0.79 - 29 Aug 2018, H.Merijn Brand
* Environmant control hardening
* ReadData () docs (opening from scalar ref: issue#21)
* Check for XLSX content on opening from plain scalar content
* Fix typo in ss-dup-tk.pl (PRC, Branislav Zahradnik)
* Allow source from command line option in xls2csv (PRC, Branislav Zahradnik)
* Allow --in-sep=tab in xlscat/xlsgrep
* Add --hash to xlscat/xlsgrep
* Help and usage for examples/xls2csv PR#23)
0.71 2018-08-28
[ADDED]
- forfactored { ... } a,b loop n=a..b setting $_=n, @_=factor(n)
- forsquarefree { ... } a,b as forfactored, but only square-free n
- forsemiprimes { ... } a,b as forcomposites, but only semiprimes
- random_factored_integer(n) random [1..n] w/ array ref of factors
- semiprime_count([lo],hi) counts semiprimes in range
[FIXES]
- Monolithic sieves beyond 30*2^32 (~ 1.2 * 10^11) overflowed.
- is_semiprime was wrong for five small values since 0.69. Fixed.
[FUNCTIONALITY AND PERFORMANCE]
- is_primitive_root much faster (doesn't need to calulate totient,
and faster rejection when n has no primitive root).
- znprimroot and znorder use Montgomery, 1.2x to 2x faster.
- slightly faster sieve_range for native size inputs (use factor_one).
- bin/primes.pl faster for palindromic primes and works for 10^17
[OTHER]
- Added ability to use -DBENCH_SEG for benchmarking sieves using
prime_count and ntheory::_segment_pi without table optimizations.
- Reorg of main factor loop. Should be identical from external view.
- Internal change to is_semiprime and is_catalan_pseudoprime.
Upstream changes:
Version 0.4-91
Fixed a bug in heatmap.circular
Version 0.4-8 2014/08/08
minusPiPlusPi now accepts missing values
Added the start.sep argument to plot.circular and points.circular. Also the internal function PointsCircularRad has changed the API.
Upstream changes:
Changes in version 1.0-8 (2018-05-31)
o pmvt(..., sigma = ) was ignored in the univariate case
(reported by Alec Stephenson)
o documentation updates
Changes in version 1.0-7 (2018-01-25)
o pmvt(..., df = ) is scalar only
Upstream changes:
1.8-3 (2018-08-29)
* Changed listOfTablesGallery vignette to exclude references to
lsmeans since Russell Lenth has deprecated lsmeans, replacing it
with emmeans which has support for tables using xtable based on
listOfTables. lsmeans removed from Suggests in DESCRIPTION also.
* Changed OtherPackagesGallery vignette example using the function
impacts from spdep due to a change in the package spdep causing a
failure ofr the example using gstslshet from sphet
* Changed error messages to extract actual value of nrow(x),
suggestion by Michael Chirico <michaelchirico4@gmail.com>
* Corrected author field to properly represent author contributions,
code supplied by Arni Magnusson <arnima@hafro.is>
* Corrected call to print.xtable inside print.xtableFtable included
arguments from call to print.xtableFtable. Absence of size
argument was advised by Lluis Ramon, email March 4, 2016
* Added patch from Martin Gubri, martin.gubri@framasoft.org to
enable use of lagImpactMat from spdep in xtable method lagImpact.
* Added patch to code in OtherPackagesGallery.Rnw supplied by Martin
Gubri to avoid warnings in the spdep package example. Also fixed the
vignette index entry.
* Fixed number of columns in \multicolumn command in print.xtableList to
deal with inclusion of row names. Previously was only appropriate for
row names not included.
Upstream changes:
Changed in xts 0.11-0:
o Fix make.index.unique() to always return a unique and sorted index. Thanks
to Chris Katsulis for the report and example (#241).
o Add window.xts() method and completely refactor the internal binary search
function it depends on. Thanks to Corwin Joy for the PR, tests, review, and
patience (#100, #240).
o Better axis tick mark locations for plots. Thanks to Dirk Eddelbuettel for
the report (#246). Also incorporate axTicksByTime2() into axTicksByTime() to
reduce code duplication from the migration of quantmod::chart_Series() to
xts::plot.xts() (#74).
o Add details to plot.xts() parameters that are periodicity, now that RStudio
has argument completion. Thanks to Evelyn Mitchell for the PR (#154).
o periodicity() now warns instead of errors if the xts object contains less
than 2 observations (#230).
o first() and last() now keep dims when they would otherwise be dropped by a
regular row subset. This is consistent with head() and tail(). Thanks to
Davis Vaughan for the report (#226).
o Fix subset when ISO8601 string is outside the valid range, so it returns no
data instead of all rows (#96).
o Avoid partial name matches from parse.side() (inside .parseISO8601())
results that are passed to firstof() and lastof(). Thanks to @gp2x for the
report and the patch (#231).
o na.locf.xts() now loops over columns of multivariate objects in C code,
instead of in R. This should improve speed and memory performance. Thanks to
Chris Katsulis and Tom Andrews for their reports and patches (#232, #233,
#234, #235, #237).
o Change plot.xts() default 'pch = 0' (rectangles) to 'pch = 1' (circles) so
it looks more like base and zoo plots (#203).
Changed in xts 0.10-2:
o na.locf.xts() and na.omit.xts() now support character xts objects. Thanks to
Ken Williams and Samo Pahor for the reports (#42).
o na.locf.xts() now honors 'x' and 'xout' arguments by dispatching to the next
method (#215). Thanks to Morten Grum for the report.
o coredata.xts() now functions the same as coredata.zoo() on zero-length
objects, and only removes xts-related attributes (#223). Thanks to Vincent
Guyader for the report.
o plot.xts() no longer ignores 'col.up' and 'col.dn' when 'type="h"' (#224).
Thanks to Charlie Friedemann for the report. This was inadvertently broken
as part of the fix for #210.
Changes from 2.6.7 to 2.6.8
---------------------------
- Add check to make sure that f_locals is not actually f_globals when we
do the f_locals clear to avoid the 310 memory leak issue.
- Compare NumPy versions using distutils.version.LooseVersion to avoid issue
312 when working with NumPy development versions.
- As part of multibuild, wheels for Python 3.7 for Linux and MacOSX are now
available on PyPI
Version 0.39.0
Here are the highlights for the Numba 0.39.0 release.
This is the first version that supports Python 3.7.
With help from Intel, we have fixed the issues with SVML support.
List has gained support for containing reference-counted types like NumPy arrays and list. Note, list still cannot hold heterogeneous types.
We have made a significant change to the internal calling-convention, which should be transparent to most users, to allow for a future feature that will permitting jumping back into python-mode from a nopython-mode function. This also fixes a limitation to print that disabled its use from nopython functions that were deep in the call-stack.
For CUDA GPU support, we added a __cuda_array_interface__ following the NumPy array interface specification to allow Numba to consume externally defined device arrays. We have opened a corresponding pull request to CuPy to test out the concept and be able to use a CuPy GPU array.
The Numba dispatcher inspect_types() method now supports the kwarg pretty which if set to True will produce ANSI/HTML output, showing the annotated types, when invoked from ipython/jupyter-notebook respectively.
The NumPy functions ndarray.dot, np.percentile and np.nanpercentile, and np.unique are now supported.
Numba now supports the use of a per-project configuration file to permanently set behaviours typically set via NUMBA_* family environment variables.
Support for the ppc64le architecture has been added.
NumPy 1.15.1:
This is a bugfix release for bugs and regressions reported following the 1.15.0
release.
* The annoying but harmless RuntimeWarning that "numpy.dtype size changed" has
been suppressed. The long standing suppression was lost in the transition to
pytest.
* The update to Cython 0.28.3 exposed a problematic use of a gcc attribute used
to prefer code size over speed in module initialization, possibly resulting in
incorrect compiled code. This has been fixed in latest Cython but has been
disabled here for safety.
* Support for big-endian and ARMv8 architectures has been improved.
The Python versions supported by this release are 2.7, 3.4-3.7. The wheels are
linked with OpenBLAS v0.3.0, which should fix some of the linalg problems
reported for NumPy 1.14.
1.14 2018-06-25 05:29:49 -0400
- Production release identical to 1.12_01
1.12_01 2018-06-25 03:34:28 +0000
- Remove dependency on Alien::Role::Alt
This Role is no longer necessary, as the capability of that role
has been merged into the Alien::Build core.
The purpose of this perl module is to calculate the median (or in
principle also other statistics) with confidence intervals on a sample.
To do that, it uses a technique called bootstrapping. In a nutshell, it
resamples the sample a lot of times and for each resample, it calculates
the median. From the distribution of medians, it then calculates the
confidence limits.
This perl class is a container class for numbers with a number of
associated symmetric and asymmetric errors. It overloads practically
all common arithmetic operations and trigonometric functions to
propagate the errors. It can do proper scientific rounding.
Upstream changes:
1.12
26 Jun 2018
- Typo found by Florian Schlichting fixed.
- Add gcd() and lcm() functions.
- New example scripts (a couple transferred over from
Math::Polynomial::Solve) in the new eg/ directory.
Gnumeric 1.12.42
Morten:
* Plug leaks.
* Introspection fixes.
* Work around gtk+ breakage re. link colors.
* Fix problems with ssconvert --export-file-per-sheet. [#694408]
* Enable ssconvert --export-file-per-sheet for html, latex, and pdf.
* Test suite improvements.
* ssconvert improvements.
* Makefile improvements.
* Don't save any configuration when running ssconvert/ssdiff/...
* Turn GnmFunc into a GObject.
* Make clipboard output deterministic.
* Fix conditional format crash [#343].
We provide easy to configure, lightweight open source C++, Java,
JavaScript, Python libraries and a LibreOffice Spreadsheet extension
for number to number name conversion, including cardinal and ordinal
numbers, ordinal indicators and money amounts with currencies in
more than 40 languages and numeral systems.
Changes from 2.6.6 to 2.6.7
* Thanks to Lehman Garrison for finding and fixing a bug that exhibited memory leak-like behavior. The use in numexpr.evaluate of sys._getframe combined with .f_locals from that frame object results an extra refcount on objects in the frame that calls numexpr.evaluate, and not evaluate’s frame. So if the calling frame remains in scope for a long time (such as a procedural script where numexpr is called from the base frame) garbage collection would never occur.
* Imports for the numexpr.test submodule were made lazy in the numexpr module.
Remove hack that had a high chance of resulting in a dysfunctional package
qttools can't be a build dependency because we link against something
in it.
XXX pkgsrc claims this package has work directory references
Summary of important user-visible changes for version 4.4 (2018-04-30):
----------------------------------------------------------------------
** A graphical Variable Editor has been added to the GUI interface.
It uses a spreadsheet-like interface for quick, intuitive editing
of variables. The Variable Editor is launched by double-clicking
on a variable name in the Workspace Window or by typing
"openvar VARIABLE_NAME" in the Command Window.
** On systems with 64-bit pointers, --enable-64 is now the default and
Octave always uses 64-bit indexing. However, if the configure
script determines that the BLAS library uses 32-bit integers, then
operations using the following libraries are limited to arrays with
dimensions that are smaller than 2^31 elements:
BLAS LAPACK QRUPDATE SuiteSparse ARPACK
Additionally, the following libraries use "int" internally, so
maximum problem sizes are always limited:
glpk Qhull
** The octave command no longer starts the GUI by default. Most users
starting Octave from a shell were expecting the command line
interface, and desktop launchers already required the `--force-gui'
option. With this change, desktop launchers should be modified to
use the new option `--gui'. The previous `--force-gui' option will
continue to work, and maps to `--gui', but it will be removed in
Octave 6.
** A known bug in Qt (https://bugreports.qt.io/browse/QTBUG-55357) is
addressed by limiting GUI sub-panel relocation capabilities for Qt
versions in the range >= 5.6.1 and < 5.7.1. However, this may not
thoroughly avoid issues on all platforms.
** A new container data type--containers.Map--is available. Map is a
key/value storage container (a.k.a, a hash) that efficiently allows
storing and retrieving values by name, rather than by position which
is how arrays work.
** The bareword "import" is now recognized in scripts and functions.
However, the functionality to import functions and classes from
other namespaces into the local scope has not yet been implemented.
Attempting to use "import" will provoke an error message.
** hex2num and num2hex now work for integer and char types and num2hex
may optionally return a cell array of strings instead of a character
array. If given a cell array of strings, hex2num now returns a
numeric array of the same size as the input cell array. Previously,
hex2num would accept a cell array of strings of arbitrary dimension
but would always return a column vector.
** New special functions cosint, sinint, and gammaincinv have been added.
** Special functions in Octave have been rewritten for larger input
domains, better accuracy, and additional options.
* gammainc now accepts negative real values for X.
* improved accuracy for gammainc, betainc, betaincinv, expint.
* gammainc has new options "scaledlower" and "scaledupper".
* betainc, betaincinv have new option "upper".
** The "names" option used in regular expressions now returns a struct
array, rather than a struct with a cell array for each field. This
change was made for Matlab compatibility.
** The quadcc function now uses both absolute tolerance and relative
tolerance to determine the stopping criteria for an integration.
To be compatible with other quadXXX functions, such as quadgk, the
calling syntax has changed to
quadcc (f, a, b, [AbsTol, [RelTol]])
To update existing code, change instances of RelTol to [0, RelTol].
quadcc (f, a, b, tol) => quadcc (f, a, b, [0, tol])
A warning that a single tolerance input is now interpreted as an
absolute tolerance will be issued in Octave versions 4.4 and 5,
after which it will be removed. The warning has ID
"Octave:quadcc:RelTol-conversion" and can be disabled with
warning ("off", "Octave:quadcc:RelTol-conversion")
** The qr function now returns a standard factorization unless
explicitly instructed to perform an economy factorization by using a
final argument of 0.
** The Qt graphics toolkit now supports offscreen printing without osmesa
if Octave was built with Qt >= 5.1.
** The built-in pager for display of large data is now disabled by
default. To re-enable it for every Octave session add the following
to your .octaverc file:
more on;
** The FLTK toolkit is no longer prioritized for development. The
number of Octave Maintainers is too small to support three different
graphic toolkits. New development will target the Qt toolkit.
While no longer prioritized, the FLTK toolkit is not deprecated and
there is no schedule for its removal.
** The graphic object property "PickableParts" has been implemented
which controls whether an object can accept mouse clicks.
** The graphic object property "Interruptible" has been fully
implemented which controls whether a running callback function can
be interrupted by another callback function.
** The graphic object property "HitTest" has been updated to be fully
compatible with Matlab.
** Text objects now implement the properties "BackgroundColor",
"EdgeColor", "LineStyle", "LineWidth", and "Margin".
** An initial implementation of alpha transparency has been made for
patch and surface objects. Printing to svg and pdf is supported.
** ishandle now returns true for both graphics handle objects and
Java objects. The latter change was made for Matlab compatibility.
Use ishghandle or isgraphics if it is important not to include Java
objects.
** The pkg command now accepts a URL as an argument, allowing a valid
Octave package to be installed from any remote host with one command,
for example
pkg install https://example.org/download/example-package.tar.gz
** The following statistical functions have been moved from core
Octave to the statistics package available from Octave Forge.
BASE
cloglog
logit
prctile
probit
qqplot
table (renamed to crosstab)
DISTRIBUTIONS
betacdf
betainv
betapdf
betarnd
binocdf
binoinv
binopdf
binornd
cauchy_cdf
cauchy_inv
cauchy_pdf
cauchy_rnd
chi2cdf
chi2inv
chi2pdf
chi2rnd
expcdf
expinv
exppdf
exprnd
fcdf
finv
fpdf
frnd
gamcdf
gaminv
gampdf
gamrnd
geocdf
geoinv
geopdf
geornd
hygecdf
hygeinv
hygepdf
hygernd
kolmogorov_smirnov_cdf
laplace_cdf
laplace_inv
laplace_pdf
laplace_rnd
logistic_cdf
logistic_inv
logistic_pdf
logistic_rnd
logncdf
logninv
lognpdf
lognrnd
nbincdf
nbininv
nbinpdf
nbinrnd
normcdf
norminv
normpdf
normrnd
poisscdf
poissinv
poisspdf
poissrnd
stdnormal_cdf
stdnormal_inv
stdnormal_pdf
stdnormal_rnd
tcdf
tinv
tpdf
trnd
unidcdf
unidinv
unidpdf
unidrnd
unifcdf
unifinv
unifpdf
unifrnd
wblcdf
wblinv
wblpdf
wblrnd
wienrnd
MODELS
logistic_regression
TESTS
anova
bartlett_test
chisquare_test_homogeneity
chisquare_test_independence
cor_test
f_test_regression
hotelling_test
hotelling_test_2
kolmogorov_smirnov_test
kolmogorov_smirnov_test_2
kruskal_wallis_test
manova
mcnemar_test
prop_test_2
run_test
sign_test
t_test
t_test_2
t_test_regression
u_test
var_test
welch_test
wilcoxon_test
z_test
z_test_2
** The following image functions have been moved from core Octave to
the image package available from Octave Forge.
ntsc2rgb
rgb2ntsc
** Other new functions added in 4.4:
bounds
camlookat
camorbit
campos
camroll
camtarget
camup
camva
camzoom
corrcoef
cosint
decic
erase
gammaincinv
getframe
groot
gsvd
hgtransform
humps
integral
integral2
integral3
isgraphics
isstring
mad
ode15i
ode15s
openvar
quad2d
repelem
rgb2gray
rticks
sinint
tfqmr
thetaticks
vecnorm
winqueryreg
xticklabels
xticks
yticklabels
yticks
zticklabels
zticks
** Deprecated functions.
The following functions have been deprecated in Octave 4.4 and will
be removed from Octave 6 (or whatever version is the second major
release after 4.4):
Function | Replacement
---------------------|------------------
chop | sprintf for visual results
desktop | isguirunning
tmpnam | tempname
toascii | double
java2mat | __java2mat__
** The following functions were deprecated in Octave 4.0 and have been
removed from Octave 4.4.
allow_noninteger_range_as_index
bicubic
delaunay3
do_braindead_shortcircuit_evaluation
dump_prefs
find_dir_in_path
finite
fmod
fnmatch
gmap40
loadaudio
luinc
mouse_wheel_zoom
nfields
octave_tmp_file_name
playaudio
saveaudio
setaudio
syl
usage
** The "Octave:undefined-return-values" warning ID is obsolete. Octave
now throws an error for any attempts to assign undefined values that
might be returned from functions.
** Deprecated graphics properties.
The following properties or allowed corresponding values have been
deprecated in Octave 4.4 and will be removed from Octave 6 (or whatever
version is the second major release after 4.4):
Object | Property | Value
---------------------|-------------------------|-------------------
figure | doublebuffer |
| mincolormap |
| wvisual |
| wvisualmode |
| xdisplay |
| xvisual |
| xvisualmode |
axes | drawmode |
annotation | edgecolor ("rectangle") |
text | fontweight | "demi" and "light"
uicontrol | fontweight | "demi" and "light"
uipanel | fontweight | "demi" and "light"
uibuttongroup | fontweight | "demi" and "light"
** The rectangle and ellipse annotation property "edgecolor" has been
deprecated and will be removed from Octave 6 (or whatever version
is the second major release after 4.4). Use the property "color"
instead.
** The header file oct-alloc.h has been removed along with the macros
that it defined (DECLARE_OCTAVE_ALLOCATOR, DEFINE_OCTAVE_ALLOCATOR,
and DEFINE_OCTAVE_ALLOCATOR2).
v0.23.4:
This is a minor bug-fix release in the 0.23.x series and includes some regression fixes, bug fixes, and performance improvements. We recommend that all users upgrade to this version.
NumPy 1.15.0 is a release with an unusual number of cleanups, many deprecations
of old functions, and improvements to many existing functions. Please read the
detailed descriptions below to see if you are affected.
For testing, we have switched to pytest as a replacement for the no longer
maintained nose framework. The old nose based interface remains for downstream
projects who may still be using it.
The Python versions supported by this release are 2.7, 3.4-3.7. The wheels are
linked with OpenBLAS v0.3.0, which should fix some of the linalg problems
reported for NumPy 1.14.
Highlights:
- NumPy has switched to pytest for testing.
- A new numpy.printoptions context manager.
- Many improvements to the histogram functions.
- Support for unicode field names in python 2.7.
- Improved support for PyPy.
- Fixes and improvements to numpy.einsum.
Algorithm
Rewrite of the core int32/avx2 implementation for (1) higher speed and
(2) reduced memory consumption. Stack allocation is now at most a few
kilobytes, even for gigantic arrays.
Internally, the sorting algorithm is now mostly bitonic to simplify
indexing, although odd-even speedups are still applied when
convenient. Lanes are complemented to take the down-up decision out of
the inner loops.
As in previous djbsort versions, data is sorted first in vector lanes
and then transposed for final merges, reducing the overall number of
vector permutations. Unlike previous versions, transposition is done
in-place. The transposition in this version is bit-reversal on the outer
6 bits (bottom 3 bits and the top 3 bits), but leaves intermediate bits
alone. Non-power-of-2 array sizes are handled by an extra, more
traditional, merge step.
Sizes 2, 3, 4, 5, 6, 7, 8, 16, 32 are now special-cased. Non-power-of-2
sizes below 256 are padded to the next power of 2.
Portable implementations: The out-of-place int32/portable1 and
int32/portable2 implementations are now gone; the in-place
int32/portable3 and int32/portable4 implementations remain.
C API
float32_sort is now supported. The arithmetic in the reduction from
float32 to int32 is int32 31-bit right shift, uint32 1-bit right shift,
xor; this is slightly more efficient than the reduction from float32 to
uint32 from 2001 Herf.
Compiling
Tests now have more variation (without much slowdown): the uint32 test
cases now deviate from int32 in more than the sign; float32 uses
floating-point numbers that aren't integers; int32 does more loops for
small cases, and some larger cases.
Internals
API for 2-input sorting is now MINMAX macro operating on two
inputs in place.
Better inline assembly from Jason Donenfeld for 2-input sorting: more
flexibility in compiler's register allocation.
The package version number is now automatically copied to version.c as
the implementation version number for implementations that don't provide
version.c.
Verification
minmax now supports more peephole optimizations for complemented bitonic
sorting and for padding: xor(s,xor(s,t)) ⇒ t; xor(-1,s) ⇒ invert(s);
Reverse(Reverse(s)) ⇒ s; signedmin(invert(s),invert(t)) ⇒
invert(signedmax(s,t)); signedmax(invert(s),invert(t)) ⇒
invert(signedmin(s,t)); invert(s)[high:low] ⇒ invert(s[high:low]);
s[bits-1:0] ⇒ s; s[high:low][high2:low2] ⇒ s[high2+low:low2+low];
Concat(...)[high:low] ⇒ ...[high-pos:low-pos] when possible;
Reverse(s)[high:low] ⇒ Reverse(s[...]) when possible; eliminate
signedmin/signedmax when one input is the minimum or maximum constant.
verifymany now includes the implementation version number on
verified lines.
machine, not on the machine preparing a binary package." (Also: "The
issues are explained in Section 8 of
https://pqcrypto.eu.org/deliverables/d2.4.pdf.")
For this to work, we install the source tree (with built objects) to
${PREFIX}/share/djbsort. Then we run tests, install to ${PREFIX}/include
and ${PREFIX}/lib, and check the installed files against pseudo-PLIST.
This means pkg_add(1) will fail if no C compiler is present, which is
unusual behavior for pkg_add but perhaps not entirely unreasonable for a
C library.
Bump PKGREVISION.
djbsort is a software library for sorting arrays of integers. It
provides the following features:
- Speed: djbsort holds new speed records for in-memory sorting.
- Security: djbsort is designed to be safe for cryptographic contexts.
- Verification: djbsort includes tools to automatically verify correctness.
These features are not separate options: there is a single sorting
function that is simultaneously fast, secure, and verified.
Packaged for wip by schmonz@
Distfiles for older R packges are moved on CRAN from contrib/ to
contrib/Archive/${R_PKGNAME}/. As a result, they may be inaccessible to
'make fetch'. Add the additional directory to MASTER_SITES in
math/R/Makefile.extension so that older distfiles will be retrieved
directly from CRAN. In addition, remove the definition of MASTER_SITES
from math/R-prob/Makefile, which is the only package directly referring to
the distfile archive. At this point all R packages should rely on
math/R/Makefile.extension to define MASTER_SITES; they should not be
defining MASTER_SITES directly.
