...
Stop printing recursive structs with 'g' format.
This gets annoying really quickly, so just terminate the recursive
struct printing right away.
Handle ref types in &foo->bar operations
For some reason, this case was left out of the usual ref type hacks
Version 2.74
Switch from debuild to pdebuild
Catch more package building problems by using pbuilder.
Fix Semaphore::wait logic (again) - partial means we've woken up
The only way to run do_Semaphore::wait with 'partial' set to true is
if the thread is waking up; in this case, the semaphore count may well
be negative if other threads are also waiting. Ignore the count in
this case and just complete the operation.
Add explicit debian source format 3.0 (native)
Keep lintian happy
Clean up some debian lintian warnings
Fix new FileVPrintf 'G' format comparison
Was comparing the pointer to the representation enum. oops.
Update debian/changelog for eventual 2.73 release
git-log has become git log
Needed to build ChangeLog
Back autoconf requirement to 2.64 so debian stable can run it
Shorten backtrace display
Don't display composite values in backtraces so that the
backtrace doesn't get flooded with giant values.
Typecheck switch expressions
Make sure switch expression and case expresssions are all type compatible.
Add is_type and has_member built-ins
These provide the ability to do run-time type comparisons without
needing full introspection in the language.
Add list.5c
A useful data type
add 'millis' function to return a clock in milliseconds.
Useful when doing things with sleep
Add Semaphore::count
Useful for checking current semaphore value without
modifying it.
Clean up do_Semaphore_wait
Make it clear that the semaphore count gets bumped down the first time
into this function.
Check for thread switch even if current thread is last
Threads can switch due to semaphores or other signals; that can leave
the current thread last in the run queue. Check for any case where
running changes instead of only when the current thread isn't last.
Make scanf not report valid conversion on blank input.
scanf was incorrectly accepting " " as a valid number, returning a
conversion of 0. Fix this by checking for empty strings in any numeric
conversion.
Add tests for scanf function
Scanf incorrectly accepts blank strings for numbers; here's a pile
of tests to validate various numeric input.
Add sort and skiplist to standard nickle library
These are too useful to just be examples
Add gamma function
Printing rational 0 in 'e' format doesn't need an exponent
Computing a negative exponent requires a non-zero value, so just skip
that if the value is zero
NaturalGcd must return a Natural* when aborting
It was returning One (an Integer) instead of one_natural;
floor() and ceil() should work on imprecise floats
They should return an approximate integer value instead of raising an exception.
Set version to 2.73 in prepartion for eventually release
Only call readline tty cleanup on signal readline is active
If readline isn't active, the cleanup functions tend to make a mess of
the tty state, so don't call them. This really only matters when
handling SIGTSTP.
Update to version 2.72
Keep readline from catching signals
This stops readline from catching signals, letting nickle handle them
all by itself.
Block in select instead of sigsuspend when waiting for I/O
The kernel doesn't appear to reliably deliver SIGIO while the
application is blocked, so sit in select instead of sigsuspend to make
sure we hear about pending I/O.
rename configure.in to configure.ac
Switch version to 2.72 in preparation for an eventual release
wait3 returns 0 when there's nothing left to do
Don't keep looping when wait3 is done
Update to version 2.71
Clean up a pile of build warnings
Signal return types, unused return values and stepping off the end of
the typePrim array (the value of which was unused anyways).
Catch attempts to use uninitialized pointer contents
Dereferencing a pointer to uninitialized storage is an error, instead
of passing this value along to callers, catch it immediately and raise
an exception. Check for this case in the ++ and -- operators to
generate a better error message (otherwise, we'll pass Void along and
generate an error much later).
Exit after two consecutive interrupts
If the first interrupt isn't received by the nickle code,
when the second one comes in, just exit
Cleanup struct type changes
Replace most parameterized macros with static inline functions
Typechecking, decent compiler warnings and smaller code.
Replace macros with static inline functions in value.h
Actual type checking, and smaller compiler output to boot.
Get rid of old-school variable length struct allocations
This confuses the new _FORTIFY_SOURCE bits in GCC, so use the
'sanctioned' form of placing a zero-length array at the end of the
struct.
gh-2973 Fix `1` is printed during numpy.test()
gh-2983 BUG: gh-2969: Backport memory leak fix 80b3a34.
gh-3007 Backport gh-3006
gh-2984 Backport fix complex polynomial fit
gh-2982 BUG: Make nansum work with booleans.
gh-2985 Backport large sort fixes
gh-3039 Backport object take
gh-3105 Backport nditer fix op axes initialization
gh-3108 BUG: npy-pkg-config ini files were missing after Bento build.
gh-3124 BUG: PyArray_LexSort allocates too much temporary memory.
gh-3131 BUG: Exported f2py_size symbol prevents linking multiple f2py
modules.
gh-3117 Backport gh-2992
gh-3135 DOC: Add mention of PyArray_SetBaseObject stealing a reference
gh-3134 DOC: Fix typo in fft docs (the indexing variable is 'm', not 'n').
gh-3136 Backport 3128
Notable changes (compared to version 1.1.8):
- New MatrixManipulation package.
- New ParallelIntegrationTools package.
- Gruntz algorithm in now used also for finite one-sided limits.
- FriCAS has now true 2-dimensional arrays (previously they were
emulated using vectors of vectors).
- Speedups in some matrix operations and in arithmetic with
algebraic expressions.
- FreeModule is now more general, it allows Comparable as second
argument.
- Changed Spad parser, it now uses common scanner with interpreter.
Spad language is now closer to interpreter language and Aldor.
'leave' is removed, 'free', 'generate' and 'goto' are now keywords.
Pile rules changed slightly, they should be more intuitve now.
Error messages from Spad parser should be slightly better.
Bug fixes, in particular:
- Fixed a few build problems.
- Eliminated division by 0 during 'normalize'.
- 'nthRootIfCan' removes leading zeros from generalized series
(this avoids problems with power series expanders).
- Fixed corruption of formal derivatives.
- Fixed two problems with fortan output.
- Fixed ')untrace' and ')undo'. Fixed ')trace' with ECL.
- Fixed problem with calling efricas if user default shell is (t)csh.
Differences from previous version (5.5.2):
2013.02.15: Changes between NTL 5.5.2 and 6.0
Replaced the old template-like macros for vectors, matrices, and pairs
with true template classes: Vec<T>, Mat<T>, and Pair<S,T>. For
backwards compatibilty, all the names that were used in previous
versions (e.g., vec_ZZ_p, mat_ZZ_p) have been replaced with
appropriate typedefs.
For many years, I resisted the temptation of using templates, because
compiler support was very inconsistent. But that no longer seems to
be the case.
This change, while rather sweeping, should create very few, if any,
incompatibilities with existing software. The biggest issue would be
for software that uses the old template-like macros: such macro
invocations can simply be replaced with appropriate typedefs.
Made the conversion interface more complete and uniform. Also, using
template notation, one can and should now write conv<ZZ>(a) instead of
to_ZZ(a) (for backward compatibility, all the old names to_XXX are
still there, but many new conversions are not available under these
old names). There are many new conversions provided. Moreover,
whenever there is a conversion from a ring R to a ring S, there is a
corresponding, coefficiet-wise conversion from the polynomial ring
R[X] to the polynomial ring R[X].
In addition, using the template mechanism, there are generic
conversions for vectors and matrices. For example, if there is a
conversion from S to T, then there is automatically a corresponding
component-wise conversion from Vec<S> to Vec<T>.
Introduced a more general mechanism for accessing GF2's in packed
structures via indexing (see the class ref_GF2 in the GF2 module).
Employed ideas from David Harvey to make the single-precision FFT
faster (about twice as fast in many cases). This speeds up many
higher-level operations.
Fixed all known bugs.
Summary of changes since 0.10.1:
This is a major release from 0.10.1 and includes many new features and
enhancements along with a large number of bug fixes. The methods of
Selecting Data have had quite a number of additions, and Dtype support
is now full-fledged. There are also a number of important API changes
that long-time pandas users should pay close attention to.
* New precision indexing fields loc, iloc, at, and iat, to reduce
occasional ambiguity in the catch-all hitherto ix method.
* Expanded support for NumPy data types in DataFrame.
* NumExpr integration to accelerate various operator evaluation.
* Improved DataFrame to CSV exporting performance.
For a full list refer to the "what's new" page.
Also fixes PLIST errors introduced in last update.
PR pkg/47783 by Litvinov Sergey.
METIS 4.0.3, 3/19/11
------------------------------------------------------------------------------
r9587 | karypis | 2011-03-19 12:22:36 -0500 (Sat, 19 Mar 2011) | 1 line
- Renamed log2() to ilog2() to remove conflicts with C99 log2() function
- Fixed I/O routines to eliminate compilation warnings
- Fixed error reporting routines to eliminate compilation warnings
METIS 4.0.2, 3/10/04
------------------------------------------------------------------------------
- Fixed a problem with weighted graphs and ometis.c
METIS 4.0.1, 11/29/98
------------------------------------------------------------------------------
This is mostly a bug-fix release
- Fixed some bugs in the multi-constraint partitioning routines
- Fixed some bugs in the volume-minimization routines
Major changes in 2.4:
- Improved HDF5 error logging management.
- Added support for the float16 data type.
- Leaf nodes now have attributes for retrieving the size of data in memory
and on disk.
- Configurable maximum number of threads for Blosc and Numexpr.
- ndim (read-only) attribute added to Leaf, Atom and Col objects.
- Added read support for variable length string attributes.
Full changelog for 2.4.0, see:
http://pytables.github.io/release-notes/RELEASE_NOTES_v2.4.x.html
Major changes in 2.3:
- Integrated functionality from PyTablesPro (re-licensed under a BSD license).
- OPSI is a powerful and innovative indexing engine allowing PyTables
to perform fast queries on arbitrarily large tables.
- A fine-tuned LRU cache for both metadata (nodes) and regular data.
Full changelog for 2.3.x, see:
http://pytables.github.io/release-notes/RELEASE_NOTES_v2.3.x.html
The new API routine glp_mincost_relax4, which is a driver to
relaxation method of Bertsekas and Tseng (RELAX-IV), was added
to the package. RELAX-IV is a code for solving minimum cost
flow problems. On large instances it is 100-1000 times faster
than the standard primal simplex method. Prof. Bertsekas, the
author of the original RELAX-IV Fortran code, kindly permitted
to include a C translation of his code in GLPK under GPLv3.
A bug (wrong dual feasibility test) was fixed in API routine
glp_warm_up. Thanks to David T. Price <dtprice@speakeasy.net>
for bug report.
Obsolete API routine lpx_check_kkt was replaced by new routine
glp_check_kkt.
IMPORTANT: All old API routines whose names begin with 'lpx_'
were removed from API level and NO MORE AVAILABLE.
File too long (should be no more than 24 lines).
Line too long (should be no more than 80 characters).
Trailing empty lines.
Trailing white-space.
Trucated the long files as best as possible while preserving the most info
contained in them.
COMMENT should not be longer than 70 characters.
COMMENT should not begin with 'A'.
COMMENT should not begin with 'An'.
COMMENT should not begin with 'a'.
COMMENT should not end with a period.
COMMENT should start with a capital letter.
pkglint warnings. Some files also got minor formatting, spelling, and style
corrections.
Math_BigInteger provices support of base-2, base-10, base-16, and base-256
numbers. Uses the GMP or BCMath extensions, if available, and an internal
implementation, otherwise.
* NArray properties:
+ Fast and easy calculation for large numerical array.
+ Accepting Elements:
8,16,32 bit integer, single/double float/complex, Ruby Object.
+ Easy extraction/substitution of array subset,
using assignment with number, range, array index.
+ Operator: +,-,*,/,%,**, etc.
+ FFTW version 2 or 3 is separately supported.
+ NImage: Image viewer class.
+ Ruby/PGPLOT: Graphics library interface (separately distributed)
X-Y Graph, Histogram, Contour map, Image map, etc.
* NArray is similar to:
+ Python/NumPy, Perl/PDL, Yorick, IDL
Libint is two things:
1. a library of C/C++ functions for efficient evaluation of
several kinds of two-body molecular integrals over Gaussian
functions;
2. the optimizing compiler that generates a Libint library.
In molecular electronic structure theory Gaussian basis sets are
standard because they allow efficient evaluation of matrix
elements of operators (molecular integrals). Modern electronic
structure programs spend considerable portion of their runtime
computing the Coulomb two-electron integrals. While anyone can
compute Gaussian integrals using simple formulas, the efficient
evaluation of many-body can be (relatively) complicated.
Libint is an open library that anyone can use to compute a
variety of two-electron integrals, most importantly the Coulomb
two-electron integrals and their arbitrary-order geometric
derivatives, over Gaussians of arbitrary angular momentum.
Among other notable features is the support for the nonstandard
two-electron integrals that appear in explicitly correlated R12
methods.
=== 0.8.2 / 28.02.2013
Author: Roque Pinel <roque.pinel@infotechfl.com>
Date: Wed Feb 27 12:10:29 2013 -0500
* Requiring BigDecimal for checking.
* Made API friendly to BigDecimal precision.
* Changes introduced by the user 'valeriusjames'.
=== 0.8.1 / 18.02.2013
* Updated Manifest.txt to include lib/spreadsheet/excel/rgb.rb
=== 0.8.0 / 18.02.2013
* Adding support for converting color palette values to RGB values (not vice-versa..yet)
* by https://github.com/dancaugherty/spreadsheet/compare/master...rgb
=== 0.7.9 / 06.02.2013
Author: Eugeniy Belyaev (zhekanax)
* You can merge if you are interested in perl-like Workbook.set_custom_color
implementation. I know it is not really a proper way to deal with custom colors, but
nevertheless it makes it possible.
* https://github.com/zdavatz/spreadsheet/pull/27
=== 0.7.8 / 06.02.2013
Author: Kenichi Kamiya <kachick1@gmail.com>
Date: Wed Feb 6 11:23:35 2013 +0900
* Link to Travis CI on README
* Remove warnings "assigned but unused variable" in test
* Remove warnings "assigned but unused variable"
* Enable $VERBOSE flag when running test
isl is a library for manipulating sets and relations of integer
points bounded by linear constraints. Supported operations on sets
include intersection, union, set difference, emptiness check, convex
hull, (integer) affine hull, integer projection, and computing the
lexicographic minimum using parametric integer programming. It also
includes an ILP solver based on generalized basis reduction.
Release date: 2013-01-22
New features:
Add data inferface to World Bank WDI pandas.io.wb (GH2592)
API Changes:
Restored inplace=True behavior returning self (same object) with
deprecation warning until 0.11 (GH1893)
HDFStore
refactored HFDStore to deal with non-table stores as objects, will
allow future enhancements
removed keyword compression from put (replaced by keyword complib
to be consistent across library)
warn PerformanceWarning if you are attempting to store types that
will be pickled by PyTables
Improvements to existing features:
HDFStore
enables storing of multi-index dataframes (closes GH1277)
support data column indexing and selection, via data_columns
keyword in append
support write chunking to reduce memory footprint, via chunksize
keyword to append
support automagic indexing via index keyword to append
support expectedrows keyword in append to inform PyTables about
the expected tablesize
support start and stop keywords in select to limit the row
selection space
added get_store context manager to automatically import with pandas
added column filtering via columns keyword in select
added methods append_to_multiple/select_as_multiple/
select_as_coordinates to do multiple-table append/selection
added support for datetime64 in columns
added method unique to select the unique values in an indexable
or data column
added method copy to copy an existing store (and possibly upgrade)
show the shape of the data on disk for non-table stores when
printing the store
added ability to read PyTables flavor tables (allows compatiblity
to other HDF5 systems)
Add logx option to DataFrame/Series.plot (GH2327, GH2565)
Support reading gzipped data from file-like object
pivot_table aggfunc can be anything used in GroupBy.aggregate (GH2643)
Implement DataFrame merges in case where set cardinalities might
overflow 64-bit integer (GH2690)
Raise exception in C file parser if integer dtype specified and have
NA values. (GH2631)
Attempt to parse ISO8601 format dates when parse_dates=True in read_csv
for major performance boost in such cases (GH2698)
Add methods neg and inv to Series
Implement kind option in ExcelFile to indicate whether it's an XLS
or XLSX file (GH2613)
Bug fixes:
Fix read_csv/read_table multithreading issues (GH2608)
HDFStore
correctly handle nan elements in string columns; serialize via the
nan_rep keyword to append
raise correctly on non-implemented column types (unicode/date)
handle correctly Term passed types (e.g. index<1000, when index is
Int64), (closes GH512)
handle Timestamp correctly in data_columns (closes GH2637)
contains correctly matches on non-natural names
correctly store float32 dtypes in tables (if not other float types
in the same table)
Fix DataFrame.info bug with UTF8-encoded columns. (GH2576)
Fix DatetimeIndex handling of FixedOffset tz (GH2604)
More robust detection of being in IPython session for wide DataFrame
console formatting (GH2585)
Fix platform issues with file:/// in unit test (GH2564)
Fix bug and possible segfault when grouping by hierarchical level that
contains NA values (GH2616)
Ensure that MultiIndex tuples can be constructed with NAs (GH2616)
Fix int64 overflow issue when unstacking MultiIndex with many levels
(GH2616)
Exclude non-numeric data from DataFrame.quantile by default (GH2625)
Fix a Cython C int64 boxing issue causing read_csv to return incorrect
results (GH2599)
Fix groupby summing performance issue on boolean data (GH2692)
Don't bork Series containing datetime64 values with to_datetime (GH2699)
Fix DataFrame.from_records corner case when passed columns, index
column, but empty record list (GH2633)
Fix C parser-tokenizer bug with trailing fields. (GH2668)
Don't exclude non-numeric data from GroupBy.max/min (GH2700)
Don't lose time zone when calling DatetimeIndex.drop (GH2621)
Fix setitem on a Series with a boolean key and a non-scalar as value
(GH2686)
Box datetime64 values in Series.apply/map (GH2627, GH2689)
Upconvert datetime + datetime64 values when concatenating frames
(GH2624)
Raise a more helpful error message in merge operations when one
DataFrame has duplicate columns (GH2649)
Fix partial date parsing issue occuring only when code is run at EOM
(GH2618)
Prevent MemoryError when using counting sort in sortlevel with
high-cardinality MultiIndex objects (GH2684)
Fix Period resampling bug when all values fall into a single bin
(GH2070)
Fix buggy interaction with usecols argument in read_csv when there is
an implicit first index column (GH2654)
version: 0.18.0
date: Thu Dec 20 17:50:41 CET 2012
changes:
- Update to isl 0.11.1
- clast annotations for openmp and vectorization
- statement-wise loop separation
- clast traversal and node filtering support
- Do not call some deprecated isl functions
- Support for OpenSCoP coordinates extension
version: 0.17.0
date: Mon Dec 12 00:51:44 CET 2011
changes:
- Support openscop as input format
- update isl backend to changes in isl 0.08
- Add CLOOG_ prefix to LANGUAGE defines in public header files
- Replace cloog_union_domain_from_isl_union_set() with
cloog_union_domain_from_isl_set()
- Allow to build CLooG from gmp build directory
- Smaller improvements
version: 0.16.3
date: Wed Jul 13 18:18:19 CEST 2011
changes:
- update isl backend to recent changes in isl
- add support for unrolling
=== 0.7.7 / 22.01.2013
Author: DeTeam <timur.deteam@gmail.com>
Date: Tue Jan 22 19:11:52 2013 +0400
* Make tests pass
* Readme updated
* RuntimeError when file is empty
* Hoe in dev deps
* Finish with bundler
* Add a Gemfile
also see: https://github.com/zdavatz/spreadsheet/pull/24
Update LICENSE
Upstream changes:
genetics 1.3.8 - 2012-12-14
---------------------------
Bug fixes:
- Regenerate broken PDF files in inst/doc.
genetics 1.3.7 - 2012-09-14
---------------------------
Enhancements:
- Improve descripiton of last examples in manual page for HWE.test().
Other Changes:
- Correct warnings issued by recent versions of R CMD CHECK.
pkgsrc change: depend on math/py-pytables.
Changes since 0.9.1:
* Delimited file parsing engine rewritten to use a fraction of memory while
being 40%+ faster.
- Much-improved Unicode handling via the encoding option.
- Column filtering (usecols)
- Dtype specification (dtype argument)
- Ability to specify strings to be recognized as True/False
- Ability to yield NumPy record arrays (as_recarray)
- High performance delim_whitespace option
- Decimal format (e.g. European format) specification
- Easier CSV dialect options: escapechar, lineterminator, quotechar, etc.
- More robust handling of many exceptional kinds of files observed in the wild
* API changes
- Deprecated DataFrame BINOP TimeSeries special case behavior
- Altered resample default behavior
- Infinity and negative infinity are no longer treated as NA by isnull and
notnull.
- Methods with the inplace option now all return None instead of the calling
object.
- pandas.merge no longer sorts the group keys (sort=False) by default.
- The default column names for a file with no header have been changed.
- Values like 'Yes' and 'No' are not interpreted as boolean by default.
- The file parsers will not recognize non-string values arising from a
converter function as NA.
- Calling fillna on Series or DataFrame with no arguments is no longer valid
code.
- Series.apply will now operate on a returned value from the applied function.
- New API functions for working with pandas options.
* New features
- Wide DataFrame Printing.
- Updated PyTables Support.
* Enhancements
- added ability to hierarchical keys.
- added mixed-dtype support!
- performance improvments on table writing.
- support for arbitrarily indexed dimensions.
- SparseSeries now has a density property.
* Bug fixes
- added Term method of specifying where conditions.
- del store['df'] now call store.remove('df') for store deletion.
- deleting of consecutive rows is much faster than before.
- in_itemsize parameter can be specified in table creation to force a minimum
size for indexing columns.
- indexing support via create_table_index (requires PyTables >= 2.3)
- appending on a store would fail if the table was not first created via put.
- fixed issue with missing attributes after loading a pickled dataframe.
- minor change to select and remove: require a table ONLY if where is also
provided.
* Compatibility
- 0.10 of HDFStore is backwards compatible for reading tables created
in a prior version of pandas, however, query terms using the prior
(undocumented) methodology are unsupported.
* N Dimensional Panels (Experimental)
Approved by wiz@
Upstream changes:
CHANGES IN R VERSION 2.15.1:
NEW FEATURES:
o source() now uses withVisible() rather than
.Internal(eval.with.vis). This sometimes alters tracebacks
slightly.
o install.packages("pkg_version.tgz") on Mac OS X now has sanity
checks that this is actually a binary package (as people have
tried it with incorrectly named source packages).
o splineDesign() and spline.des() in package splines have a new
option sparse which can be used for efficient construction of a
sparse B-spline design matrix (_via_ Matrix).
o norm() now allows type = "2" (the 'spectral' or 2-norm) as well,
mainly for didactical completeness.
o pmin() and pmax()) now also work when one of the inputs is of
length zero and others are not, returning a zero-length vector,
analogously to, say, +.
o colorRamp() (and hence colorRampPalette()) now also works for the
boundary case of just one color when the ramp is flat.
o qqline() has new optional arguments distribution, probs and
qtype, following the example of lattice's panel.qqmathline().
o .C() gains some protection against the misuse of character vector
arguments. (An all too common error is to pass character(N),
which initializes the elements to "", and then attempt to edit
the strings in-place, sometimes forgetting to terminate them.)
o Calls to the new function globalVariables() in package utils
declare that functions and other objects in a package should be
treated as globally defined, so that CMD check will not note
them.
o print(packageDescription(*)) trims the Collate field by default.
o The included copy of zlib has been updated to version 1.2.7.
o A new option "show.error.locations" has been added. When set to
TRUE, error messages will contain the location of the most recent
call containing source reference information. (Other values are
supported as well; see ?options.)
o The NA warning messages from e.g. pchisq() now report the call to
the closure and not that of the .Internal.
o Added Polish translations by <c5><81>ukasz Daniel.
PERFORMANCE IMPROVEMENTS:
o In package parallel, makeForkCluster() and the multicore-based
functions use native byte-order for serialization (deferred from
2.15.0).
o lm.fit(), lm.wfit(), glm.fit() and lsfit() do less copying of
objects, mainly by using .Call() rather than .Fortran().
o .C() and .Fortran() do less copying: arguments which are raw,
logical, integer, real or complex vectors and are unnamed are not
copied before the call, and (named or not) are not copied after
the call. Lists are no longer copied (they are supposed to be
used read-only in the C code).
o tabulate() makes use of .C(DUP = FALSE) and hence does not copy
bin. (Suggested by Tim Hesterberg.) It also avoids making a
copy of a factor argument bin.
o Other functions (often or always) doing less copying include
cut(), dist(), the complex case of eigen(), hclust(), image(),
kmeans(), loess(), stl() and svd(LINPACK = TRUE).
o There is less copying when using primitive replacement functions
such as names(), attr() and attributes().
DEPRECATED AND DEFUNCT:
o The converters for use with .C() (see ?getCConverterDescriptions)
are deprecated: use the .Call() interface instead. There are no
known examples (they were never fully documented).
UTILITIES:
o For R CMD check, a few people have reported problems with
junctions on Windows (although they were tested on Windows 7, XP
and Server 2008 machines and it is unknown under what
circumstances the problems occur). Setting the environment
variable R_WIN_NO_JUNCTIONS to a non-empty value (e.g. in
~/.R/check.Renviron) will force copies to be used instead.
INSTALLATION:
o R CMD INSTALL with _R_CHECK_INSTALL_DEPENDS_ set to a true value
(as done by R CMD check --as-cran) now restricts the packages
available when lazy-loading as well as when test-loading (since
packages such as ETLUtils and agsemisc had top-level calls to
library() for undeclared packages).
This check is now also available on Windows.
C-LEVEL FACILITIES:
o C entry points mkChar and mkCharCE now check that the length of
the string they are passed does not exceed 2^31-1 bytes: they
used to overflow with unpredictable consequences.
o C entry points R_GetCurrentSrcref and R_GetSrcFilename have been
added to the API to allow debuggers access to the source
references on the stack.
WINDOWS-SPECIFIC CHANGES:
o Windows-specific changes will now be announced in this file
(NEWS). Changes up and including R 2.15.0 remain in the CHANGES
file.
o There are two new environment variables which control the
defaults for command-line options.
If R_WIN_INTERNET2 is set to a non-empty value, it is as if
--internet2 was used.
If R_MAX_MEM_SIZE is set, it gives the default memory limit if
--max-mem-size is not specified: invalid values being ignored.
BUG FIXES:
o lsfit() lost the names from the residuals.
o More cases in which merge() could create a data frame with
duplicate column names now give warnings. Cases where names
specified in by match multiple columns are errors.
o Nonsense uses such as seq(1:50, by = 5) (from package plotrix)
and seq.int(1:50, by = 5) are now errors.
o The residuals in the 5-number summary printed by summary() on an
"lm" object are now explicitly labelled as weighted residuals
when non-constant weights are present. (Wish of PR#14840.)
o tracemem() reported that all objects were copied by .C() or
.Fortran() whereas only some object types were ever copied.
It also reported and marked as copies _some_ transformations such
as rexp(n, x): it no longer does so.
o The plot() method for class "stepfun" only used the optional xval
argument to compute xlim and not the points at which to plot (as
documented). (PR#14864)
o Names containing characters which need to be escaped were not
deparsed properly. (PR#14846)
o Trying to update (recommended) packages in R_HOME/library without
write access is now dealt with more gracefully. Further, such
package updates may be skipped (with a warning), when a newer
installed version is already going to be used from .libPaths().
(PR#14866)
o hclust() is now fast again (as up to end of 2003), with a
different fix for the "median"/"centroid" problem. (PR#4195).
o get_all_vars() failed when the data came entirely from vectors in
the global environment. (PR#14847)
o R CMD check with _R_CHECK_NO_RECOMMENDED_ set to a true value (as
done by the --as-cran option) could issue false errors if there
was an indirect dependency on a recommended package.
o formatC() uses the C entry point str_signif which could write
beyond the length allocated for the output string.
o Missing default argument added to implicit S4 generic for
backsolve(). (PR#14883)
o Some bugs have been fixed in handling load actions that could
fail to export assigned items or generate spurious warnings in
CMD check on loading.
o For tiff(type = "windows"), the numbering of per-page files
except the last was off by one.
o On Windows, loading package stats (which is done for a default
session) would switch line endings on stdout and stderr from CRLF
to LF. This affected Rterm and R CMD BATCH.
o On Windows, the compatibility function x11() had not kept up with
changes to windows(), and issued warnings about bad parameters.
(PR#14880)
o On Windows, the Sys.glob() function did not handle UNC paths as
it was designed to try to do. (PR#14884)
o In package parallel, clusterApply() and similar failed to handle
a (pretty pointless) length-1 argument. (PR#14898)
o Quartz Cocoa display reacted asynchronously to dev.flush() which
means that the redraw could be performed after the plot has been
already modified by subsequent code. The redraw is now done
synchronously in dev.flush() to allow animations without sleep
cycles.
o Source locations reported in traceback() were incorrect when
byte-compiled code was on the stack.
o plogis(x, lower = FALSE, log.p = TRUE) no longer underflows early
for large x (e.g. 800).
o ?Arithmetic's "1 ^ y and y ^ 0 are 1, _always_" now also applies
for integer vectors y.
o X11-based pixmap devices like png(type = "Xlib") were trying to
set the cursor style, which triggered some warnings and hangs.
o Code executed by the built-in HTTP server no longer allows other
HTTP clients to re-enter R until the current worker evaluation
finishes, to prevent cascades.
o The plot() and Axis() methods for class "table" now respect
graphical parameters such as cex.axis. (Reported by Martin
Becker.)
o Under some circumstances package.skeleton() would give out
progress reports that could not be translated and so were
displayed by question marks. Now they are always in English.
(This was seen for CJK locales on Windows, but may have occurred
elsewhere.)
o The evaluator now keeps track of source references outside of
functions, e.g. when source() executes a script.
o The replacement method for window() now works correctly for
multiple time series of class "mts". (PR#14925)
o is.unsorted() gave incorrect results on non-atomic objects such
as data frames. (Reported by Matthew Dowle.)
o The value returned by tools::psnice() for invalid pid values was
not always NA as documented.
o Closing an X11() window while locator() was active could abort
the R process.
o getMethod(f, sig) produced an incorrect error message in some
cases when f was not a string).
o Using a string as a "call" in an error condition with
options(showErrorCalls=TRUE) could cause a segfault. (PR#14931)
o The string "infinity" allowed by C99 was not accepted as a
numerical string value by e.g. scan() and as.character().
(PR#14933)
o In legend(), setting some entries of lwd to NA was inconsistent
(depending on the graphics device) in whether it would suppress
those lines; now it consistently does so. (PR#14926)
o by() failed for a zero-row data frame. (Reported by Weiqiang
Qian)
o Yates correction in chisq.test() could be bigger than the terms
it corrected, previously leading to an infinite test statistic in
some corner cases which are now reported as NaN.
o xgettext() and related functions sometimes returned items that
were not strings for translation. (PR#14935)
o plot(<lm>, which=5) now correctly labels the factor level
combinations for the special case where all h[i,i] are the same.
(PR#14837)
CHANGES IN R VERSION 2.15.0:
SIGNIFICANT USER-VISIBLE CHANGES:
o The behaviour of unlink(recursive = TRUE) for a symbolic link to
a directory has changed: it now removes the link rather than the
directory contents (just as rm -r does).
On Windows it no longer follows reparse points (including
junctions and symbolic links).
NEW FEATURES:
o Environment variable RD2DVI_INPUTENC has been renamed to
RD2PDF_INPUTENC.
o .Deprecated() becomes a bit more flexible, getting an old
argument.
o Even data-only packages without R code need a namespace and so
may need to be installed under R 2.14.0 or later.
o assignInNamespace() has further restrictions on use apart from at
top-level, as its help page has warned. Expect it to be disabled
from programmatic use in the future.
o system() and system2() when capturing output report a non-zero
status in the new "status" attribute.
o kronecker() now has an S4 generic in package methods on which
packages can set methods. It will be invoked by X %x% Y if
either X or Y is an S4 object.
o pdf() accepts forms like file = "|lpr" in the same way as
postscript().
o pdf() accepts file = NULL. This means that the device does NOT
create a PDF file (but it can still be queried, e.g., for font
metric info).
o format() (and hence print()) on "bibentry" objects now uses
options("width") to set the output width.
o legend() gains a text.font argument. (Suggested by Tim Paine,
PR#14719.)
o nchar() and nzchar() no longer accept factors (as integer
vectors). (Wish of PR#6899.)
o summary() behaves slightly differently (or more precisely, its
print() method does). For numeric inputs, the number of NAs is
printed as an integer and not a real. For dates and datetimes,
the number of NAs is included in the printed output (the latter
being the wish of PR#14720).
The "data.frame" method is more consistent with the default
method: in particular it now applies zapsmall() to
numeric/complex summaries.
o The number of items retained with options(warn = 0) can be set by
options(nwarnings=).
o There is a new function assignInMyNamespace() which uses the
namespace of the function it is called from.
o attach() allows the default name for an attached file to be
overridden.
o bxp(), the work horse of boxplot(), now uses a more sensible
default xlim in the case where at is specified differently from
1:n, see the discussion on R-devel, <URL:
https://stat.ethz.ch/pipermail/r-devel/2011-November/062586.html>.
o New function paste0(), an efficient version of paste(*, sep=""),
to be used in many places for more concise (and slightly more
efficient) code.
o Function setClass() in package methods now returns, invisibly, a
generator function for the new class, slightly preferred to
calling new(), as explained on the setClass help page.
o The "dendrogram" method of str() now takes its default for
last.str from option str.dendrogram.last.
o New simple fitted() method for "kmeans" objects.
o The traceback() function can now be called with an integer
argument, to display a current stack trace. (Wish of PR#14770.)
o setGeneric() calls can be simplified when creating a new generic
function by supplying the default method as the def argument.
See ?setGeneric.
o serialize() has a new option xdr = FALSE which will use the
native byte-order for binary serializations. In scenarios where
only little-endian machines are involved (these days, close to
universal) and (un)serialization takes an appreciable amount of
time this may speed up noticeably transferring data between
systems.
o The internal (un)serialization code is faster for long vectors,
particularly with XDR on some platforms. (Based on a suggested
patch by Michael Spiegel.)
o For consistency, circles with zero radius are omitted by points()
and grid.circle(). Previously this was device-dependent, but
they were usually invisible.
o NROW(x) and NCOL(x) now work whenever dim(x) looks appropriate,
e.g., also for more generalized matrices.
o PCRE has been updated to version 8.30.
o The internal R_Srcref variable is now updated before the browser
stops on entering a function. (Suggestion of PR#14818.)
o There are 'bare-bones' functions .colSums(), .rowSums(),
.colMeans() and .rowMeans() for use in programming where ultimate
speed is required.
o The formerly internal function .package_dependencies() from
package tools for calculating (recursive) (reverse) dependencies
on package databases has been renamed to package_dependencies()
and is now exported.
o There is a new function optimHess() to compute the (approximate)
Hessian for an optim() solution if hessian = TRUE was forgotten.
o .filled.contour() is a 'bare-bones' function to add a
filled-contour rectangular plot to an already prepared plot
region.
o The stepping in debugging and single-step browsing modes has
changed slightly: now left braces at the start of the body are
stepped over for if statements as well as for for and while
statements. (Wish of PR#14814.)
o library() no longer warns about a conflict with a function from
package:base if the function has the same code as the base one
but with a different environment. (An example is Matrix::det().)
o When deparsing very large language objects, as.character() now
inserts newlines after each line of approximately 500 bytes,
rather than truncating to the first line.
o New function rWishart() generates Wishart-distributed random
matrices.
o Packages may now specify actions to be taken when the package is
loaded (setLoadActions()).
o options(max.print = Inf) and similar now give an error (instead
of warnings later).
o The "difftime" replacement method of units tries harder to
preserve other attributes of the argument. (Wish of PR#14839.)
o poly(raw = TRUE) no longer requires more unique points than the
degree. (Requested by John Fox.)
PACKAGE parallel:
o There is a new function mcmapply(), a parallel version of
mapply(), and a wrapper mcMap(), a parallel version of Map().
o A default cluster can be registered by the new function
setDefaultCluster(): this will be used by default in functions
such as parLapply().
o clusterMap() has a new argument .scheduling to allow the use of
load-balancing.
o There are new load-balancing functions parLapplyLB() and
parSapplyLB().
o makePSOCKCluster() has a new option useXDR = FALSE which can be
used to avoid byte-shuffling for serialization when all the nodes
are known to be little-endian (or all big-endian).
PACKAGE INSTALLATION:
o Non-ASCII vignettes without a declared encoding are no longer
accepted.
o C/C++ code in packages is now compiled with -NDEBUG to mitigate
against the C/C++ function assert being called in production use.
Developers can turn this off during package development with
PKG_CPPFLAGS = -UNDEBUG.
o R CMD INSTALL has a new option --dsym which on Mac OS X (Darwin)
dumps the symbols alongside the .so file: this is helpful when
debugging with valgrind (and especially when installing packages
into R.framework). [This can also be enabled by setting the
undocumented environment variable PKG_MAKE_DSYM, since R 2.12.0.]
o R CMD INSTALL will test loading under all installed
sub-architectures even for packages without compiled code, unless
the flag --no-multiarch is used. (Pure R packages can do things
which are architecture-dependent: in the case which prompted
this, looking for an icon in a Windows R executable.)
o There is a new option install.packages(type = "both") which tries
source packages if binary packages are not available, on those
platforms where the latter is the default.
o The meaning of install.packages(dependencies = TRUE) has changed:
it now means to install the essential dependencies of the named
packages plus the Suggests, but only the essential dependencies
of dependencies. To get the previous behaviour, specify
dependencies as a character vector.
o R CMD INSTALL --merge-multiarch is now supported on OS X and
other Unix-alikes using multiple sub-architectures.
o R CMD INSTALL --libs-only now by default does a test load on
Unix-alikes as well as on Windows: suppress with --no-test-load.
UTILITIES:
o R CMD check now gives a warning rather than a note if it finds
inefficiently compressed datasets. With bzip2 and xz compression
having been available since R 2.10.0, it only exceptionally makes
sense to not use them.
The environment variable _R_CHECK_COMPACT_DATA2_ is no longer
consulted: the check is always done if _R_CHECK_COMPACT_DATA_ has
a true value (its default).
o Where multiple sub-architectures are to be tested, R CMD check
now runs the examples and tests for all the sub-architectures
even if one fails.
o R CMD check can optionally report timings on various parts of the
check: this is controlled by environment variable
_R_CHECK_TIMINGS_ documented in 'Writing R Extensions'. Timings
(in the style of R CMD BATCH) are given at the foot of the output
files from running each test and the R code in each vignette.
o There are new options for more rigorous testing by R CMD check
selected by environment variables - see the 'Writing R
Extensions' manual.
o R CMD check now warns (rather than notes) on undeclared use of
other packages in examples and tests: increasingly people are
using the metadata in the DESCRIPTION file to compute information
about packages, for example reverse dependencies.
o The defaults for some of the options in R CMD check (described in
the 'R Internals' manual) have changed: checks for unsafe and
.Internal() calls and for partial matching of arguments in R
function calls are now done by default.
o R CMD check has more comprehensive facilities for checking
compiled code and so gives fewer reports on entry points linked
into .so/.dll files from libraries (including C++ and Fortran
runtimes).
Checking compiled code is now done on FreeBSD (as well as the
existing supported platforms of Linux, Mac OS X, Solaris and
Windows).
o R CMD build has more options for --compact-vignettes: see R CMD
build --help.
o R CMD build has a new option --md5 to add an MD5 file (as done by
CRAN): this is used by R CMD INSTALL to check the integrity of
the distribution.
If this option is not specified, any existing (and probably
stale) MD5 file is removed.
DEPRECATED AND DEFUNCT:
o R CMD Rd2dvi is now defunct: use R CMD Rd2pdf.
o Options such --max-nsize, --max-vsize and the function
mem.limits() are now defunct. (Options --min-nsize and
--min-vsize remain available.)
o Use of library.dynam() without specifying all the first three
arguments is now disallowed.
Use of an argument chname in library.dynam() including the
extension .so or .dll (which was never allowed according to the
help page) is defunct. This also applies to
library.dynam.unload() and to useDynLib directives in NAMESPACE
files.
o The internal functions .readRDS() and .saveRDS() are now defunct.
o The off-line help() types "postscript" and "ps" are defunct.
o Sys.putenv(), replaced and deprecated in R 2.5.0, is finally
removed.
o Some functions/objects which have been defunct for five or more
years have been removed completely. These include .Alias(),
La.chol(), La.chol2inv(), La.eigen(), Machine(), Platform(),
Version, codes(), delay(), format.char(), getenv(), httpclient(),
loadURL(), machine(), parse.dcf(), printNoClass(), provide(),
read.table.url(), restart(), scan.url(), symbol.C(), symbol.For()
and unix().
o The ENCODING argument to .C() is deprecated. It was intended to
smooth the transition to multi-byte character strings, but can be
replaced by the use of iconv() in the rare cases where it is
still needed.
INSTALLATION:
o Building with a positive value of --with-valgrind-instrumentation
now also instruments logical, complex and raw vectors.
C-LEVEL FACILITIES:
o Passing R objects other than atomic vectors, functions, lists and
environments to .C() is now deprecated and will give a warning.
Most cases (especially NULL) are actually coding errors. NULL
will be disallowed in future.
.C() now passes a pairlist as a SEXP to the compiled code. This
is as was documented, but pairlists were in reality handled
differently as a legacy from the early days of R.
o call_R and call_S are deprecated. They still exist in the
headers and as entry points, but are no longer documented and
should not be used for new code.
BUG FIXES:
o str(x, width) now obeys its width argument also for function
headers and other objects x where deparse() is applied.
o The convention for x %/% 0L for integer-mode x has been changed
from 0L to NA_integer_. (PR#14754)
o The exportMethods directive in a NAMESPACE file now exports S4
generics as necessary, as the extensions manual said it does.
The manual has also been updated to be a little more informative
on this point.
It is now required that there is an S4 generic (imported or
created in the package) when methods are to be exported.
o Reference methods cannot safely use non-exported entries in the
namespace. We now do not do so, and warn in the documentation.
o The namespace import code was warning when identical S4 generic
functions were imported more than once, but should not (reported
by Brian Ripley, then Martin Morgan).
o merge() is no longer allowed (in some ways) to create a data
frame with duplicate column names (which confused PR#14786).
o Fixes for rendering raster images on X11 and Windows devices when
the x-axis or y-axis scale is reversed.
o getAnywhere() found S3 methods as seen from the utils namespace
and not from the environment from which it was called.
o selectMethod(f, sig) would not return inherited group methods
when caching was off (as it is by default).
o dev.copy2pdf(out.type = "cairo") gave an error. (PR#14827)
o Virtual classes (e.g., class unions) had a NULL prototype even if
that was not a legal subclass. See ?setClassUnion.
o The C prototypes for zdotc and zdotu in R_ext/BLAS.h have been
changed to the more modern style rather than that used by f2c.
(Patch by Berwin Turlach.)
o isGeneric() produced an error for primitives that can not have
methods.
o .C() or .Fortran() had a lack-of-protection error if the
registration information resulted in an argument being coerced to
another type.
o boxplot(x=x, at=at) with non finite elements in x and non integer
at could not generate a warning but failed.
o heatmap(x, symm=TRUE, RowSideColors=*) no longer draws the colors
in reversed order.
o predict(<ar>) was incorrect in the multivariate case, for p >= 2.
o print(x, max=m) is now consistent when x is a "Date"; also the
"reached ... max.print .." messages are now consistently using
single brackets.
o Closed the <li> tag in pages generated by Rd2HTML(). (PR#14841.)
o Axis tick marks could go out of range when a log scale was used.
(PR#14833.)
o Signature objects in methods were not allocated as S4 objects
(caused a problem with trace() reported by Martin Morgan).
Upstream changes:
0.15 9 December 2012
- Lots of internal changes to Ei, li, Zeta, and R functions:
- Native Zeta and R have slightly more accurate results.
- For bignums, use Math::MPFR if possible. MUCH faster.
Also allows extended precision while still being fast.
- Better accuracy for standard bignums.
- All four functions do:
- XS if native input.
- MPFR to whatever accuracy is desired, if Math::MPFR installed.
- BigFloat versions if no MPFR and BigFloat input.
- standard version if no MPFR and not a BigFloat.
- Add tests for primorial, jordan_totient, and divisor_sum.
- Revamp of the random_prime internals. Also fixes some issues with
random n-bit and maurer primes.
- The random prime and primorial functions now will return a Math::BigInt
object if the result is greater than the native size. This includes
loading up the Math::BigInt library if necessary.
Notable changes in FriCAS 1.1.8 (compared to version 1.1.7):
- Improvements of pattern matching integrator, it can now integrate
in terms of Fresnel integrals and better handles integrals in terms
of Si and Ci.
- Better integration of symbolic derivatives.
- Better normalization of Liouvillian functions.
- New package for computing limits using Gruntz algorithm.
- Faster removal of roots from denominators.
- New domains for mutivariate Ore algebras and partial differential
operators.
- New package for noncommutative Groebner bases.
- New domain for univariate power series with arbitrary exponents.
- New special functions: Shi and Chi.
- New package for noncommutative Groebner bases.
- New domain for univariate power series with arbitrary exponents.
- New special functions: Shi and Chi.
- Several aggregates (in particular tables) allow more general
parameter types.
- New domain for hash tables using equality from underlying
domain.
Bug fixes, in particular:
- Fixed problem with gcd failing due to bad reduction.
- Fixed series of 'acot' and Puiseux series of several special functions.
- Fixed wrong factorization of differential operators.
- Fixed build problem on recent Mac OS X.
Notable changes in FriCAS 1.1.7 (compared to version 1.1.6):
- Improved integration in terms of special functions.
- Updated new graphics framework and graph theory package.
- Added routines for numerical evaluation of several special
functions.
- Added modular method for computing polynomial gcd over algebraic extensions.
- Derivatives of fresnelC and fresnelS are changed to agree
with established convention.
- When printing floats groups of digits are now separated by
underscores (previously were separated by spaces).
- Added C code for removing directories, this speeds up full
build and should avoid build problems on Mac OSX.
Bug fixes, in particular:
- Series expansion now handle poles of Gamma.
- Fixed derivatives of meijerG.
Upstream changes:
Release Notes for 0.7.2New Page Edit Page Page History
These are the release notes for SymPy 0.7.2. SymPy 0.7.2 was released on October 16, 2012.
Major Changes
Python 3 support
SymPy now supports Python 3. The officially supported versions are 3.2 and 3.3, but 3.1 should also work in a pinch. The Python 3-compatible tarballs will be provided separately, but it is also possible to download Python 2 code and convert it manually, via the bin/use2to3 utility. See the README for more
PyPy support
All SymPy tests pass in recent nightlies of PyPy, and so it should have full support as of the next version after 1.9.
Combinatorics
A new module called Combinatorics was added which is the result of a successful GSoC project. It attempts to replicate the functionality of Combinatorica and currently has full featured support for Permutations, Subsets, Gray codes and Prufer codes.
In another GSoC project, facilities from computational group theory were added to the combinatorics module, mainly following the book "Handbook of computational group theory". Currently only permutation groups are supported. The main functionalities are: basic properties (orbits, stabilizers, random elements...), the Schreier-Sims algorithm (three implementations, in increasing speed: with Jerrum's filter, incremental, and randomized (Monte Carlo)), backtrack searching for subgroups with certain properties.
Definite Integration
A new module called meijerint was added, which is also the result of a successful GSoC project. It implements a heuristic algorithm for (mainly) definite integration, similar to the one used in Mathematica. The code is automatically called by the standard integrate() function. This new algorithm allows computation of important integral transforms in many interesting cases, so helper functions for Laplace, Fourier and Mellin transforms were added as well.
Random Variables
A new module called stats was added. This introduces a RandomSymbol type which can be used to model uncertainty in expressions.
Matrix Expressions
A new matrix submodule named expressions was added. This introduces a MatrixSymbol type which can be used to describe a matrix without explicitly stating its entries. A new family of expression types were also added: Transpose, Inverse, Trace, and BlockMatrix. ImmutableMatrix was added so that explicitly defined matrices could interact with other SymPy expressions.
Sets
A number of new sets were added including atomic sets like FiniteSet, Reals, Naturals, Integers, UniversalSet as well as compound sets like ProductSet and TransformationSet. Using these building blocks it is possible to build up a great variety of interesting sets.
Classical Mechanics
A physics submodule named machanics was added which assists in formation of equations of motion for constrained multi-body systems. It is the result of 3 GSoC projects. Some nontrivial systems can be solved, and examples are provided.
Quantum Mechanics
Density operator module has been added. The operator can be initialized with generic Kets or Qubits. The Density operator can also work with TensorProducts as arguments. Global methods are also added that compute entropy and fidelity of states. Trace and partial-trace operations can also be performed on these density operators.
To enable partial trace operations a Tr module has been added to the core library. While the functionality should remain same, this module is likely to be relocated to an alternate folder in the future. One can currently also use sympy.core.Tr to work on general trace operations, but this module is what is needed to work on trace and partial-trace operations on any sympy.physics.quantum objects.
The Density operators, Tr and Partial trace functionality was implemented as part of student participation in GSoC 2012
Expanded angular momentum to include coupled-basis states and product-basis states. Operators can also be treated as acting on the coupled basis (default behavior) or on one component of the tensor product states. The methods for coupling and uncoupling these states can work on an arbitrary number of states. Representing, rewriting and applying states and operators between bases has been improved.
Commutative Algebra
A new module agca was started which seeks to support computations in commutative algebra (and eventually algebraic geometry) in the style of Macaulay2 and Singular. Currently there is support for computing Groebner bases of modules over a (generalized) polynomial ring over a field. Based on this, there are algorithms for various standard problems in commutative algebra, e.g., computing intersections of submodules, equality tests in quotient rings, etc....
Plotting Module
A new plotting module has been added which uses Matplotlib as its back-end. The plotting module has functions to plot the following:
2D line plots
2D parametric plots.
2D implicit and region plots.
3D surface plots.
3D parametric surface plots.
3D parametric line plots.
Differential Geometry
Thanks to a GSoC project the beginning of a new module covering the theory of differential geometry was started. It can be imported with sympy.diffgeom. It is based on "Functional Differential Geometry" by Sussman and Wisdom. Currently implemented are scalar, vector and form fields over manifolds as well as covariant and other derivatives.
Upstream changes:
0.14 29 November 2012
- Compilation and test issues:
Fix compilation on NetBSD
Try to fix compilation on Win32 + MSVC
Speed up some testing, helps a lot with Cygwin on slow machines
Speed up a lot of slow PP areas, especially used by test suite
- XS AKS extended from half-word to full-word.
- Add functions:
jordan_totient generalization of Euler Totient
divisor_sum run coderef for every divisor
- Allow environment variables MPU_NO_XS and MPU_NO_GMP to turn off XS and
GMP support respectively if they are defined and equal to 1.
- Lehmer prime count for Pure Perl code, including use in nth_prime.
prime count 10^9 using sieve:
71.9s PP sieve
0.47s XS sieve
prime count 10^9 using Lehmer:
0.70s PP lehmer
0.03s XS lehmer
- Moved bignum Zeta and R to separate file, only loaded when needed.
Helpful to get the big rarely-used tables out of the main loading.
- Quote arguments to Math::Big{Int,Float} in a few places it wasn't.
Math::Big* coerces the input to a signed value if it isn't a string,
which causes us all sorts of grief.
0.13 19 November 2012
- Fix an issue with prime count, and make prime count available as a
standalone program using primesieve.
0.12 17 November 2012
- Add bin/primes.pl and bin/factor.pl
- Add functions:
primorial product of primes <= n
pn_primorial product of first n primes
prime_set_config set config options
RiemannZeta export and make accurate for small reals
is_provable_prime prove primes after BPSW
is_aks_prime prove prime via AKS
- Add 'assume_rh' configuration option (default: false) which can be set
to allow functions to assume the Riemann Hypothesis.
- Use the Schoenfeld bound for Pi(x) (x large) if assume_rh is true.
- valgrind testing
- Use long doubles for math functions.
- Some fixes and speedups for ranged primes().
- In the PP code, use 2 MR bases for more numbers when possible.
- Fixup of racing SQUFOF, and switch to use it in factor().
- Complete rewrite of XS p-1 factor routine, includes second stage.
- bug fix for prime_count on edge of cache.
- prime_count will use Lehmer prime counting algorithm for largish
sizes (above 4 million). This is MUCH faster than sieving.
- nth_prime now uses the fast Lehmer prime count below the lower limit,
then sieves up from there. This makes a big speed difference for inputs
over 10^6 or so -- over 100x faster for 10^9 and up.
Upstream changes:
Changes in Version 1.7-9
o Added ggplot2 interface through autplot() and fortify() methods. Also
support function facet_free().
Changes in Version 1.7-8
o Added rollsum.
o Bugfix in src/lag.c for the case of k > NROW.
* Fix deadlock bug in MPI transforms (thanks to Michael Pippig for the
bug report and patch, and to Graham Dennis for the bug report).
* Use 128-bit ARM NEON instructions instead of 64-bits. This change
appears to speed up even ARM processors with a 64-bit NEON pipe.
* Speed improvements for single-precision AVX.
* Speed up planner on machines without "official" cycle counters, such as ARM.
pandas is an open source, BSD-licensed library providing
high-performance, easy-to-use data structures and data analysis tools
for the Python programming language.
Upstream changes:
Version 2.01 - 24 October 2012 (bug fix release)
* Fixed error in electronmass
* New definition for au
* Fixed DESTDIR support for installation
* Changed configure script for success with Solaris
* Small changes to manual
* Fix error reporting not working for certain types of error
* Add shadow around display
* Remove reference to removed source file
* Replace lex/bison parser with hand-written parser
* Use g_warning not g_error when unable to parse currency file
* Set window icon correctly
* Port to GtkApplication
* Replace menubar with a GMenu
* Only show thousands separators in decimal mode
* Translation updates
(unimpressed by https://bugzilla.gnome.org/show_bug.cgi?id=670098)
Changes in 5.1.23
Bug fixes
* [ES] removed *86 specific optimizations (rep. #2154)
* [ES] renamed RMS per cent error -> relative error (rep. #2192)
* [ES] a workaround for a bug in recent Xorg not releasing grab of popup menus
* [ES] accept -graphtype chart instead of bar. List possible values in the
help output
* [TK] fix building against png-1.5
* [SM] a grace_np fix
* [ES] IsoLatin5.enc was not included in the distribution
math/p5-Math-Prime-Util.
A set of utilities related to prime numbers. These include multiple sieving
methods, is_prime, prime_count, nth_prime, approximations and bounds for
the prime_count and nth prime, next_prime and prev_prime, factoring
utilities, and more.
