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2018-09-29Disable float128 support on DragonFly BSD as well.sevan1-2/+2
As per https://mail-index.netbsd.org/pkgsrc-users/2018/02/03/msg026233.html
2018-09-29sundials: Needs python for build. Fix PLIST. Bump.tnn2-17/+20
2018-09-27py-Theano: REPLACE_INTERPRETER+=bashtnn1-1/+6
2018-09-24py-numpy: updated to 1.15.2adam2-7/+7
NumPy 1.15.2: This is a bugfix release for bugs and regressions reported following the 1.15.1 release. * The matrix PendingDeprecationWarning is now suppressed in pytest 3.8. * The new cached allocations machinery has been fixed to be thread safe. * The boolean indexing of subclasses now works correctly. * A small memory leak in PyArray_AdaptFlexibleDType has been fixed. 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.
2018-09-24math/py-pandas-datareader: Update to 0.7.0minskim3-18/+48
Changes: * Reintroduced support for Yahoo! price, dividends, and splits data for stocks and currency pairs. * A new data connector for data provided by Alpha Vantage was introduced to obtain Foreign Exchange (FX) data * A new data connector for data provided by Alpha Vantage was introduced to obtain historical time series data. * A new data connector for data provided by Alpha Vantage was introduced to obtain sector performance data. * A new data connector for data provided by Alpha Vantage was introduced to obtain real-time Batch Stock Quotes. * Immediate deprecation of Google finance and Morningstar for historical price data, as these API endpoints are no longer supported by their respective providers. Alternate methods are welcome via pull requests, as PDR would like to restore these features. * Removal of EDGAR, which was deprecated in v0.6.0.
2018-09-23math/ruby-spreadsheet: update to 1.1.8taca2-7/+7
### 1.1.8 / 20.08.2018 Author: VitaliyAdamkov <adamkov@tex.ua> Date: Mon Aug 20 09:48:31 2018 +0300 * Cancel :lazy usage * Use lazy select to speed up a little * Omit rails :try usage * stub for :postread_worksheet method * sometimes it selects empty array.. Author: 545ch4 <s@rprojekt.org> Date: Wed Mar 28 15:33:04 2018 +0200 * [ruby-2.4] Fix weird first line of spreadsheet.gemspec * Doesn't seem to be a valid .gemspec command/field.
2018-09-17Add package R-RNetCDF version 1.9-1maya5-1/+68
An R interface to the NetCDF file format designed by Unidata for efficient storage of array-oriented scientific data and descriptions. The R interface is closely based on the C API of the NetCDF library, and it includes calendar conversions from the Unidata UDUNITS library. The current implementation supports all operations on NetCDF datasets in classic and 64-bit offset file formats, and NetCDF4-classic format is supported for reading and modification of existing files. From Kai-Uwe Eckhardt, updated as the previous distfile wasn't available. PR pkg/51607
2018-09-04math/R-igraph: Needs a C compilerminskim1-2/+2
2018-09-03math/py-numba: Add ALTERNATIVESminskim3-4/+14
2018-09-03*: recursive bump for vala-0.42.wiz1-2/+2
2018-09-03py-scipy: add upstream bug reportswiz2-3/+8
2018-09-03py-scipy: remove obsolete patch; HAVE_OPEN_MEMSTREAM is defined to 1 nowadays.wiz2-17/+1
2018-09-03py-scipy: remove reference to non-existent filewiz1-2/+1
2018-09-02gnumeric: update to 1.12.43.wiz3-55/+57
Changes not found
2018-09-02p5-Spreadsheet-Read: update to 0.79.wiz2-8/+7
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)
2018-09-02p5-Math-Prime-Util: update to 0.71.wiz2-8/+7
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.
2018-08-31py-scipy: add missing test dependencywiz1-5/+5
Update comment about upstream bug reports about test failures.
2018-08-30Update to 0.4.93wen2-7/+9
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.
2018-08-30Update to 1.0.8wen2-7/+7
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
2018-08-30Update to 1.8.3wen2-7/+7
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.
2018-08-30Update to 0.11.0wen2-7/+7
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.
2018-08-30Update to 1.8.3wen2-8/+8
2018-08-30py-powerlaw: updated to 1.4.4adam3-10/+10
1.4.4: Unknown changes
2018-08-30py-numexpr: updated to 2.6.8adam2-7/+7
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
2018-08-28py-numba: updated to 0.39.0adam3-16/+48
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.
2018-08-28Update to 20.4.14. The changelog, while extremely long, only reaches backschmonz41-1140/+393
to 20.0. Please consult https://fractint.org/ftp/current/dos/whatsnew.txt for an approximate understanding of what's new since 3.10 (the previous version in pkgsrc).
2018-08-27py-numpy: updated to 1.15.1adam4-16/+9
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.
2018-08-22Recursive bump for perl5-5.28.0wiz76-129/+152
2018-08-22Recursive bump for perl5-5.28.0wiz2-3/+4
2018-08-21p5-Statistics-Descriptive: update to 3.0701.wiz2-7/+7
3.0701 2018-07-14 - Typo corrections thanks to Debian 3.0700 2018-07-13 - Typo corrections thanks to Debian - Added the ->summary() method to Statistics::Descriptive::Full. - https://rt.cpan.org/Public/Bug/Display.html?id=82852 - Thanks to Su-Shee
2018-08-21p5-Alien-GMP: update to 1.14.wiz2-10/+7
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.
2018-08-21math/Makefile: + p5-Statistics-CaseResamplingwiz1-1/+2
2018-08-21math/p5-Statistics-CaseResampling: import p5-Statistics-CaseResampling-0.15wiz3-0/+28
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.
2018-08-21math/Makefile: + p5-Number-WithErrorwiz1-1/+2
2018-08-21math/p5-Number-WithError: import p5-Number-WithError-1.01wiz3-0/+32
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.
2018-08-20BUILD_DEPENDS+= -> TEST_DEPENDS+=szptvlfn1-3/+2
2018-08-20Update to 1.12wen2-7/+7
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.
2018-08-19py-roman: updated to 3.0adam2-10/+9
3.0: Added support for Python 3.5, 3.6 and PyPy3. Dropped support for Python 2.6 and 3.3.
2018-08-17math/octave: Fix CHECK_WRKREF_SKIP patternsminskim1-3/+3
2018-08-16revbump after boost-libs updateadam15-28/+30
2018-08-16octave: PRINT_PLIST_AWK to avoid a recurrence of a broken PLIST.maya1-1/+2
From wiz, thanks.
2018-08-16octave: don't make netbsd references in PLIST, accidentally went in withmaya2-33/+35
the update. skip checking for workdir references for liboctinterp which doesn't seem to actually make references (maybe it's debug info?)
2018-08-16gnumeric: update to 1.12.42.wiz3-14/+55
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].
2018-08-16math/gnumeric*: remove two obsolete versions of gnumeric.wiz21-2103/+1
Use math/gnumeric112 instead.
2018-08-15Add libnumbertextryoon1-1/+2
2018-08-15math/libnumbertext: import libnumbertext-1.0.3ryoon5-0/+52
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.
2018-08-14py-numexpr: updated to 2.6.7adam2-7/+7
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 evaluateā€™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.
2018-08-14py-simpleeval: updated to 0.9.6adam2-7/+7
0.9.6: Unknown changes.
2018-08-12LAPACK: build deprecated functions. Allows me to build unmodifiedmaya1-1/+3
octave forge control, sparing the need to understand how to patch fortran 77 code. Fixes PR pkg/52449. bump PKGREVISION.
2018-08-12Remove unused patches.maya3-51/+0