Merge pull request #92 from RcppCore/feature/eigen-3.3.9

Update to Eigen 3.3.9 (closes #91)

Author: eddelbuettel

.travis.yml

@@ -2,26 +2,36 @@
 
 language: c
 sudo: required
-dist: trusty
+dist: focal
+
+jobs:
+  include:
+    - name: linux
+      os: linux
+    #- name: macOS
+    #  os: osx
+
+env:
+  global:
+    - USE_BSPM="true"
+    - _R_CHECK_FORCE_SUGGESTS_="false"
 
 before_install:
-  - curl -OLs https://eddelbuettel.github.io/r-travis/run.sh && chmod 0755 run.sh
-  # add our launchpad repo which has additional packages -- not needed here
-  # - sudo add-apt-repository -y ppa:edd/r-3.5
+  - curl -OLs https://eddelbuettel.github.io/r-ci/run.sh && chmod 0755 run.sh
   - ./run.sh bootstrap
 
 install:
-  - ./run.sh install_aptget r-cran-rcpp r-cran-matrix r-cran-inline r-cran-tinytest r-cran-pkgkitten r-cran-microbenchmark
+  - ./run.sh install_all
 
 script:
   - ./run.sh run_tests
 
-#after_success:
-#  - ./run.sh coverage
-
 after_failure:
   - ./run.sh dump_logs
 
+#after_success:
+#  - ./run.sh coverage
+
 notifications:
   email:
     on_success: change

ChangeLog

@@ -1,3 +1,18 @@
+2020-12-05  Dirk Eddelbuettel  <edd@debian.org>
+
+	* DESCRIPTION (Version, Date): Release 0.3.3.9.0
+
+	* inst/include/Eigen: Upgraded to Eigen 3.3.9
+	* inst/include/unsupported/Eigen: Idem
+	* patches/eigen-3.3.9.diff: Carried local CRAN patches forward
+
+	* .travis.yml: Switch to r-ci using focal and bspm
+
+	* README.md: Updated URLs to https and/or redirect location
+	* inst/CITATION: Idem
+	* man/RcppEigen-package.Rd: Idem
+	* man/fastLm.Rd: Idem
+
 2020-08-16  Dirk Eddelbuettel  <edd@debian.org>
 
 	* README.md: Add JSS badge

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: RcppEigen
 Type: Package
 Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library
-Version: 0.3.3.7.0
-Date: 2019-11-16
+Version: 0.3.3.9.0
+Date: 2020-12-05
 Author: Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu;
  the authors of Eigen for the included version of Eigen
 Maintainer: Dirk Eddelbuettel <edd@debian.org>
@@ -21,7 +21,6 @@ Description: R and 'Eigen' integration using 'Rcpp'.
  later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
  the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
 License: GPL (>= 2) | file LICENSE
-Depends: R (>= 2.15.1)
 LazyLoad: yes
 LinkingTo: Rcpp
 Imports: Matrix (>= 1.1-0), Rcpp (>= 0.11.0), stats, utils

README.md

@@ -1,13 +1,13 @@
 ## RcppEigen: Rcpp Integration for the Eigen Templated Linear Algebra Library
 
 [![Build Status](https://travis-ci.org/RcppCore/RcppEigen.svg)](https://travis-ci.org/RcppCore/RcppEigen)
-[![License](http://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html)
-[![License](http://img.shields.io/badge/license-MPL2-brightgreen.svg?style=flat)](http://www.mozilla.org/MPL/2.0/)
-[![CRAN](http://www.r-pkg.org/badges/version/RcppEigen)](https://cran.r-project.org/package=RcppEigen)
+[![License](https://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](https://www.gnu.org/licenses/gpl-2.0.html)
+[![License](https://img.shields.io/badge/license-MPL2-brightgreen.svg?style=flat)](https://www.mozilla.org/MPL/2.0/)
+[![CRAN](https://www.r-pkg.org/badges/version/RcppEigen)](https://cran.r-project.org/package=RcppEigen)
 [![Dependencies](https://tinyverse.netlify.com/badge/RcppEigen)](https://cran.r-project.org/package=RcppEigen)
 [![Debian package](https://img.shields.io/debian/v/r-cran-rcppeigen/sid?color=brightgreen)](https://packages.debian.org/sid/r-cran-rcppeigen)
 [![Last Commit](https://img.shields.io/github/last-commit/RcppCore/RcppEigen)](https://github.com/RcppCore/RcppEigen)  
-[![Downloads](http://cranlogs.r-pkg.org/badges/RcppEigen?color=brightgreen)](http://www.r-pkg.org/pkg/RcppEigen)
+[![Downloads](https://cranlogs.r-pkg.org/badges/RcppEigen?color=brightgreen)](https://www.r-pkg.org:443/pkg/RcppEigen)
 [![CRAN use](https://jangorecki.gitlab.io/rdeps/RcppEigen/CRAN_usage.svg?sanitize=true)](https://cran.r-project.org/package=RcppEigen)
 [![BioConductor use](https://jangorecki.gitlab.io/rdeps/RcppEigen/BioC_usage.svg?sanitize=true)](https://cran.r-project.org/package=RcppEigen)
 [![StackOverflow](https://img.shields.io/badge/stackoverflow-rcpp-orange.svg)](https://stackoverflow.com/questions/tagged/rcpp)
@@ -16,19 +16,19 @@
 
 ### Synopsis
 
-[Eigen](http://eigen.tuxfamily.org) is a C++ template library for linear algebra:
+[Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) is a C++ template library for linear algebra:
 matrices, vectors, numerical solvers and related algorithms.  It supports dense and sparse
 matrices on integer, floating point and complex numbers, decompositions of such matrices,
 and solutions of linear systems. Its performance on many algorithms is comparable with
 some of the best implementations based on `Lapack` and level-3 `BLAS`.
 
-RcppEigen provides an interface from R to and from [Eigen](http://eigen.tuxfamily.org) by
+RcppEigen provides an interface from R to and from [Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) by
 using the facilities offered by the [Rcpp](http://dirk.eddelbuettel.com/code/rcpp.html)
 package for seamless R and C++ integration.
 
 ### Examples
 
-A few examples are over at the [Rcpp Gallery](http://gallery.rcpp.org/tags/eigen/). A simple one is
+A few examples are over at the [Rcpp Gallery](https://gallery.rcpp.org/tags/eigen/). A simple one is
 
 ```c++
 #include <RcppEigen.h>
@@ -55,13 +55,13 @@ sourceCpp("eigenExample.cpp")
 
 due to the two Rcpp directives to use headers from the RcppEigen package, and to export
 the `getEigenValues()` function -- but read [the full
-post](http://gallery.rcpp.org/articles/eigen-eigenvalues/) for details.
+post](https://gallery.rcpp.org/articles/eigen-eigenvalues/) for details.
 
 
 ### Status
 
 The package is mature and under active development, following the
-[Eigen](http://eigen.tuxfamily.org) release cycle.
+[Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) release cycle.
 
 ### Documentation
 

inst/CITATION

@@ -9,11 +9,11 @@ citEntry(entry = "Article",
   volume       = "52",
   number       = "5",
   pages        = "1--24",
-  url          = "http://www.jstatsoft.org/v52/i05/",
+  url          = "https://www.jstatsoft.org/v52/i05/",
 
   textVersion  =
   paste("Douglas Bates, Dirk Eddelbuettel (2013).",
         "Fast and Elegant Numerical Linear Algebra Using the RcppEigen Package.",
         "Journal of Statistical Software, 52(5), 1-24.",
-        "URL http://www.jstatsoft.org/v52/i05/.")
+        "URL https://www.jstatsoft.org/v52/i05/.")
 )

inst/include/Eigen/Core

@@ -279,7 +279,10 @@
 #include <cmath>
 #include <cassert>
 #include <functional>
-#include <iosfwd>
+#include <sstream>
+#ifndef EIGEN_NO_IO
+  #include <iosfwd>
+#endif
 #include <cstring>
 #include <string>
 #include <limits>
@@ -375,7 +378,9 @@ using std::ptrdiff_t;
 
 #if defined EIGEN_VECTORIZE_AVX512
   #include "src/Core/arch/SSE/PacketMath.h"
+  #include "src/Core/arch/SSE/MathFunctions.h"
   #include "src/Core/arch/AVX/PacketMath.h"
+  #include "src/Core/arch/AVX/MathFunctions.h"
   #include "src/Core/arch/AVX512/PacketMath.h"
   #include "src/Core/arch/AVX512/MathFunctions.h"
 #elif defined EIGEN_VECTORIZE_AVX

inst/include/Eigen/Eigenvalues

@@ -10,14 +10,14 @@
 
 #include "Core"
 
-#include "src/Core/util/DisableStupidWarnings.h"
-
 #include "Cholesky"
 #include "Jacobi"
 #include "Householder"
 #include "LU"
 #include "Geometry"
 
+#include "src/Core/util/DisableStupidWarnings.h"
+
 /** \defgroup Eigenvalues_Module Eigenvalues module
   *
   *

inst/include/Eigen/Geometry

@@ -10,12 +10,12 @@
 
 #include "Core"
 
-#include "src/Core/util/DisableStupidWarnings.h"
-
 #include "SVD"
 #include "LU"
 #include <limits>
 
+#include "src/Core/util/DisableStupidWarnings.h"
+
 /** \defgroup Geometry_Module Geometry module
   *
   * This module provides support for:

inst/include/Eigen/QR

@@ -10,12 +10,12 @@
 
 #include "Core"
 
-#include "src/Core/util/DisableStupidWarnings.h"
-
 #include "Cholesky"
 #include "Jacobi"
 #include "Householder"
 
+#include "src/Core/util/DisableStupidWarnings.h"
+
 /** \defgroup QR_Module QR module
   *
   *

inst/include/Eigen/SparseQR

@@ -28,7 +28,6 @@
   * 
   */
 
-#include "OrderingMethods"
 #include "src/SparseCore/SparseColEtree.h"
 #include "src/SparseQR/SparseQR.h"