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2019-09-09eigen2: fix headers to avoid introducing errors in dependent packages.maya3-5/+31
Fixes PR pkg/54108: misc/step fails build under -current 8.99.37 bump PKGREVISION.
2019-09-06Revbump due to XmHTML updatenros1-2/+2
2019-09-05py-ephem: updated to 3.7.7.0adam3-10/+8
Version 3.7.7.0: Upgraded libastro to 3.7.7. The internal star catalog now includes all 57 navigational stars. The rise, culminate, and set returned by next_pass() are now consecutive values for a single pass. Pass singlepass=False to return the original next_rise, next_culminate, next_set even if next_set < next_rise (the satellite is already up). ephem.delta_t('0') now returns the correct value, instead of misbehaving for that particular input.
2019-09-02Changed PYTHON_VERSIONS_INCOMPATIBLE to PYTHON_VERSIONS_ACCEPTED; needed for ↵adam7-14/+14
future Python 3.8
2019-09-02p5-Math-Calc-Units: remove PLIST since PERL5_PACKLIST is in useadam1-19/+0
2019-08-27py-quadprog: updated to 0.1.7adam3-9/+9
0.1.7: Unknown changes
2019-08-26Add TEST_TARGET.alnsn1-2/+5
Current score on -current amd64: Pass: 861, Fail: 171.
2019-08-24Make pkglint happy.alnsn1-2/+2
2019-08-24Add yices2 to the build.alnsn1-1/+2
2019-08-24Initial import of Yices 2, version 2.6.1.alnsn10-0/+361
Yices 2 is an SMT solver that decides the satisfiability of formulas containing uninterpreted function symbols with equality, real and integer arithmetic, bitvectors, scalar types, and tuples. Yices 2 supports both linear and nonlinear arithmetic. Yices 2 can process input written in the SMT-LIB notation (both versions 2.0 and 1.2 are supported). Alternatively, you can write specifications using Yices 2's own specification language, which includes tuples and scalar types. You can also use Yices 2 as a library in your software.
2019-08-22Recursive revbump from boost-1.71.0ryoon16-31/+32
2019-08-14Recursive bump of all packages using Go after Go 1.12.8 update.bsiegert2-4/+4
2019-08-14Update to 3.6.1wen2-8/+7
Upstream changes: CHANGES IN R 3.6.1: INSTALLATION on a UNIX-ALIKE: * The default detection of the shell variable libNN is overridden for derivatives of Debian Linux, some of which have started to have a /usr/lib64 directory. (E.g. Ubuntu 19.04.) As before, it can be specified in config.site. UTILITIES: * R CMD config knows the values of AR and RANLIB, often set for LTO builds. DEPRECATED AND DEFUNCT: * The use of a character vector with .Fortran() is formally deprecated and gives a non-portability warning. (It has long been strongly discouraged in 'Writing R Extensions'.) BUG FIXES: * On Windows, GUI package installation via menuInstallPkgs() works again, thanks to Len Weil's and Duncan Murdoch's PR#17556. * R CMD check on data() fixing PR#17558 thanks to Duncan Murdoch. * quasi(*, variance = list(..)) now works more efficiently, and should work in all cases fixing PR#17560. Further, quasi(var = mu(1-mu)) and quasi(var = "mu ^ 3") now work, and quasi(variance = "log(mu)") now gives a correct error message. * Creation of lazy loading database during package installation is again robust to Rprofile changing the current working directory (PR#17559). * boxplot(y ~ f, horizontal=TRUE) now produces correct x- and y-labels. * rbind.data.frame() allows to keep <NA> levels from factor columns (PR#17562) via new option factor.exclude. Additionally, it works in one more case with matrix-columns which had been reported on 2017-01-16 by Krzysztof Banas. * Correct messaging in C++ pragma checks in tools code for R CMD check, fixing PR#17566 thanks to Xavier Robin. * print()ing and auto-printing no longer differs for functions with a user defined print.function, thanks to Bill Dunlap's report. * On Windows, writeClipboard(.., format = <n>) now does correctly pass format to the underlying C code, thanks to a bug report (with patch) by Jenny Bryan. * as.data.frame() treats 1D arrays the same as vectors, PR#17570. * Improvements in smoothEnds(x, *) working with NAs (towards runmed() working in that case, in the next version of R). * vcov(glm(<quasi>), dispersion = *) works correctly again, fixing PR#17571 thanks to Pavel Krivitsky. * R CMD INSTALL of binary packages on Windows now works also with per-directory locking. * R CMD INSTALL and install.packages() on Windows are now more robust against a locked file in an earlier installation of the package to be installed. The default value of option install.lock on Windows has been changed to TRUE. * On Unix alikes (when readline is active), only expand tilde (~) file names starting with a tilde, instead of almost all tildes. * In R documentation (*.Rd) files, \item [..] is no longer treated specially when rendered in LaTeX and hence pdf, but rather shows the brackets in all cases.
2019-08-11Bump PKGREVISIONs for perl 5.30.0wiz80-146/+160
2019-08-09R-tidyr: initial commitbrook4-1/+35
An evolution of 'reshape2'. It's designed specifically for data tidying (not general reshaping or aggregating) and works well with 'dplyr' data pipelines.
2019-08-09R-dplyr: initial commitbrook4-1/+35
A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
2019-08-09R-compositions: initial commitbrook4-1/+31
Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.
2019-08-09R-robustbase: initial commitbrook4-1/+30
"Essential" Robust Statistics. Tools allowing to analyze data with robust methods. This includes regression methodology including model selections and multivariate statistics where we strive to cover the book "Robust Statistics, Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
2019-08-09R-tensorA: initial commitbrook4-1/+27
Provides convenience functions for advanced linear algebra with tensors and computation with datasets of tensors on a higher level abstraction. It includes Einstein and Riemann summing conventions, dragging, co- and contravariate indices, parallel computations on sequences of tensors.
2019-08-09R-DEoptimR: initial commitbrook4-1/+29
Differential Evolution (DE) stochastic algorithms for global optimization of problems with and without constraints. The aim is to curate a collection of its state-of-the-art variants that (1) do not sacrifice simplicity of design, (2) are essentially tuning-free, and (3) can be efficiently implemented directly in the R language. Currently, it only provides an implementation of the 'jDE' algorithm by Brest et al. (2006) <doi:10.1109/TEVC.2006.872133>.
2019-08-09R-energy: initial commitbrook4-1/+33
E-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, k-groups and hierarchical clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.
2019-08-08Update all R packages to canonical form.brook1-6/+4
The canonical form [1] of an R package Makefile includes the following: - The first stanza includes R_PKGNAME, R_PKGVER, PKGREVISION (as needed), and CATEGORIES. - HOMEPAGE is not present but defined in math/R/Makefile.extension to refer to the CRAN web page describing the package. Other relevant web pages are often linked from there via the URL field. This updates all current R packages to this form, which will make regular updates _much_ easier, especially using pkgtools/R2pkg. [1] http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html
2019-08-08Update all R packages to canonical form.brook100-594/+397
The canonical form [1] of an R package Makefile includes the following: - The first stanza includes R_PKGNAME, R_PKGVER, PKGREVISION (as needed), and CATEGORIES. - HOMEPAGE is not present but defined in math/R/Makefile.extension to refer to the CRAN web page describing the package. Other relevant web pages are often linked from there via the URL field. This updates all current R packages to this form, which will make regular updates _much_ easier, especially using pkgtools/R2pkg. [1] http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html
2019-08-07Add 'R' to the cateogries for R packages.brook1-2/+2
The category 'R' is used to denote R packages, just as 'perl5' and 'python' are used in other cases. To ensure consistency, add that to CATEGORIES in Makefile.extension rather than in each individual R package. This was discussed in http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html.
2019-08-06py-numba: updated to 0.45.1adam2-7/+7
Version 0.45.1 This patch release addresses some regressions reported in the 0.45.0 release and adds support for NumPy 1.17: * accept scalar/0d-arrays * Fix. Parfors reduction vars not deleted. * Use process level locks for fork() only. * Try to fix. * Fix np1.17 isnan, isinf, isfinite ufuncs * Fix np.interp for np1.17 nan handling * Fix nump1.17 random function non-aliasing Version 0.45.0 In this release, Numba gained an experimental numba.typed.List container as a future replacement of the reflected list. In addition, functions decorated with parallel=True can now be cached to reduce compilation overhead associated with the auto-parallelization. Enhancements from user contributed PRs (with thanks!): James Bourbeau added the Numba version to reportable error messages, added the signature parameter to inspect_types, improved the docstring of normalize_signatur, and fixed by adding reference counting to register_dispatcher Guilherme Leobas implemented the dominator tree and dominance frontier algorithms Nick White fixed the issue with round in the CUDA target. Joshua Adelman added support for determining if a value is in a range (i.e. x in range(...)), and added windowing functions (np.bartlett, np.hamming, np.blackman, np.hanning, np.kaiser) from NumPy. Lucio Fernandez-Arjona added support for np.select Rob Ennis added support for np.flatnonzero Keith Kraus extended the __cuda_array_interface__ with an optional mask attribute. Gregory R. Lee replaced deprecated use of inspect.getargspec
2019-08-06math/bc-gh: Update to 2.1.0gdt2-7/+7
Upstream changes: This release is a production release. The following bugs were fixed: A dc bug that caused stack mishandling was fixed. A warning on OpenBSD was fixed. Bugs in ctrl+arrow operations in history were fixed. The ability to paste multiple lines in history was added. A bc bug, mishandling of array arguments to functions, was fixed. A crash caused by freeing the wrong pointer was fixed. A dc bug where strings, in a rare case, were mishandled in parsing was fixed. In addition, the following changes were made: Division was slightly optimized. An option was added to the build to disable printing of prompts. The special case of empty arguments is now handled. This is to prevent errors in scripts that end up passing empty arguments. A harmless bug was fixed. This bug was that, with the pop instructions (mostly) removed (see below), bc would leave extra values on its stack for void functions and in a few other cases. These extra items would not affect anything put on the stack and would not cause any sort of crash or even buggy behavior, but they would cause bc to take more memory than it needed. On top of the above changes, the following optimizations were added: The need for pop instructions in bc was removed. Extra tests on every iteration of the interpreter loop were removed. Updating function and code pointers on every iteration of the interpreter loop was changed to only updating them when necessary. Extra assignments to pointers were removed. Altogether, these changes sped up the interpreter by around 2x. NOTE: This is the last release with new features because this bc is now considered complete. From now on, only bug fixes and new translations will be added to this bc.
2019-08-01R-RandomFieldsUtils: add a missing buildlink3.mk file.brook1-0/+12
2019-07-31R-zoo: update to version 1.8.6.brook2-10/+11
Update to the canonical form of an R package.
2019-07-31R-xts: update to version 0.11.2.brook3-14/+14
Update to the canonical form of an R package and fix the LICENSE field.
2019-07-31R-xtable: update to version 1.8.4.brook2-11/+10
Update to the canonical form of an R package and fix the LICENSE field.
2019-07-31R-wle: update to canonical form of an R package.brook1-5/+5
2019-07-31R-tibble: update to version 2.1.3.brook2-13/+14
Update to the canonical form of an R package.
2019-07-31R-statmod: update to version 1.4.32.brook2-10/+10
Update to the canonical form of an R package and fix the LICENSE field.
2019-07-31R-stabledist: update to canonical form of an R package.brook1-3/+3
Update to the canonical form of an R package and fix the LICENSE field.
2019-07-31R-splancs: update to version 2.01.40.brook2-10/+11
Update to the canonical form of an R package.
2019-07-31R-spacetime: update to version 1.2.2.brook2-10/+13
Update to the canonical form of an R package and fix the LICENSE field.
2019-07-31R-sp: update to canonical form of an R package.brook1-2/+4
2019-07-31R-shapefiles: update to canonical form of an R package.brook1-5/+6
Update to the canonical form of an R package and fix the LICENSE field.
2019-07-31R-sgeostat: update to version 1.0.27.brook2-9/+9
Update to the canonical form of an R package and fix the LICENSE field.
2019-07-31R-reshape2: update to canonical form of an R package.brook1-5/+6
Update to the canonical form of an R package and fix the LICENSE field.
2019-07-31R-randomForest: update to version 4.6.14.brook2-10/+10
Update to the canonical form of an R package and fix the LICENSE field.
2019-07-31R-quantreg: update to version 5.42.1.brook2-14/+13
Update to the canonical form of an R package.
2019-07-31R-quadprog: update to version 1.5.7.brook2-10/+9
Update to the canonical form of an R package and fix the LICENSE field.
2019-07-31R-prob: update to version 1.0.1.brook2-11/+11
Update to the canonical form of an R package.
2019-07-31R-prettyunits: update to canonical form of an R package.brook1-6/+8
2019-07-31R-poweRlaw: update to version 0.70.2.brook2-11/+11
Update to the canonical form of an R package and fix the LICENSE field.
2019-07-31R-plyr: update to canonical form of an R package.brook1-2/+2
2019-07-31R-pixmap: update to canonical form of an R package.brook1-2/+4
2019-07-31R-pbkrtest: update to canonical form of an R package.brook1-7/+6
Update to the canonical form of an R package and fix the LICENSE field.
2019-07-31R-numDeriv: update to version 2016.8.1.1.brook3-11/+10
Update to the canonical form of an R package.
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