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out-of-date information.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.
Provided by Kai-Uwe Eckhardt in private mail.
version: 0.17.1
date: Fri May 6 12:02:48 CEST 2016
changes:
- fix bug in coalescing treatment
---
version: 0.17
date: Tue May 3 14:26:43 CEST 2016
changes:
- optionally combine SCCs incrementally in scheduler
- optionally maximize coincidence in scheduler
- optionally avoid loop coalescing in scheduler
- fix handling of nested integer divisions
- optionally detect min/max expressions during AST generation
- minor AST generator improvements
- simplify stride constraints
- improve support for expansions in schedule trees
---
version: 0.16.1
date: Thu Jan 14 18:08:06 CET 2016
changes:
- fix bug in simplification
---
version: 0.16
date: Tue Jan 12 09:56:16 CET 2016
changes:
- add 32 bit integer optimization for IMath
- minor AST generator improvements
- add isl_union_flow_get_full_{may,must}_dependence
- minor improvements to Python bindings
- minor improvements to set and map printing
---
version: 0.15
date: Thu Jun 11 12:45:33 CEST 2015
changes:
- improve coalescing
- add isl_union_access_info_compute_flow
- add mark nodes in AST
- add isl_union_pw_aff and isl_multi_union_pw_aff
- add schedule trees
- deprecate band forests
- deprecate separation_class AST generation option
- introduce isl_bool and isl_stat types
Feb 5th, 2016
v1.0
-- Bump to 1.0
-- Dirkjan Bussink provided a faster version of mp_expt_d()
-- Moritz Lenz contributed a fix to mp_mod()
and provided mp_get_long() and mp_set_long()
-- Fixed bugs in mp_read_radix(), mp_radix_size
Thanks to shameister, Gerhard R,
-- Christopher Brown provided mp_export() and mp_import()
-- Improvements in the code of mp_init_copy()
Thanks to ramkumarkoppu,
-- lomereiter provided mp_balance_mul()
-- Alexander Boström from the heimdal project contributed patches to
mp_prime_next_prime() and mp_invmod() and added a mp_isneg() macro
-- Fix build issues for Linux x32 ABI
-- Added mp_get_long_long() and mp_set_long_long()
-- Carlin provided a patch to use arc4random() instead of rand()
on platforms where it is supported
-- Karel Miko provided mp_sqrtmod_prime()
Changes from version 3.1.4 to version 3.1.5:
- C++11 compatibility.
- Bug fixes (see <http://www.mpfr.org/mpfr-3.1.4/#fixed> and ChangeLog file).
- More tests.
we pass and assume a given MACHINE_GNU_PLATFORM, but this package did not
use this value due to an error.
the guess it had for linux (x86_64-unknown-linux-gnu) is different, and
this seems to trample over our own tools, see:
https://mail-index.netbsd.org/pkgsrc-users/2014/03/26/msg019464.html
add this patch to the original m4 script too, not just the resulting configure
file, so it won't be accidentially forgotten (and can be upstreamed).
patch originally by Iain Morgan
reminded by Dr. Thomas Orgis
Ixion is a general purpose formula parser & interpreter that can
calculate multiple named targets, or "cells".
The goal of this project is to create a library for calculating
the results of formula expressions stored in multiple named targets,
or "cells". The cells can be referenced from each other, and the
library takes care of resolving their dependencies automatically
upon calculation. The caller can run the calculation routine either
in a single-threaded mode, or a multi-threaded mode. The library
also supports re-calculations where the contents of one or more
cells have been modified since the last calculation, and a partial
calculation of only the affected cells need to be calculated.
Set LICENSE.
Still does not build with guile20, so leave it at 1.8.
Version 1.1.11
* Fixed issue with linking Lex library.
Version 1.1.10
* Fixed memory leak in evaluator_create function implementation.
Version 1.1.9
* Fixed bug in math_step function implementation.
* Updated manual.
Eigen 3.2.9
Released on July 18, 2016
Changes since 3.2.8:
* Main fixes and improvements:
+ Improve numerical robustness of JacobiSVD (backported from 3.3)
+ Bug 1017: prevents underflows in makeHouseholder
+ Fix numerical accuracy issue in the extraction of complex
eigenvalue pairs in real generalized eigenvalue problems.
+ Fix support for vector.homogeneous().asDiagonal()
+ Bug 1238: fix SparseMatrix::sum() overload for un-compressed mode
+ Bug 1213: workaround gcc linking issue with anonymous enums.
+ Bug 1236: fix possible integer overflow in sparse-sparse product
+ Improve detection of identical matrices when applying a
permutation (e.g., mat = perm * mat)
+ Fix usage of nesting type in blas_traits. In practice, this
fixes compilation of expressions such as A*(A*A)^T
+ CMake: fixes support of Ninja generator
+ Add a StorageIndex typedef to sparse matrices and expressions
to ease porting code to 3.3 (see
http://eigen.tuxfamily.org/index.php?title=3.3#Index_typedef)
+ Bug 1200: make aligned_allocator c++11 compatible (backported from 3.3)
+ Bug 1182: improve generality of abs2 (backported from 3.3)
+ Bug 537: fix compilation of Quaternion with Apples's compiler
+ Bug 1176: allow products between compatible scalar types
+ Bug 1172: make valuePtr and innerIndexPtr properly return null
for empty sparse matrices.
+ Bug 1170: skip calls to memcpy/memmove for empty inputs.
* Others:
+ Bug 1242: fix comma initializer with empty matrices.
+ Improves support for MKL's PARDISO solver.
+ Fix a compilation issue with Pastix solver.
+ Add some missing explicit scalar conversions
+ Fix a compilation issue with matrix exponential (unsupported
MatrixFunctions module).
+ Bug 734: fix a storage order issue in unsupported Spline module
+ Bug 1222: fix a compilation issue in AutoDiffScalar
+ Bug 1221: shutdown some GCC6's warnings.
+ Bug 1175: fix index type conversion warnings in sparse to
dense conversion.
Eigen 3.2.8
Released on February 16, 2016
Changes since 3.2.7:
* Main fixes and improvements:
+ Make FullPivLU::solve use rank() instead of nonzeroPivots().
+ Add EIGEN_MAPBASE_PLUGIN
+ Bug 1166: fix issue in matrix-vector products when the
destination is not a vector at compile-time.
+ Bug 1100: Improve cmake/pkg-config support.
+ Bug 1113: fix name conflict with C99's "I".
+ Add missing delete operator overloads in
EIGEN_MAKE_ALIGNED_OPERATOR_NEW
+ Fix (A*B).maxCoeff(i) and similar.
+ Workaround an ICE with VC2015 Update1 x64.
+ Bug 1156: fix several function declarations whose arguments
were passed by value instead of being passed by reference
+ Bug 1164: fix std::list and std::deque specializations such
that our aligned allocator is automatically activatived only
when the user did not specified an allocator (or specified the
default std::allocator).
* Others:
+ Fix BLAS backend (aka MKL) for empty matrix products.
+ Bug 1134: fix JacobiSVD pre-allocation.
+ Bug 1111: fix infinite recursion in
sparse-column-major.row(i).nonZeros() (it now produces a
compilation error)
+ Bug 1106: workaround a compilation issue in Sparse module for
msvc-icc combo
+ Bug 1153: remove the usage of __GXX_EXPERIMENTAL_CXX0X__ to
detect C++11 support
+ Bug 1143: work-around gcc bug in COLAMD
+ Improve support for matrix products with empty factors.
+ Fix and clarify documentation of Transform wrt
operator*(MatrixBase)
+ Add a matrix-free conjugate gradient example.
+ Fix cost computation in CwiseUnaryView (internal)
+ Remove custom unaligned loads for SSE.
+ Some warning fixes.
+ Several other documentation clarifications.
Fix isnan() checks to declare main() returning 'int' and use floating
argument to isnan() avoiding recent (gcc 5) compiler noise.
Since last update:
../../.. version 5.5.2.1
- fixed a small error in new and improved MIP_stepOF function to find integer solutions.
../../.. version 5.5.2.2
- For integer models with semi-cont variables it happened sometimes that a message
"fillbranches_BB: Inconsistent equal-valued bounds for ..." occured and that the semi-cont condition
was not respected.
- New functions added: get_accuracy to get the numeric accuracy after solve.
- New functions added: set_break_numeric_accuracy, get_break_numeric_accuracy to let lp_solve return ACCURACYERROR
instead of FEASIBLE when numerical accuracy if worse then the provided values.
In the past, lp_solve only returned a non-optimal status in case of very severe numerical instability.
Now it will return already ACCURACYERROR when it finds a relative inaccuracy of 5e-7
- When reading a model from the lp-format and important issues are detected such as already bounds on variables being overruled
later with for example a bin keyword, this is now reported in the default verbose level such that this is seen easier.
08/05/16 version 5.5.2.3
- For some models with integer variables, lp_solve did not find the most optimal solution.
* What is new in gsl-2.2.1:
** reverted gsl_linalg_cholesky_decomp to its previous behavior
so it is backward compatible; new cholesky routine is
gsl_linalg_cholesky_decomp1
* What is new in gsl-2.2:
** updated gsl_linalg_cholesky_invert to use Level-2 BLAS
and added function gsl_linalg_pcholesky_invert
** added function gsl_linalg_invtri for inverting
triangular matrices
** fix GSL_EIGEN_SORT_VAL_{ASC,DESC} for nonsymmetric
eigensystems (Victor Zverovich)
** added complete orthogonal decomposition routines
(gsl_linalg_COD)
** bug fix where median calculation wasn't reset in
gsl_rstat_reset(); added gsl_rstat_quantile_reset() function
(reported by Pedro Donato)
** added multivariate Gaussian random distribution
gsl_ran_multivariate_gaussian (Timothée Flutre)
** added functions to estimate the 1-norm reciprocal condition
number for various matrix factorizations:
* gsl_linalg_cholesky_rcond
* gsl_linalg_QRPT_rcond
** added functions gsl_linalg_QRPT_{lssolve,lssolve2} to
compute least squares solutions with the QRPT decomposition
** added function gsl_permute_matrix()
** added modified Cholesky factorization (gsl_linalg_mcholesky)
to handle symmetric indefinite matrices
** added pivoted Cholesky factorization (gsl_linalg_pcholesky)
for ill-conditioned matrices
** rewrote (real) Cholesky decomposition to use
a Level-2 blas algorithm instead of Level-1. Flop
count is about the same but the code is much simpler
and easier to follow
** completely rewritten nonlinear least squares module,
including support for large problems; the user may
now control the linear solver used, the trust region
updating strategy, and the scaling method. In addition,
support has been added for the geodesic acceleration
step (Transtrum 2011) which can speed up convergence
on a wide class of problems.
** added gsl_rstat_rms() for root mean square
** optimized lmniel nonlinear least squares solver
(bug #46369)
** improved precision in Bessel K0/K1 near x = 2
(Pavel Holoborodko, bug #47401)
** added support for compressed row storage sparse
matrices (Alexis Tantet)
** bug fix in convergence check of hypergeometric 2F1
function (bug #45926)
** added gsl_multilarge_linear_lcurve() to compute
the L-curve for large linear systems
** updated multilarge normal equations method to use
new Cholesky scaling for better numerical stability
** added scaling to Cholesky routines to reduce the
condition number prior to factorization
Autograd can automatically differentiate native Python and Numpy
code. It can handle a large subset of Python's features, including
loops, ifs, recursion and closures, and it can even take derivatives
of derivatives of derivatives. It uses reverse-mode differentiation
(a.k.a. backpropagation), which means it can efficiently take
gradients of scalar-valued functions with respect to array-valued
arguments. The main intended application is gradient-based
optimization.
Apart from translation updates, this is the same as the "stable"
3.20.2, but with history-view.ui and history-entry.ui now included
in the tarball. Since glib fixed
673101 resource compiler dependency generation not working for generated files
gnome-calculator will not compile without the missing files.
Overview of changes in gnome-calculator 3.21.90
* Updated Hebrew translation (Yosef Or Boczko)
* Added 'period' keypress when the delete key on the numpad is
pressed. (Myridium)
* Updated Spanish translation (Daniel Mustieles)
* also in 3.20.2: lib: prevents segfault when elements of
division to zero have null assigned tokens (fixes#769364)
(Alberto Ruiz)
* Add Language headers to po files (Piotr Drg)
* Updated Swedish translation (Anders Jonsson)
* Updated Friulian translation (Fabio Tomat)
* Updated Indonesian translation (cherry picked from commit
da3a093148c5f9340c6566fe35d5a38b5aa04e6b) (Andika Triwidada)
* Updated Occitan translation (Cédric Valmary)
Overview of changes in gnome-calculator 3.21.2
* Updated Norwegian bokmål translation. (Kjartan Maraas)
* Updated Friulian translation (Fabio Tomat)
* Updated Friulian translation (Fabio Tomat)
* Updated Friulian translation (Fabio Tomat)
* Added Friulian translation (Fabio Tomat)
* Distribute history-view.ui (Robert Ancell)
* Distribute history-entry.ui (Robert Ancell)
* Updated Occitan translation (Cédric Valmary)
