Add missing DEPENDS
Upstream changes:
NetworkX 1.9
Release date: 21 June 2014
Support for Python 3.1 is dropped in this release.
Highlights
Completely rewritten maximum flow and flow-based connectivity algorithms with backwards incompatible interfaces
Community graph generators
Stoer-Wagner minimum cut algorithm
Linear-time Eulerian circuit algorithm
Linear algebra package changed to use SciPy sparse matrices
Algebraic connectivity, Fiedler vector, spectral ordering algorithms
Link prediction algorithms
Goldberg-Radzik shortest path algorithm
Semiconnected graph and tree recognition algorithms
NEW FEATURES:
* When attach() reports conflicts, it does so compatibly with
library() by using message().
* R CMD Sweave no longer cleans any files by default, compatibly
with versions of R prior to 3.1.0. There are new options
--clean, --clean=default and --clean=keepOuts.
* tools::buildVignette() and tools::buildVignettes() with clean =
FALSE no longer remove any created files. buildvignette() gains
a keep argument for more cleaning customization.
* The Bioconductor 'version' used by setRepositories() can now be
set by environment variable R_BIOC_VERSION at runtime, not just
when R is installed. (It has been stated that Bioconductor will
switch from 'version' 2.14 to 'version' 3.0 during the lifetime
of the R 3.1 series.)
* Error messages from bugs in embedded Sexpr code in Sweave
documents now report the source location.
* type.convert(), read.table() and similar read.*() functions get a
new numerals argument, specifying how numeric input is converted
when its conversion to double precision loses accuracy. The
default value, "allow.loss" allows accuracy loss, as in R
versions before 3.1.0.
* For some compilers, integer addition could overflow without a
warning. R's internal code for both integer addition and
subtraction is more robust now.
* The function determining the default number of knots for
smooth.spline() is now exported, as .nknots.smspl().
* dbeta(, a,b), pbeta(), qbeta() and rbeta() are now defined also
for a = 0, b = 0, or infinite a and b (where they typically
returned NaN before).
* Many package authors report that the RStudio graphics device does
not work correctly with their package's use of dev.new(). The
new option dev.new(noRStudioGD = TRUE) replaces the RStudio
override by the default device as selected by R itself, still
respecting environment variables R_INTERACTIVE_DEVICE and
R_DEFAULT_DEVICE.
* readRDS() now returns visibly.
* Modifying internal logical scalar constants now results in an
error instead of a warning.
* install.packages(repos = NULL) now accepts http:// or ftp:// URLs
of package archives as well as file paths, and will download as
required. In most cases repos = NULL can be deduced from the
extension of the URL.
* The warning when using partial matching with the $ operator on
data frames is now only given when
options("warnPartialMatchDollar") is TRUE.
* Package help requests like package?foo now try the package foo
whether loaded or not.
* General help requests now default to trying all loaded packages,
not just those on the search path.
* Added a new function promptImport(), to generate a help page for
a function that was imported from another package (and presumably
re-exported, or help would not be needed).
--0.19--
Released June 10, 2014
* Moved issue tracking to github and the main website to mpmath.org.
Several URLs and issue numbers were updated in the documentation
(Sergey B Kirpichev)
* Enabled automatic testing with Travis CI (Sergey B Kirpichev)
* Fixed many doctest issues (Sergey B Kirpichev)
* Converted line endings to LF (Ondrej Certik)
* Made polyroots() more robust (Ondrej Certik)
This is two major releases since 0.12.0. Changes include API changes, new
features, enhancements, and performance improvements along with a large
number of bug fixes.
For the detailed list of changes see
http://pandas.pydata.org/pandas-docs/stable/whatsnew.html
* Optional features required versions now builtin
* Updated copyright to 2014
* Prefer Data::Peek over Data::Dumper
* Support (and prefer) Spreadsheet::ParseXLSX for .xlsx
* Store CSV parse error - if any - in $ss->[0]{error}
* Link xlsgrep during install
* Added xlsgrep to examples
* Allow -C B,D for xlscat
* More prominent reference to xlscat in docs
* /dev/null cannot be used for tests on Windows
* Improve documentation consistency (RT#80409)
* Updated copyright to 2013
* Force old(er) tar format (ustar) - assumes GNU tar on release box
* Fix yml/json optional_features
* Install utilities from example by default
* Several minor changes (for maint)
* Note that empty sheets are skipped when clip is true (RT#75277)
* Allow undef as valid value for the options (Max Maischein)
* Don't generate warnings when stripping whitespace and only
generating one of cells or rc. (Max Maschein)
* Fix test warning under perl-5.17.x
* Updated copyright to 2012
* Support passing attributes to the underlying parser
* Do not strip fields in sheets with no cells at all (RT#74976)
CHANGELOG:
0.2
---
* Added `Hashable` and `Data` support.
* Will build as full-fledged `Safe` Haskell if you configure with -f-hashable, merely `Trustworthy` otherwise.
* Allow for manual removal of the `hashable` dependency to support advanced sandbox users who explicitly want to avoid compiling certain dependencies
they know they aren't using.
We will fix bugs caused by any combination of these package flags, but the API of the package should be considered the default build
configuration with all of the package dependency flags enabled.
Update LICENSE
Upstream changes:
30 May 2014: statmod 1.4.20
- Considerable work on the inverse Gaussian functions dinvgauss(),
pinvgauss(), qinvgauss() and rinvgauss(). The parameter arguments
are changed to mean, shape and dispersion instead of mu and lambda.
The functions now include arguments lower.tail and log.p, meaning
that right-tailed probabilities can be used and probabilities can
be specified on the log-scale. Good numerical precision is
maintained in these case. The functions now respect attributes,
so that a matrix argument for example will produce a matrix result.
Checking is now done for missing values and invalid parameter
values on an element-wise basis. A technical report has been
written to describe the methodology behind qinvgauss().
- This file has been renamed to NEWS instead of changelog.txt.
- The introductory help page previously called 1.Introduction is now
named statmod-package.
13 April 2014: statmod 1.4.19
- qinvgauss() now uses a globally convergent Newton iteration, which
produces accurate values for a greater range of parameter values.
- glmnb.fit() now supports weights.
Update LICENSE
Upstream changes:
Changes in Version 1.7-11
o Extended the license from "GPL-2" to "GPL-2 | GPL-3".
o Avoid duplications in Suggests/Imports/Depends in the package's
DESCRIPTION. Use only :: instead of ::: to access certain functions
from other namespaces.
o Added as.list() methods for yearmon/yearqtr.
o Added workaround in Ops.zoo if first argument is not a zoo series
(prompted by Josh Ulrich).
o The transform() method for zoo series now does what method for
data.frame does (instead of just calling it) in order to get
non-standard evaluation.
Upstream changes:
Networkx-1.8.1
Release date: 4 August 2013
Bugfix release for missing files in source packaging
Networkx-1.8
Release date: 28 July 2013
Highlights
Faster (linear-time) graphicality tests and Havel-Hakimi graph generators
Directed Laplacian matrix generator
Katz centrality algorithm
Functions to generate all simple paths
Improved shapefile reader
More flexible weighted projection of bipartite graphs
Faster topological sort, decendents and ancestors of DAGs
Scaling parameter for force-directed layout
Bug Fixes
Error with average weighted connectivity for digraphs, correct normalized laplacian with self-loops, load betweenness for single node graphs, isolated nodes missing from dfs/bfs trees, normalize HITS using l1, handle density of graphs with self loops
Cleaner handling of current figure status with Matplotlib, Pajek files now don't write troublesome header line, default alpha value for GEXF files, read curved edges from yEd GraphML
Upstream changes:
--0.18--
Released December 31, 2013
Linear algebra:
* added qr() for matrix QR factorization (contributed by Ken Allen)
* added functions eigsy(), eighe(), eig() to compute matrix
eigenvalues (contributed by Timo Hartmann)
* added functions svd(), svd_r(), svd_c() for singular value
decomposition of matrices (contributed by Timo Hartmann)
* added calculation of Gaussian quadrature rules for various weight
functions (contributed by Timo Hartmann)
* improved precision selection in exp_pade() (contributed by
Mario Pernici)
Special functions:
* fixed ellippi() to return an inf instead of raising an exception
* fixed a crash in zeta() with huge arguments
* added functions for computing Stirling numbers
(stirling1(), stirling2())
* improved the computation of zeros of zeta at high precision
(contributed by Juan Arias de Reyna)
* fixed zeta(-x) raising an exception for tiny x
* recognize when lerchphi() can call zeta() or polylog(),
handling those cases faster
Compatibility:
* fixed gmpy2 compatibility issues (contributed by Case Van Horsen)
* better solutions for python 2/3 compatibility,
using Benjamin Peterson's six.py
* fixes to allow mpmath to run in non-sage mode when sage is available
* support abstract base classes (contributed by Stefan Krastanov)
* use new-style classes to improve pypy performance
Other:
* added Levin, Sidi-S and Cohen/Villegas/Zagier series
transformations (contributed by Timo Hartmann)
* added isfinite() utility function
* fixed a problem with bisection root-finding
* fixed several documentation errors
* corrected number of coefficients returned by diffs() with
method='quad'
* fixed repr(constant) being slow at high precision
* made intervals hashable
packaged for wip.
A Scientific number is an arbitrary-precision floating-point number
represented using scientific notation.
A scientific number with coefficient c and base10Exponent e corresponds to
the Fractional number: fromInteger c * 10 ^^ e
Its primary use-case is to serve as the target of parsing floating point
numbers. Since the textual representation of floating point numbers use
scientific notation they can be efficiently parsed to a Scientific number.
Do it for all packages that
* mention perl, or
* have a directory name starting with p5-*, or
* depend on a package starting with p5-
like last time, for 5.18, where this didn't lead to complaints.
Let me know if you have any this time.
NEW FEATURES:
* type.convert() (and hence by default read.table()) returns a
character vector or factor when representing a numeric input as a
double would lose accuracy. Similarly for complex inputs.
If a file contains numeric data with unrepresentable numbers of
decimal places that are intended to be read as numeric, specify
colClasses in read.table() to be "numeric".
* tools::Rdiff(useDiff = FALSE) is closer to the POSIX definition
of diff -b (as distinct from the description in the man pages of
most systems).
* New function anyNA(), a version of any(is.na(.)) which is fast
for atomic vectors, based on a proposal by Tim Hesterberg.
* arrayInd(*, useNames = TRUE) and, analogously, which(*, arr.ind =
TRUE) now make use of names(.dimnames) when available.
* is.unsorted() now also works for raw vectors.
* The "table" method for as.data.frame() (also useful as
as.data.frame.table()) now passes sep and base arguments to
provideDimnames().
* uniroot() gets new optional arguments, notably extendInt,
allowing to auto-extend the search interval when needed. The
return value has an extra component, init.it.
* switch(f, ...) now warns when f is a factor, as this typically
happens accidentally where the useR meant to pass a character
string, but f is treated as integer (as always documented).
* The parser has been modified to use less memory.
* The way the unary operators (+ - !) handle attributes is now more
consistent. If there is no coercion, all attributes (including
class) are copied from the input to the result: otherwise only
names, dims and dimnames are.
* colorRamp() and colorRampPalette() now allow non-opaque colours
and a ramp in opacity via the new argument alpha = TRUE.
(Suggested by Alberto Krone-Martins, but optionally as there are
existing uses which expect only RGB values.)
* grid.show.layout() and grid.show.viewport() get an optional vp.ex
argument.
* There is a new function find_gs_cmd() in the tools package to
locate a GhostScript executable. (This is an enhanced version of
a previously internal function there.)
* object.size() gains a format() method.
* There is a new family, "ArialMT", for the pdf() and postscript()
devices. This will only be rendered correctly on viewers which
have access to Monotype TrueType fonts (which are sometimes
requested by journals).
* The text and PDF news files, including NEWS and NEWS.2, have been
moved to the doc directory.
* combn(x, simplify = TRUE) now gives a factor result for factor
input x (previously user error).
* Added utils::fileSnapshot() and utils::changedFiles() functions
to allow snapshots and comparison of directories of files.
* make.names(names, unique=TRUE) now tries to preserve existing
names.
* New functions cospi(x), sinpi(x), and tanpi(x), for more accurate
computation of cos(pi*x), etc, both in R and the C API. Using
these gains accuracy in some cases, e.g., inside lgamma() or
besselI().
* print.table(x, zero.print = ".") now also has an effect when x is
not integer-valued.
* There is more support to explore the system's idea of time-zone
names. Sys.timezone() tries to give the current system setting
by name (and succeeds at least on Linux, OS X, Solaris and
Windows), and OlsonNames() lists the names in the system's Olson
database. Sys.timezone(location = FALSE) gives the previous
behaviour.
* Platforms with a 64-bit time_t type are allowed to handle
conversions between the "POSIXct" and "POSIXlt" classes for
date-times outside the 32-bit range (before 1902 or after 2037):
the existing workarounds are used on other platforms. (Note that
time-zone information for post-2037 is speculative at best, and
the OS services are tested for known errors and so not used on OS
X.)
Currently time_t is usually long and hence 64-bit on Unix-alike
64-bit platforms: however it several cases the time-zone database
is 32-bit. On R for Windows it is 64-bit (for both architectures
as from this version).
* The "save.defaults" option can include a value for
compression_level.
* colSums() and friends now have support for arrays and data-frame
columns with 2^31 or more elements.
* as.factor() is faster when f is an unclassed integer vector (for
example, when called from tapply()).
* fft() now works with longer inputs, from the 12 million
previously supported up to 2 billion.
* Complex svd() now uses LAPACK subroutine ZGESDD, the complex
analogue of the routine used for the real case.
* Sweave now outputs .tex files in UTF-8 if the input encoding is
declared to be UTF-8, regardless of the local encoding. The
UTF-8 encoding may now be declared using a LaTeX comment
containing the string %\SweaveUTF8 on a line by itself.
* file.copy() gains a copy.date argument.
* Printing of date-times will make use of the time-zone
abbreviation in use at the time, if known. For example, for
Paris pre-1940 this could be LMT, PMT, WET or WEST. To enable
this, the "POSIXlt" class has an optional component "zone"
recording the abbreviation for each element.
For platforms which support it, there is also a component
"gmtoff" recording the offset from GMT where known.
* (On Windows, by default on OS X and optionally elsewhere.) The
system C function strftime has been replaced by a more
comprehensive version with closer conformance to the POSIX 2008
standard.
* dnorm(x, log = FALSE) is more accurate (but somewhat slower) for
|x| > 5.
* Some versions of the tiff() device have further compression
options.
* read.table(), readLines() and scan() have a new argument to
influence the treatment of embedded nuls.
* Avoid duplicating the right hand side values in complex
assignments when possible. This reduces copying of replacement
values in expressions such as Z$a <- a0 and ans[[i]] <- tmp: some
package code has relied on there being copies.
Also, a number of other changes to reduce copying of objects; all
contributed by or based on suggestions by Michael Lawrence.
* The fast argument of KalmanLike(), KalmanRun() and
KalmanForecast() has been replaced by update, which instead of
updating mod in place, optionally returns the updated model in an
attribute "mod" of the return value.
* arima() and makeARIMA() get a new optional argument SSinit,
allowing the choice of a different *s*tate *s*pace initialization
which has been observed to be more reliable close to
non-stationarity.
* warning() has a new argument noBreaks., to simplify
post-processing of output with options(warn = 1).
* pushBack() gains an argument encoding, to support reading of
UTF-8 characters using scan(), read.table() and related functions
in a non-UTF-8 locale.
* all.equal.list() gets a new argument use.names which by default
labels differing components by names (if they match) rather than
by integer index. Saved R output in packages may need to be
updated.
* The methods for all.equal() and attr.all.equal() now have
argument check.attributes after ... so it cannot be partially nor
positionally matched (as it has been, unintentionally).
A side effect is that some previously undetected errors of
passing empty arguments (no object between commas) to all.equal()
are detected and reported.
There are explicit checks that check.attributes is logical,
tolerance is numeric and scale is NULL or numeric. This catches
some unintended positional matching.
The message for all.equal.numeric() reports a "scaled difference"
only for scale != 1.
* all.equal() now has a "POSIXt" method replacing the "POSIXct"
method.
* The "Date" and "POSIXt" methods of seq() allows by = "quarter"
for completeness (by = "3 months" always worked).
* file.path() removes any trailing separator on Windows, where they
are invalid (although sometimes accepted). This is intended to
enhance the portability of code written by those using POSIX file
systems (where a trailing / can be used to confine path matching
to directories).
* New function agrepl() which like grepl() returns a logical
vector.
* fifo() is now supported on Windows.
* sort.list(method = "radix") now allows negative integers
* Some functionality of print.ts() is now available in
.preformat.ts() for more modularity.
* mcparallel() gains an option detach = TRUE which allows execution
of code independently of the current session. It is based on a
new estranged = TRUE argument to mcfork() which forks child
processes such that they become independent of the parent
process.
* The pdf() device omits circles and text at extremely small sizes,
since some viewers were failing on such files.
* The rightmost break for the "months", "quarters" and "years"
cases of hist.POSIXlt() has been increased by a day.
* The handling of DF[i,] <- a where i is of length 0 is improved.
* hclust() gains a new method "ward.D2" which implements Ward's
method correctly. The previous "ward" method is "ward.D" now,
with the old name still working. Thanks to research and
proposals by Pierre Legendre.
* The sunspot.month dataset has been amended and updated from the
official source, whereas the sunspots and sunspot.year datasets
will remain immutable. The documentation and source links have
been updated correspondingly.
* The summary() method for "lm" fits warns if the fit is
essentially perfect, as most of the summary may be computed
inaccurately (and with platform-dependent values).
Programmers who use summary() in order to extract just a
component which will be reliable (e.g. $cov.unscaled) should wrap
their calls in suppressWarnings().
version: 0.13
date: Mon Apr 14 11:08:45 CEST 2014
changes:
- deprecate isl_int
- improved support for multi piecewise quasi-affine expressions
- allow the user to impose a bound on the number of low-level operations
- add isl_id_to_ast_expr and isl_id_to_pw_aff
- add isl_schedule_constraints
- hide internal structure of isl_vec
- remove support for piplib
