Change bl3 to pdflib-lite to fix binary package distribution.
Grace-5.1.25
- killing set data from GUI and scripts now clears set comments
- undid "always overwrite set comments when reading data in" from 5.1.24
- fixed Fourier transform DC-term amplitude (rep. #630)
- newer versions of "make" tried to regenerate documentation (rep. #2240)
Grace-5.1.24
- fixed detection of dynamic loading libraries (rep. # 2238)
- install PDF docs instead of the DVI ones
- added cephes/COPYING (from Debian)
- a workaround for broken input of non-ASCII text under UTF8 locales
- always overwrite set comments when reading data in
==========================
NumPy 1.11.3 Release Notes
==========================
Numpy 1.11.3 fixes a bug that leads to file corruption when very large files
opened in append mode are used in ``ndarray.tofile``. It supports Python
versions 2.6 - 2.7 and 3.2 - 3.5. Wheels for Linux, Windows, and OS X can be
found on PyPI.
Contributors to maintenance/1.11.3
==================================
A total of 2 people contributed to this release. People with a "+" by their
names contributed a patch for the first time.
- Charles Harris
- Pavel Potocek +
Pull Requests Merged
====================
- `#8341 <https://github.com/numpy/numpy/pull/8341>`__: BUG: Fix ndarray.tofile large file corruption in append mode.
- `#8346 <https://github.com/numpy/numpy/pull/8346>`__: TST: Fix tests in PR #8341 for NumPy 1.11.x
Upstream changes:
gtools 3.5.0 - 2015-04-28
-------------------------
New Functions:
- New roman2int() functon to convert roman numerals to integers
without the range restriction of utils::as.roman().
- New asc() and chr() functions to convert between ASCII codes and
characters. (Based on the 'Data Debrief' blog entry for 2011-03-09
at http://datadebrief.blogspot.com/2011/03/ascii-code-table-in-r.html).
- New unByteCode() and unByteCodeAssign() functions to convert a
byte-code functon to an interpeted code function.
- New assignEdgewise() function for making assignments into locked
environments. (Used by unByteCodeAssign().)
Enhacements:
- mixedsort() and mixedorder() now have arguments 'decreasing',
'na.last', and 'blank.last' arguments to control sort ordering.
- mixedsort() and mixedirdeR() now support Roman numerals via the
arguments 'numeric.type', and 'roman.case'. (Request by David
Winsemius, suggested code changes by Henrik Bengtsson.)
- speed up mixedorder() (and hence mixedsort()) by moving
suppressWarnings() outside of lapply loops. (Suggestion by Henrik
Bengtsson.)
- The 'q' argument to quantcut() now accept an integer
indicating the number of equally spaced quantile groups to
create. (Suggestion and patch submitted by Ryan C. Thompson.)
Bug fixes:
- Removed stray browser() call in smartbind().
- ddirichlet(x, alpha) was incorrectly returning NA when for any i,
x[i]=0 and alpha[i]=1. (Bug report by John Nolan.)
Other changes:
- Correct typographical errors in package description.
gtools 3.4.2 - 2015-04-06
-------------------------
New features:
- New function loadedPackages() to display name, version, and path of
loaded packages (package namespaces).
- New function: na.replace() to replace missing values within a
vector with a specified value.`
Bug fixes:
- Modify keywords() to work properly in R 3.4.X and later.
gtools 3.4.1 - 2014-05-27
-------------------------
Bug fixes:
- smartbind() now converts all non-atomic type columns (except factor)
to type character instead of generating an opaque error message.
Other changes:
- the argument to ASCIIfy() is now named 'x' instead of 'string'.
- minor formatting changes to ASCIIfy() man page.
gtools 3.4.0 - 2014-04-14
-------------------------
New features:
- New ASCIIfy() function to converts character vectors to ASCII
representation by escaping them as \x00 or \u0000 codes.
Contributed by Arni Magnusson.
gtools 3.3.1 - 2014-03-01
-------------------------
Bug fixes:
- 'mixedorder' (and hence 'mixedsort') not properly handling
single-character strings between numbers, so that '1a2' was being
handled as a single string rather than being properly handled as
c('1', 'a', '2').
gtools 3.3.0 - 2014-02-11
-------------------------
New features:
- Add the getDependencies() function to return a list of dependencies
for the specified package(s). Includes arguments to control whether
these dependencies should be constructed using information from
locally installed packages ('installed', default is TRUE), avilable
CRAN packages ('available', default is TRUE) and whether to include
base ('base', default=FALSE) and recommended ('recommended', default
is FALSE) packages.
Bug fixes:
- binsearch() was returning the wrong endpoint & value when the found
value was at the upper endpoint.
gtools 3.2.1 - 2014-01-13
-------------------------
Bug fixes:
- Resolve circular dependency with gdata
gtools 3.2.0 - 2014-01-11
-------------------------
New features:
- The keywords() function now accepts a function or function name as
an argument and will return the list of keywords associated with the
named function.
- New function stars.pval() which will generate p-value significance
symbols ('***', '**', etc.)
Bug fixes:
- R/mixedsort.R: mixedorder() was failing to correctly handle numbers
including decimals due to a faulty regular expression.
Other changes:
- capture() and sprint() are now defunct.
gtools 3.1.1 - 2013-11-06
-------------------------
Bug fixes:
- Fix problem with mixedorder/mixedsort when there is zero or one
elements in the argument vector.
gtools 3.1.0 - 2013-09-22
-------------------------
Major changes:
- The function 'addLast()' (deprecated since gtools 3.0.0) is no
longer available, and has been marked defunct.
Bug fixes:
- Modified 'mixedorder()' to use Use 'suppressWarnings() instead of
'options(warn=-1)'. This will avoid egregious warning messages when
called from within a nested environment, such as when run from
within 'knitr'
gtools 3.0.0 - 2013-07-06
-------------------------
Major changes:
- The function 'addLast()' has been deprecated because it directly
manipulates the global environment, which is expressly prohibited by
the CRAN policies.
- A new function, 'lastAdd()' has been created to replace 'addLast()'.
The name has been changed because the two functions require
different syntax. 'addLast()' was used like this:
byeWorld <- function() cat("\nGoodbye World!\n")
addLast(byeWorld)
The new 'lastAdd()' function is used like this:
byeWorld <- function() cat("\nGoodbye World!\n")
.Last <- lastAdd(byeWorld)
Bug fixes:
- Update checkRVersion() to work with R version 3.0.0 and later.
Other changes:
- Remove cross-reference to (obsolete?) moc package
- The function 'assert()' (deprecated since gtools 2.5.0) is no longer
available and has been marked defunct.
gtools 2.7.1 - 2013-03-17
-------------------------
Bug fixes:
- smartbind() was not properly handling factor columns when the first
data frame did not include the relevant column.
gtools 2.7.0 - 2012-06-19
-------------------------
New features:
- smartbind() has a new 'sep' argument to allow specification of the
character(s) used to separate components of constructed column names
- smartbind() has a new 'verbose' argument to provide details on how
coluumns are being processed
Bug fixes:
- smartbind() has been enhanced to improve handling of factor and
ordered factor columns.
* What is new in gsl-2.3:
** bug fix in documentation for gsl_linalg_LU_refine
(bug #49728, Joey De Pauw)
** added gsl_multifit_linear_tsvd and gsl_multifit_wlinear_tsvd
to give user more control over cutoff for truncated SVD
** added routines for Generalized Cross Validation for
regularized linear least squares
** improved rstat example program and added documentation for
gsl_rstat_sd_mean (Jonathan Leto)
** added function gsl_multifit_linear_rank
** bug fix in nonlinear least squares when using data weights with
finite-difference Jacobian
** add 2D subspace method for large systems (multilarge_nlinear)
** bug fix in gsl_ran_beta for small parameters
(bug #47646, Yu Liu)
** bug fix in gsl_complex_tan for negative imaginary arguments
(bug #47347, Yu Liu)
** doc bug fix: value of golden ratio
** fixed scaling issue in 2D subspace nonlinear least squares
method
** optimize dogleg methods to calculate Gauss-Newton point
only when needed
Linking lapack with the gold linker fails with this error:
fatal error: --sysroot=: must take a non-empty argument
Similar to recent fixes to math/blas and math/lapack
Linking lapack with the gold linker fails with this error:
fatal error: --sysroot=: must take a non-empty argument
DragonFly has been using the gold linker by default for a while now.
Since I don't have time to track down this linking problem, I'm going
to restore the build on DragonFly by setting an environment variable
that forces DF to use the classic GNU linker instead.
This was already fixed on math/blas which uses the lapack common
makefile, so just relocate the fix to lapack.
Linking blas with the gold linker fails with this error:
fatal error: --sysroot=: must take a non-empty argument
DragonFly has been using the gold linker by default for a while now.
Since I don't have time to track down this linking problem, I'm going
to restore the build on DragonFly by setting an environment variable
that forces DF to use the classic GNU linker instead.
At this point in time, I don't know if BLAS is unique or if LAPACK
and others need the same workaround. If the latter, this variable
may need to be moved to the common LAPACK makefile.
Upstream changes:
0.60 2016-10-09
[ADDED]
- vecfirstidx { expr } @n returns first index with expr true
[FUNCTIONALITY AND PERFORMANCE]
- Expanded and modified prime count sparse tables. Prime counts from 30k
to 90M are 1.2x to 2.5x faster. It has no appreciable effect on the
speed of prime counts larger than this size.
- fromdigits works with bigint first arg, no need to stringify.
Slightly faster for bigints, but slower than desired.
- Various speedups and changes for fromdigits, todigits, todigitstring.
- vecprod in PP for negative high-bit would return double not bigint.
- Lah numbers added as Stirling numbers of the third kind. They've been
in the GMP code for almost 2 years now. Also for big results, directly
call the GMP code and objectify the result.
- Small performance change to AKS (r,s) selection tuning.
- On x86_64, use Montgomery math for Pollard/Brent Rho. This speeds up
factoring significantly for large native inputs (e.g. 10-20 digits).
- Use new GMP zeta and riemannr functions if possible, making some of
our operations much faster without Math::MPFR.
- print_primes with large args will try GMP sieve for big speedup. E.g.
use bigint; print_primes(2e19,2e19+1e7);
goes from 37 minutes to 7 seconds. This also removes a mistaken blank
line at the end for certain ranges.
- PP primes tries to use GMP. Only for calls from other PP code.
- Slightly more accuracy in native ExponentialIntegral.
- Slightly more accuracy in twin_prime_count_approx.
- nth_twin_prime_approx was incorrect over 1e10 and over 2e16 would
infinite loop due to Perl double conversion.
- nth_twin_prime_approx a little faster and more accurate.
Upstream changes:
2016-11-23 v1.999801 pjacklam
* Fix, hopefully once and for all, the longstanding problem of handling undef
as an operand to mathematical methods. The only method that accepts undef as
an operand is blog(), where the second operand might be undef, as in
$x->blog() or $x->blog($b), where $b is undef. The undef signifies that
Euler's number should be used as the base. With this fix, we should be able
to get Math::BigInt::Lite working again.
* Add least common multiple method _lcm() to Math::BigInt::Lib, and add
corresponding test file t/author-lib-arithmetic-binary-_lcm.t and test data
file t/author-lib-arithmetic-binary-_lcm.dat.
* Remove internal function __lcm() which has become redundant now that _lcm()
is in the library.
* Make it possible to use bgcd() and blcm() as class methods, since other
methods can be used as class methods. This applies to both Math::BigInt and
Math::BigFloat.
* Fix blcm() with negative input. The LCM should always be non-negative. This
applies to both Math::BigInt and Math::BigFloat.
* Add tests for bgcd() and blcm() in t/bigintpm.t and t/bigfltpm.t.
* Fix tests for blcm() assuming that LCM(0,0) should be a NaN. LCM(0,0) is 0
by convention.
* Prefer Class->config('option') over Class->config()->{option}. However, this
does not seem to be working for all options. It seems that this won't work
properly until we move the global variables into the OO interface.
* Explicitly specify the library in all test files that are shared between
Math-BigInt and the library distributions (FaatCalc, GMP, Pari, ...) with,
e.g., "use Math::BigInt only => 'Calc';". This way, it will fail immediately
if the specified library can't be loaded rather than using the fallback
library.
pkgsrc changes: removed all patches to do with qt5 support, upstream
code does it now. blindly moved some patches that were replacing
INSTALL_PROGRAM to INSTALL_LIB as the build changed. added patch
replacing struct tm_zone with timezone_t to accommodate for missing
type in NetBSD - same as libgnu does.
ok adam
Summary of important user-visible changes for version 4.2:
---------------------------------------------------------
** The parser has been extended to accept, but ignore, underscore
characters in numbers. This facilitates writing more legible code
by using '_' as a thousands separator or to group nibbles into bytes
in hex constants.
Examples: 1_000_000 == 1e6 or 0xDE_AD_BE_EF
** The parser has been extended to understand binary numbers which
begin with the prefix '0b' or '0B'. The value returned is Octave's
default numeric class of double, not at unsigned integer class.
Therefore numbers greater than flintmax, i.e., 2^53, will lose some
precision.
Examples: 0b101 == 5 or 0B1100_0001 == 0xC1
** gnuplot 4.4 is now the minimum version supported by Octave.
** The default set of colors used to plot lines has been updated to be
compatible with Matlab's new default color scheme. The line plot
color scheme can be set with the axes property "ColorOrder".
** The default colormap is now set to "viridis" which is also the
default colormap in matplotlib. This new colormap fixes some of the
main issues with the old default colormap "jet" such as its bad
"luminance profile" and is also more similar to Matlab's new default
colormap "parula".
** The colormap function no longer supports the input argument "list"
to show built-in colormaps. Use "help colormap" to find the
built-in colormaps.
** The graphics command "hold on" now ensures that each new plot added
to an existing plot has a different color or linestyle according to
the "ColorOrder" and/or "LineStyleOrder" properties. This is
equivalent to the old command "hold all" and was made for Matlab
compatibility. Existing code *may* produce differently colored
plots if it did not specify the color for a plot and relied on each
new plot having the default first color in the "ColorOrder"
property.
** When starting, Octave now looks in the function path for a file
startup.m and executes any commands found there. This change was
made to accommodate Matlab users. Octave has it's own configuration
system based on the file .octaverc which is preferred.
** Octal ('\NNN') and hex ('\xNN') escape sequences in single quoted
strings are now interpreted by the function do_string_escapes().
The *printf family of functions now supports octal and hex escape
sequences in single-quoted strings for Matlab compatibility.
** Special octal and hex escape sequences for the pattern and
replacement strings in regular expressions are now interpreted for
Matlab compatibility.
octal: '\oNNN' or '\o{NNN}'
hex : '\xNN' or '\x{NN}'
** Unknown escape sequences in the replacement string for regexprep are
now substituted with their unescaped version and no warning is
emitted. This change was made for Matlab compatibility.
Example: regexprep ('a', 'a', 'x\yz')
=> 'xyz'
** mkfifo now interprets the MODE argument as an octal, not decimal,
integer. This is consistent with the equivalent shell command.
** linspace now returns an empty matrix if the number of requested
points is 0 or a negative number. This change was made to be
compatible with Matlab releases newer than 2011. In addition,
Octave no longer supports matrix inputs for A or B.
** The cov function now returns the complex conjugate of the result
from previous versions of Octave. This change was made for
compatibility with Matlab.
** condest now works with a normest1 compatible syntax.
** The griddata function no longer plots the interpolated mesh if no
output argument is requested, instead the vector or array of
interpolated values is always returned for Matlab compatibility.
** The new function "light" and the corresponding graphics object
provide light and shadow effects for patch and surface objects.
** The surfnorm function now returns unnormalized (magnitude != 1)
normal vectors for compatibility with Matlab.
** The normal vectors returned from isonormals have been reversed to
point towards smaller values for compatibility with Matlab.
** The quadl function now uses an absolute, rather than relative,
tolerance for Matlab compatibility. The default tolerance is 1e-6
which may result in lower precision results than previous versions
of Octave which used eps as the relative tolerance. The quadl
function has also been extended to return a second output with the
total number of function evaluations.
** The textscan function is now built-in and is much faster and much
more Matlab-compatible than the previous m-file version.
** Dialog boxes--errordlg, helpdlg, inputdlg, listdlg, msgbox,
questdlg, and warndlg--now exclusively use Qt for rendering.
Java based versions have been removed.
** The axes properties "TitleFontSizeMultiplier" and "TitleFontWeight"
are now implemented which control the default appearance of text
created with title().
The axes property "LabelFontSizeMultiplier" is now implemented
which controls the default appearance of text created with
xlabel(), ylabel(), or zlabel().
** The graphics property "box" for axes now defaults to "off".
To obtain equivalent plots to previous versions of Octave use
set (0, "DefaultAxesBox", "on");
in your .octaverc file.
** The graphics property "boxstyle" has been implemented. The default
is "back" which draws only the back planes in a 3-D view. If the
option is "full" then all planes are drawn.
** The graphics property "erasemode" has been hidden, and will
eventually be removed. This property has also been removed
from Matlab, and was never implemented in Octave.
** The graphics property "graphicssmoothing" for figures now controls
whether anti-aliasing will be used for lines. The default is "on".
** The value "zero" for the axes properties "xaxislocation" and
"yaxislocation" has been deprecated and will be removed from
Octave 4.6. Use "origin" instead.
** The publish function allows easy publication of Octave script files
in HTML or other formats, including figures and output created by
this script. It comes with its counterpart grabcode, which lets one
literally grab the HTML published code from a remote website, for
example.
** The value of the MEX variable TrapFlag now defaults to 0, which will
cause Octave to abort execution of a MEX file and return to the
prompt if an error is encountered in mexCallMATLAB.
** The MEX API now includes the function mexCallMATLABWithTrap. This
function will not abort if an error occurs during mexCallMATLAB, but
instead will return execution to the MEX function for error
handling.
** The MEX API functions for input validation that begin with "mxIs"
(e.g., mxIsDouble, mxIsEmpty, etc.) now return type bool rather than
type int.
** The functions mxAssert and mxAssertS for checking assertions have
been added. In order to avoid a performance penalty they are only
compiled in to debug versions of a MEX file, i.e., that are produced
when the '-g' option is given to mex or mkoctfile.
** Other new MEX API functions include mexEvalStringWithTrap,
mxIsScalar, mxCreateUninitNumericArray, mxCreateUninitNumericMatrix.
** Other new functions added in 4.2:
audioformats
camlight
condeig
deg2rad
dialog
evalc
hash
im2double
isocaps
lighting
localfunctions
material
normest1
ode23
ode45
odeget
odeplot
odeset
padecoef
profexport
psi
rad2deg
reducepatch
reducevolume
smooth3
uibuttongroup
** Deprecated functions.
The following functions have been deprecated in Octave 4.2 and will
be removed from Octave 4.6 (or whatever version is the second major
release after 4.2):
Function | Replacement
---------------------|------------------
bitmax | flintmax
mahalanobis | mahal in Octave-Forge statistics pkg
md5sum | hash
octve_config_info | __octave_config_info__
onenormest | normest1
sleep | pause
usleep | pause
wavread | audioread
wavwrite | audiowrite
** The following functions were deprecated in Octave 3.8 and have been
removed from Octave 4.2.
default_save_options java_new
gen_doc_cache java_unsigned_conversion
interp1q javafields
isequalwithequalnans javamethods
java_convert_matrix re_read_readline_init_file
java_debug read_readline_init_file
java_invoke saving_history
** The global error_state variable in Octave's C++ API has been
deprecated and will be removed in a future version. Now the error
and print_usage functions throw an exception
(octave::execution_exception) after displaying the error message.
This makes the error and print_usage functions in C++ work more like
the corresponding functions in the scripting language.
** The default error handlers in liboctave have been updated to use
exceptions. After displaying an error message they no longer return
control to the calling program. The error handler function can be
customized through the global variables
"current_liboctave_error_handler" and
"current_liboctave_error_with_id_handler". If a programmer has
installed their own custom error handling routines when directly
linking with liboctave then these must be updated to throw an
exception and not return to the calling program.
** The system for common errors and warnings has been renamed from
gripe_XXX to either err_XXX if error is called or warn_XXX if
warning is called. The gripe_XXX functions are deprecated and will
be removed in version 4.6.
** New configure option, --enable-address-sanitizer-flags, to build
Octave with memory allocator checks (similar to those in valgrind)
built in.
Upstream changes:
2016-11-04 v1.999727 pjacklam
* Skip test exceeding the range of VAX floating point number in t/bigintpm.inc
(CPAN RT 118468).
* Fix typo in lib/Math/BigInt.pm (CPAN RT 118550).
2016-11-15 v1.999800 pjacklam
* Upgrade bundled Module::Install from version 1.16 to version 1.17.
* Add Math::BigInt::Lib (lib/Math/BigInt/Lib.pm), a parent class for
Math::BigInt backend libraries.
* Use objects in Math::BigInt::Calc, not just array refs. Also use OO-style,
i.e., use $class->_add($x, $y) rather than _add($class, $x, $y).
* Not all library methods modify the invocand, so call library methods as,
e.g, $x = $LIB->method($x, $y) rather than just $LIB->method($x, $y).
* Math::BigInt::Calc is now a subclass of Math::BigInt::Lib.
* Add Math::BigInt::Lib::Minimal (t/Math/BigInt/Lib/Minimal.pm) for testing
inheritance from Math::BigInt::Lib.
* Minor simplification in Math::BigInt::Calc->_str().
* Speed up Math::BigInt::Calc->_root().
* Remove test files that were included in the previous release by accident.
* Add more tests and use more verbose output in some tests.
* Fix typo in lib/Math/BigFloat.pm
* Fix documentation error in lib/Math/Calc.pm
* Use Config::Tiny and an .ini file to handle the library specific
configuration for the author-lib*.t test files.
Prompted by beta.repology.org.
Changes from 2.6.0 to 2.6.1
* Fixed a performance regression in some situations as consequence of
increasing too much the BLOCK_SIZE1 constant. After more careful
benchmarks (both in VML and non-VML modes), the value has been set
again to 1024 (down from 8192). The benchmarks have been made with
a relatively new processor (Intel Xeon E3-1245 v5 @ 3.50GHz), so
they should work well for a good range of processors again.
* Added NetBSD support to CPU detection. Thanks to Thomas Klausner.
Upstream changes:
28 August 2016: statmod 1.4.26
- Fortran function gaussq2 updated to Fortran 77.
5 August 2016: statmod 1.4.25
- Add CITATION file.
- pinvgauss() now uses an asymptotic approximation to compute right
tail probabilities for extreme large quantiles. This allows it to
give correct right tail probabilities for virtually any quantile.
- Fix to qinvgauss() to avoid NA values when computing extreme tail
quantiles where the inverse Gaussian density is subject to floating
underflow.
- Bug fix to qresiduals() and qresid.invgauss() for the inverse
Guassian distribution.
Upstream changes:
Changes in Version 1.7-13
o The window() method erroneously dropped the dimension in case of
1-column zoo series. Fixed now.
o Bug fix in NA handling of rollmax() pointed out by Cory Fletcher.
o A few as.yearmon/as.yearqtr methods were not registered in
the NAMESPACE but are now.
o If there are less then two non-NAs in na.approx() then approx()
cannot be applied. Instead of throwing an error (as up to version
1.7-12) simply no NAs are replaced now.
o Bug fix for lag(z, k = k, na.pad = TRUE) which ignored na.pad = TRUE
if 'k' was a vector of lags.
Upstream changes:
CHANGES IN R 3.3.2:
NEW FEATURES:
* extSoftVersion() now reports the version (if any) of the readline
library in use.
* The version of LAPACK included in the sources has been updated to
3.6.1, a bug-fix release including a speedup for the
non-symmetric case of eigen().
* Use options(deparse.max.lines=) to limit the number of lines
recorded in .Traceback and other deparsing activities.
* format(<AsIs>) looks more regular, also for non-character atomic
matrices.
* abbreviate() gains an option named = TRUE.
* The online documentation for package methods is extensively
rewritten. The goals are to simplify documentation for basic
use, to note old features not recommended and to correct
out-of-date information.
* Calls to setMethod() no longer print a message when creating a
generic function in those cases where that is natural: S3
generics and primitives.
INSTALLATION and INCLUDED SOFTWARE:
* Versions of the readline library >= 6.3 had been changed so that
terminal window resizes were not signalled to readline: code has
been added using a explicit signal handler to work around that
(when R is compiled against readline >= 6.3). (PR#16604)
* configure works better with Oracle Developer Studio 12.5.
UTILITIES:
* R CMD check reports more dubious flags in files
src/Makevars[.in], including -w and -g.
* R CMD check has been set up to filter important warnings from
recent versions of gfortran with -Wall -pedantic: this now
reports non-portable GNU extensions such as out-of-order
declarations.
* R CMD config works better with paths containing spaces, even
those of home directories (as reported by Ken Beath).
DEPRECATED AND DEFUNCT:
* Use of the C/C++ macro NO_C_HEADERS is deprecated (no C headers
are included by R headers from C++ as from R 3.3.0, so it should
no longer be needed).
BUG FIXES:
* The check for non-portable flags in R CMD check could be stymied
by src/Makevars files which contained targets.
* (Windows only) When using certain desktop themes in Windows 7 or
higher, Alt-Tab could cause Rterm to stop accepting input.
(PR#14406; patch submitted by Jan Gleixner.)
* pretty(d, ..) behaves better for date-time d (PR#16923).
* When an S4 class name matches multiple classes in the S4 cache,
perform a dynamic search in order to obey namespace imports.
This should eliminate annoying messages about multiple hits in
the class cache. Also, pass along the package from the
ClassExtends object when looking up superclasses in the cache.
* sample(NA_real_) now works.
* Packages using non-ASCII encodings in their code did not install
data properly on systems using different encodings.
* merge(df1, df2) now also works for data frames with column names
"na.last", "decreasing", or "method". (PR#17119)
* contour() caused a segfault if the labels argument had length
zero. (Reported by Bill Dunlap.)
* unique(warnings()) works more correctly, thanks to a new
duplicated.warnings() method.
* findInterval(x, vec = numeric(), all.inside = TRUE) now returns
0s as documented. (Reported by Bill Dunlap.)
* (Windows only) R CMD SHLIB failed when a symbol in the resulting
library had the same name as a keyword in the .def file.
(PR#17130)
* pmax() and pmin() now work with (more ?) classed objects, such
as "Matrix" from the Matrix package, as documented for a long
time.
* axis(side, x = D) and hence Axis() and plot() now work correctly
for "Date" and time objects D, even when "time goes backward",
e.g., with decreasing xlim. (Reported by William May.)
* str(I(matrix(..))) now looks as always intended.
* plot.ts(), the plot() method for time series, now respects cex,
lwd and lty. (Reported by Greg Werbin.)
* parallel::mccollect() now returns a named list (as documented)
when called with wait = FALSE. (Reported by Michel Lang.)
* If a package added a class to a class union in another package,
loading the first package gave erroneous warnings about
"undefined subclass".
* c()'s argument use.names is documented now, as belonging to the
(C internal) default method. In "parallel", argument recursive
is also moved from the generic to the default method, such that
the formal argument list of base generic c() is just (...).
* rbeta(4, NA) and similarly rgamma() and rnbinom() now return
NaN's with a warning, as other r<dist>(), and as documented.
(PR#17155)
* Using options(checkPackageLicense = TRUE) no longer requires
acceptance of the licence for non-default standard packages such
as compiler. (Reported by Mikko Korpela.)
* split(<very_long>, *) now works even when the split off parts are
long. (PR#17139)
* min() and max() now also work correctly when the argument list
starts with character(0). (PR#17160)
* Subsetting very large matrices (prod(dim(.)) >= 2^31) now works
thanks to Michael Schubmehl's PR#17158.
* bartlett.test() used residual sums of squares instead of
variances, when the argument was a list of lm objects. (Reported
by Jens Ledet Jensen).
* plot(<lm>, which = *) now correctly labels the contour lines for
the standardized residuals for which = 6. It also takes the
correct p in case of singularities (also for which = 5).
(PR#17161)
* xtabs(~ exclude) no longer fails from wrong scope, thanks to
Suharto Anggono's PR#17147.
* Reference class calls to methods() did not re-analyse previously
defined methods, meaning that calls to methods defined later
would fail. (Reported by Charles Tilford).
* findInterval(x, vec, left.open = TRUE) misbehaved in some cases.
(Reported by Dmitriy Chernykh.)
NumPy 1.11.2 Release Notes
**************************
Numpy 1.11.2 supports Python 2.6 - 2.7 and 3.2 - 3.5. It fixes bugs and
regressions found in Numpy 1.11.1 and includes several build related
improvements. Wheels for Linux, Windows, and OS X can be found on PyPI.
Pull Requests Merged
====================
Fixes overridden by later merges and release notes updates are omitted.
- #7736 BUG: Many functions silently drop 'keepdims' kwarg.
- #7738 ENH: Add extra kwargs and update doc of many MA methods.
- #7778 DOC: Update Numpy 1.11.1 release notes.
- #7793 BUG: MaskedArray.count treats negative axes incorrectly.
- #7816 BUG: Fix array too big error for wide dtypes.
- #7821 BUG: Make sure npy_mul_with_overflow_<type> detects overflow.
- #7824 MAINT: Allocate fewer bytes for empty arrays.
- #7847 MAINT,DOC: Fix some imp module uses and update f2py.compile docstring.
- #7849 MAINT: Fix remaining uses of deprecated Python imp module.
- #7851 BLD: Fix ATLAS version detection.
- #7896 BUG: Construct ma.array from np.array which contains padding.
- #7904 BUG: Fix float16 type not being called due to wrong ordering.
- #7917 BUG: Production install of numpy should not require nose.
- #7919 BLD: Fixed MKL detection for recent versions of this library.
- #7920 BUG: Fix for issue #7835 (ma.median of 1d).
- #7932 BUG: Monkey-patch _msvccompile.gen_lib_option like other compilers.
- #7939 BUG: Check for HAVE_LDOUBLE_DOUBLE_DOUBLE_LE in npy_math_complex.
- #7953 BUG: Guard against buggy comparisons in generic quicksort.
- #7954 BUG: Use keyword arguments to initialize Extension base class.
- #7955 BUG: Make sure numpy globals keep identity after reload.
- #7972 BUG: MSVCCompiler grows 'lib' & 'include' env strings exponentially.
- #8005 BLD: Remove __NUMPY_SETUP__ from builtins at end of setup.py.
- #8010 MAINT: Remove leftover imp module imports.
- #8020 BUG: Fix return of np.ma.count if keepdims is True and axis is None.
- #8024 BUG: Fix numpy.ma.median.
- #8031 BUG: Fix np.ma.median with only one non-masked value.
- #8044 BUG: Fix bug in NpyIter buffering with discontinuous arrays.
LAPACK 3.6.1: What’s new
[Mark Gates, UTK] blocked back-transformation for the non-symmetric eigenvalue problem
It blocks NB gemv calls into one gemm call inside trevc. To do
that, it needs a new routine, trevc3, because unfortunately the
lwork was not passed into trevc. Attached is the performance speedup
for dgeev. It gives a nice 1.5x speedup for N=20000, and that
appears to still be increasing with N. This is not the improvements
that Greg Henry recently provided for doing the triangular solves
as BLAS-3 instead of BLAS-1. That will take a while to process,
but we expect another, even larger increase in performance when
those changes are applied. This also does not include doing multiple
(BLAS-1) triangular solves in parallel, which is available in MAGMA,
since that requires OpenMP or pthreads.
### 1.1.3 / 06.08.2016
Author: Alexandre Balon-Perin <abalonperin@gilt.jp>
Date: Fri Aug 5 17:19:29 2016 +0900
* Fix issue with iconv on Ubuntu 12.04
* This fix is related to a bug in the iconv implementation packaged in libc6 on Ubuntu 12.04
* For some reasons, the encoding options //TRANSLIT//IGNORE are improperly applied.
* When //TRANSLIT is specified, instead of rescuing errors related to //TRANSLIT and checking if the //IGNORE is set, the code simply crashes.
### 1.1.2 / 29.03.2016
Author: Aleksandr Boykov <aleksandr.boykov@parelio.com>
Date: Mon Mar 28 14:07:35 2016 -0400
fixes compact! method when the excel document has dates
AFAIR, pkgsrc's ruby23-base dose not met below problem but here is changes:
* Gem was not compiling on Ruby 2.3.0 due to non-availability of
correct headers. This minor release fixes that problem.
A Python Approximate Bayesian Computing (ABC) Population Monte Carlo
(PMC) implementation based on Sequential Monte Carlo (SMC) with Particle
Filtering techniques.
