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
