2024-02-28 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.4.0.0 2024-02-12 Tomas Kalibera * inst/include/unsupported/Eigen/CXX11/src/ThreadPool/ThreadYield.h: Support clang on Windows by including 'sched.h' header 2024-01-17 Yixuan Qiu * DESCRIPTION (Version, Date): Release candidate 0.3.3.99.0 * inst/include/Eigen: Upgraded to Eigen 3.4.0 * inst/include/unsupported/Eigen: Idem * patches/eigen-3.4.0.diff: Carried local CRAN patches forward * patches/howToDiff.md: Idem 2023-11-01 Dirk Eddelbuettel * DESCRIPTION (Version, Date): CRAN Release 0.3.3.9.4 * inst/NEWS.Rd: Release 0.3.3.9.4 2023-10-05 Mikael Jagan * DESCRIPTION: Package 'Matrix' is now only a Suggests: * NAMESPACE: Remove unconditional imports from package Matrix * inst/include/Eigen/CholmodSupport: No longer need to include RcppEigenCholmod.h * inst/include/Eigen/src/CholmodSupport/CholmodSupport.h: Small wrapper adjustments conditional on Matrix use * inst/include/RcppEigenCholmod.h: Updated * inst/include/RcppEigenForward.h: Simplified * inst/include/RcppEigenWrap.h: Ditto * inst/include/RcppEigenStubs.cpp: New shorter helper * inst/include/RcppEigenStubs.h: Removed 2023-07-21 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll micro version and date * README.md: Add r-universe badge 2023-07-20 Dirk Eddelbuettel * src/RcppEigen.cpp (EigenNbThreads): Add simple threads reporter * R/fastLm.R (fastLmPure): Simpler call to `fastLm_Impl()` * src/init.c: Replaced by auto-generated section in RcppExports.cpp * src/RcppExports.cpp: Regenerated * R/RcppExports.R: Idem * src/Makevars: Document possible use of '-fopenmp' * src/Makevars.win: Idem 2023-04-18 Dirk Eddelbuettel * README.md: Use app.codecov.io as base for codecov link 2023-03-10 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll minor version * R/RcppEigen.package.skeleton.R: No longer set Imports: RcppEigen in DESCRIPTION and NAMESPACE 2023-02-12 Dirk Eddelbuettel * inst/CITATION: Convert to bibentry() style with person() 2022-11-04 Dirk Eddelbuettel * DESCRIPTION (Version, Date): CRAN Release 0.3.3.9.3 * inst/NEWS.Rd: Release 0.3.3.9.3 * src/init.c: Add 'void' for proper prototype pleasing clang-15 * R/fastLm.R (summary.fastLm,print.fastLm): Refer to correct and full variable name df.residual in the returned object * .github/workflows/ci.yaml (jobs): Update to actions/checkout@v3 2022-09-15 Jonah Gabry * inst/skeleton/rcppeigen_hello_world.cpp: Correct typo 2022-04-08 Dirk Eddelbuettel * DESCRIPTION (Depends): Add a versioned dependency on R 3.6.0 or later because of our use of FCONE to support USE_FC_LEN_T 2022-04-05 Dirk Eddelbuettel * DESCRIPTION (Version, Date): CRAN Release 0.3.3.9.2 * inst/NEWS.Rd: Release 0.3.3.9.2 2022-04-04 Dirk Eddelbuettel * src/fastLm.cpp: Add FCONE in two calls for improved Fortran and C character interface per Writing R Extensions, Section 6.6.1 2022-01-16 Dirk Eddelbuettel * inst/tinytest/test_wrap.R: Added (optional) large memory wrap tests * inst/tinytest/cpp/wrap.cpp: Added C++ part of test * .codecov.yml: Added to not trigger PR fail for small additions 2022-01-16 Mikael Jagan * inst/include/RcppEigenWrap.h: Refine use plain dense wrap() change 2022-01-15 Mikael Jagan * inst/include/RcppEigenWrap.h: Use R_xlen_t for vectors rows + cols 2021-12-29 Dirk Eddelbuettel * README.md: Add total downloads badge 2021-12-08 Dirk Eddelbuettel * README.md: Remove unused continuous integration artifact and badge 2021-10-13 Dirk Eddelbuettel * inst/CITATION: Refinment of doi use 2021-10-10 Dirk Eddelbuettel * inst/CITATION: Switch JSS url to doi form per JSS request * README.md: Idem 2021-07-19 Dirk Eddelbuettel * inst/include/RcppEigenWrap.h: Two more #nocov tags * src/fastLm.cpp: One more #nocov tag 2021-07-18 Dirk Eddelbuettel * inst/tinytest/test_fastLm.R: Add tests for summary * src/fastLm.cpp: Add a few #nocov tags 2021-07-17 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll minor version * R/RcppEigen.package.skeleton.R (RcppEigen.package.skeleton): Also import RcppEigen in DESCRIPTION 2021-06-07 Dirk Eddelbuettel * DESCRIPTION (Date, Version): Roll minor version * inst/tinytest/test_misc.R: New test file * inst/tinytest/test_fastLm.R: Added tests * R/fastLm.R: Add single one-line nocov tag * .Rbuildignore: Add .covignore and .codecov.yml 2021-06-06 Dirk Eddelbuettel * README.md: Added coverage badge * .github/workflows/ci.yaml (jobs): Turn on coverage * .covrignore: Added * .codecov.yml (ignore): Idem * R/RcppEigen.package.skeleton.R: Set nocov 2021-05-09 Dirk Eddelbuettel * DESCRIPTION (URL): Add GitHub repo to URL field 2021-01-02 Dirk Eddelbuettel * R/RcppEigen.package.skeleton.R: Wrap any() around grepl() 2020-12-25 Dirk Eddelbuettel * .github/workflows/ci.yaml: Small tweaks to CI YAML file 2020-12-17 Dirk Eddelbuettel * DESCRIPTION (Version, Date): CRAN Release 0.3.3.9.1 (following coordinated update of reverse dependency StanHeaders) * inst/NEWS.Rd: Release 0.3.3.9.1 2020-12-14 Dirk Eddelbuettel * .github/workflows/ci.yaml: Add CI runner using r-ci * README.md: Add new badge 2020-12-05 Dirk Eddelbuettel * 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 * README.md: Add JSS badge 2020-03-29 Dirk Eddelbuettel * README.md: Added commit badge, edited 2020-01-22 Dirk Eddelbuettel * README.md: README.md: Add a Debian badge 2019-11-16 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.3.7.0 * inst/include/Eigen: Upgraded to Eigen 3.3.7 * inst/include/unsupported/Eigen: Idem * patches/eigen-3.3.7.diff: Carried local CRAN patches forward 2019-11-01 Dirk Eddelbuettel * R/unit.test.R (compile_unit_tests): Removed as no longer needed 2019-10-31 Dirk Eddelbuettel * inst/tinytest/test_transform.R: Switch from RUnit to tinytest * inst/tinytest/test_wrap.R: Idem * inst/tinytest/cpp/transform.cpp: Added using Rcpp Attributes * inst/tinytest/cpp/wrap.cpp: Idem * inst/tinytest/cpp/sparse.cpp: More idiomatic Eigen code * inst/tinytest/test_sparse.R: Idem * .editorconfig: Added 2019-10-30 Dirk Eddelbuettel * DESCRIPTION (Suggests): Switch from RUnit to tinytest * .travis.yml (install): Ditto * tests/tinytest.R: Converted to tinytest * test_sparse.R: Converted to tinytest * cpp/sparse.cpp: Added using Rcpp Attributes 2019-10-29 Dirk Eddelbuettel * test_fastLm.R: Converted to tinytest * test_RcppEigen.R: Idem * test_solution.R: Idem * cpp/rcppeigen.cpp: Added using Rcpp Attributes * cpp/solution.cpp: Idem 2019-10-28 Dirk Eddelbuettel * tests/tinytest.R: Renamed from tests/doRUnit.R * inst/tinytest/test_fastLm.R: Renamed from inst/unitTests/runit* * inst/tinytest/test_RcppEigen.R: Idem * inst/tinytest/test_solution.R: Idem * inst/tinytest/test_sparse.R: Idem * inst/tinytest/test_transform.R: Idem * inst/tinytest/test_wrap.R: Idem 2019-10-13 Dirk Eddelbuettel * README.md: Added CRAN + BioConductor badges for reverse depends, add StackOverflow badge to recommend help searches under 'Rcpp' * DESCRIPTION (Version, Date): Roll minor version * R/RcppEigen.package.skeleton.R (RcppEigen.package.skeleton): Test for example_code outside of haveKitten test; remove force argument if unused 2019-05-24 Dirk Eddelbuettel * vignettes/RcppEigen-Introduction.Rnw: Update vignette to use RcppEigen:::eigen_version() instead of .Call() 2019-03-29 Dirk Eddelbuettel * inst/skeleton/rcppeigen_hello_world.cpp: Rework first example to not rely on Eigen RNG which R CMD check would complain about. 2019-02-16 James Joseph Balamuta * R/runit.RcppEigen.R: Removed listing RcppEigen in Imports during skeleton package creation. 2018-11-24 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.3.5.0 2018-11-23 Dirk Eddelbuettel * inst/include/Eigen: Updated to release 3.3.5 * inst/include/unsupported: Idem * patches/eigen-3.3.5.diff: Diff of local patches 2018-09-02 Dirk Eddelbuettel * .travis.yml: Switch Travis CI to R 3.5 repo 2018-05-30 Michael Weylandt * inst/examples/lmBenchmark.R: Update benchmark script to use microbenchmark and to use exposed fastLm functions from Rcpp packages rather than invoking .Call directly 2018-05-25 Ralf Stubner * inst/include/RcppEigenWrap.h: Use Rf_xlength and R_xlen_t to support long vectors 2018-02-07 Dirk Eddelbuettel * patches/eigen-3.3.4.diff: Diff to upstream Eigen 3.3.4, cherry-picked in the 3.3.4 branch of Yixuan 2018-02-05 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.3.4.0 * inst/include/Eigen/src/Core/arch/CUDA/Half.h (Eigen): Condition use of long long and unsigned long on C++11 * inst/include/Eigen/src/Core/arch/SSE/Complex.h (Eigen): Comment-out use of diagnostic-suppressing pragma for gcc + clang to satisfy CRAN * inst/include/Eigen/src/Core/util/DisableStupidWarnings.h: Idem 2018-02-04 Yixuan Qiu [ In RcppEigen 0.3.3.* branch ] * inst/include/Eigen: Updated to the upstream 3.3 branch of Eigen based on version 3.3.4 * inst/include/unsupported: Idem * DESCRIPTION: Idem * README.md: Idem * inst/include/Eigen/src/Core/util/DisableStupidWarnings.h: Patch from upstream Eigen that has not been ported to the 3.3 branch (cf GitHub issue #48) 2017-11-19 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.3.3.1 * R/inline.R: Use '::' not ':::' for Rcpp.plugin.maker 2017-08-26 Dirk Eddelbuettel * .travis.yml (before_install): Use https for curl fetch 2017-06-06 Yu Gong * inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h: Also permit compilation under Haiku-OS 2017-05-28 Dirk Eddelbuettel * inst/examples/lmBenchmark.R (do_bench): Remove spurious argument in call to RcppEigen:::Eigen_SSE() (cf github issue #44) 2017-04-29 Dirk Eddelbuettel * DESCRIPTION: Release 0.3.3.3.0 [ which again owes a very big thank you to Yixuan for doing the work! ] 2017-04-27 Dirk Eddelbuettel * .travis.yml: Switch to using run.sh for Travis CI 2017-04-27 Yixuan Qiu [ In RcppEigen 0.3.3.* branch ] * inst/include/Eigen/src/Core/arch/CUDA/Half.h: Fixed compiler warning on 'long long' type in C++ 98 mode 2017-03-14 Dirk Eddelbuettel * DESCRIPTION (Version, Date): Release 0.3.2.9.1 * src/init.c (R_init_RcppEigen): Call R_registerRoutines() and R_useDynamicSymbols() * NAMESPACE: Use .registration=TRUE on useDynLib * R/fastLm.R (fastLmPure): Remove erroneous fourth argument from .Call 2017-03-13 Martin Maechler * inst/include/RcppEigenCholmod.h: Synchronize with Matrix package 2017-02-21 Yixuan Qiu [ In RcppEigen 0.3.3.* branch ] * inst/include/Eigen: Updated to release 3.3.3 of Eigen * inst/include/unsupported: Idem * DESCRIPTION: Idem * README.md: Idem 2017-01-20 Yixuan Qiu [ In RcppEigen 0.3.3.* branch ] * inst/include/Eigen: Updated to release 3.3.2 of Eigen * inst/include/unsupported: Idem * DESCRIPTION: Idem * README.md: Idem * inst/unitTests/runit.RcppEigen.R, inst/unitTests/runit.sparse.R: Explicitly convert matrix size to `double` type such that Rcpp can properly return the value to R, thanks to ChingChuan and Dirk 2017-01-20 ChingChuan Chen [ In RcppEigen 0.3.3.* branch ] * inst/include/Eigen: Updated to release 3.3.1 of Eigen * inst/include/unsupported: Idem * DESCRIPTION: Idem * inst/examples/lmBenchmark.R: Fixed function names 2016-12-22 Dirk Eddelbuettel * DESCRIPTION (URL, BugReports): Added / updated 2016-11-12 Yixuan Qiu [ In RcppEigen 0.3.3.* branch ] * inst/include/Eigen: Updated to release 3.3.0 of Eigen * inst/include/unsupported: Idem * DESCRIPTION: Idem * README.md: Idem * inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: Added exporters for the new Map > type * inst/unitTests/runit.sparse.R: Unit tests for the new type 2016-08-20 Dirk Eddelbuettel * DESCRIPTION: Release 0.3.2.9.0 with big thanks to Yixuan for doing the work! 2016-08-19 Yixuan Qiu * inst/include/Eigen: Updated to release 3.2.9 of Eigen * README.md: Updated version number and fixed the NOTE from CRAN URL check 2016-04-30 Dirk Eddelbuettel * README.md: Expanded 2016-04-28 James Joseph Balamuta * inst/include/RcppEigenWrap.h: Added an exporter class for Map::RowVectorX per http://stackoverflow.com/questions/36920689/ * inst/include/unitTests/runit.RcppEigen.R: Added row exporter unit test. 2016-02-29 Dirk Eddelbuettel * DESCRIPTION (Version): Release 0.3.2.8.1 * inst/NEWS.Rd: Release 0.3.2.8.1 * debian/*: Changes for Debian release of 0.3.2.8.1 2016-02-28 Yixuan Qiu * inst/include/Eigen/src/SparseCore/CompressedStorage.h, inst/include/Eigen/src/SparseCore/SparseBlock.h, inst/include/Eigen/src/SparseCore/SparseMatrix.h, inst/include/Eigen/src/SparseCore/SparseRedux.h, inst/include/Eigen/src/SparseCore/SparseVector.h: Another patch from upstream to fix UBSAN null pointer errors 2016-02-23 Dirk Eddelbuettel * DESCRIPTION (Version): Release 0.3.2.8.0 * DESCRIPTION (Author): Added Yixuan Qiu * inst/NEWS.Rd: Release 0.3.2.8.0 2016-02-22 Yixuan Qiu * inst/include/Eigen: Updated to release 3.2.8 of Eigen * inst/include/unsupported: Idem * DESCRIPTION: Idem * README.md: Idem * inst/include/Eigen/src/SparseCore/CompressedStorage.h, inst/include/Eigen/src/Core/util/Memory.h: Applied patch from upstream to fix UBSAN errors 2016-01-20 Dirk Eddelbuettel * DESCRIPTION: Release 0.3.2.7.0 * debian/*: Changes for Debian release of 0.3.2.7.0 2016-01-19 Dirk Eddelbuettel * inst/unitTests/runit.sparse.R (test.sparseCholesky.R): Accomodate stricter as.vector() requirements in R-devel 2016-01-18 Yixuan Qiu * inst/include/Eigen: Updated to release 3.2.7 of Eigen * inst/include/unsupported: Idem * DESCRIPTION: Idem * README.md: Idem 2015-11-01 Alexey Stukalov * src/fastLm.cpp: Do not include R's LAPACK header if MKL defined 2015-09-23 Dirk Eddelbuettel * DESCRIPTION: Release 0.3.2.5.1 * debian/*: Changes for Debian release of 0.3.2.5.1 2015-09-21 Dirk Eddelbuettel * inst/include/Eigen/src/SparseCore/CompressedStorage.h: Added somewhat adapted code from upstream PR #118 to address UBSAN 2015-08-21 Dirk Eddelbuettel * src/RcppEigen.cpp: Updated code to use Rcpp Attributes * src/fastLm.cpp: Ditto * src/fastLm.h: Ditto * R/fastLm.R: Ditto * inst/unitTests/runit.fastLm.R: Ditto 2015-08-04 Dirk Eddelbuettel * R/RcppEigen.package.skeleton.R: Correct kitten() use based on patch kindly supplied by Grant Brown (cf GitHub issue #21) 2015-07-13 Dirk Eddelbuettel * DESCRIPTION: Version 0.3.2.5.0 2015-07-13 Yixuan Qiu * inst/include/Eigen/src/Core/Assign.h: Applied patch from upstream Eigen that will appear in the next release 2015-07-12 Dirk Eddelbuettel * DESCRIPTION: Added more explicitly quoting per R CMD check * NAMESPACE: Explicitly importFrom() stats and utils packages 2015-07-11 Yixuan Qiu * inst/include/Eigen: Updated to release 3.2.5 of Eigen * inst/include/unsupported: Idem * DESCRIPTION: Idem * README.md: Idem * inst/include/RcppEigenWrap.h: Fixed three incorrect error messages 2015-06-06 Dirk Eddelbuettel * R/RcppEigen.package.skeleton.R: Correct use of requireNamespace() 2015-02-26 Dirk Eddelbuettel * DESCRIPTION: Version 0.3.2.4.0 * debian/*: Updated 2015-02-23 Dirk Eddelbuettel * inst/include/Eigen: Updated to release 3.2.4 of Eigen * DESCRIPTION: Updated Version: and Date: * README.md: Idem * .travis.yml: Switch to ppa:edd/misc for binaries * R/RcppEigen.package.skeleton.R: Use pkgKitten::kitten, if installed * inst/skeleton/rcppeigen_hello_world.Rd: Added new page * inst/skeleton/Makevars: Minor edits * inst/skeleton/Makevars.win: Idem * DESCRIPTION: Added Suggests: for pkgKitten * .travis.yml: Also install pkgKitten 2014-12-22 Yixuan Qiu * inst/include/Eigen: Updated to release 3.2.3 of Eigen * DESCRIPTION: Idem * README.md: Idem 2014-11-23 Yixuan Qiu * inst/unitTests/runit.wrap.R: Added a number of unit tests * inst/unitTests/runit.transform.R: Idem * inst/unitTests/runit.sparse.R: Idem 2014-10-20 Dirk Eddelbuettel * inst/examples/lmBenchmark.R: Updated RcppArmadillo .Call in example 2014-08-21 Dirk Eddelbuettel * DESCRIPTION: New version 0.3.2.2.0 which was prepared expertly by Yixuan Qiu in a nice and clean pull request -- a big thank you for that! * DESCRIPTION: Adjusting Date: as well 2014-08-19 Yixuan Qiu * inst/include/Eigen: Updated to release 3.2.2 of Eigen * inst/unitTests/runit.wrap.R: More unit tests to reflect changes in as() exporters 2014-05-29 Yixuan Qiu * inst/include/RcppEigenWrap.h: Added as() conversion from R vector to Eigen::Array * inst/include/RcppEigenWrap.h: Fixed incorrect as() exporters * inst/include/RcppEigenWrap.h: Check matrix type of "dgCMatrix" instead of "CsparseMatrix" * inst/include/RcppEigenWrap.h, inst/include/RcppEigenForward.h: Added as() conversion from "dgRMatrix" to Eigen::MappedSparseMatrix 2014-05-01 Dirk Eddelbuettel * inst/include/Eigen/src/Core/util/Memory.h: Applied patch by Gael Guennebaud created in response to Doug's bug report (#803) which in turn is based on the UBSAN report at CRAN by Brian Ripley 2014-03-06 Dirk Eddelbuettel * DESCRIPTION: New version 0.3.2.1.1 2014-03-05 Dirk Eddelbuettel * inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h: Better, more general test for DIRENT feature thanks to Brian Ripley 2014-03-04 Dirk Eddelbuettel * inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h: (re-)add another #ifndef excluding a line on Solaris 2014-03-03 Dirk Eddelbuettel * DESCRIPTION: New release version 0.3.2.1.0 2014-03-03 Douglas Bates * inst/include/Eigen: Update to release 3.2.1 of Eigen 2014-03-01 Dirk Eddelbuettel * DESCRIPTION: New minor version 3.2.0.3 * DESCRIPTION: Switched to 'Imports: Rcpp (>= 0.11.0)' * src/Makevars: Updated for Rcpp 0.11.0 * src/Makevars.win: Ditto * R/RcppEigen.package.skeleton.R: Updated for Rcpp 0.11.0, also updated for current R versions by removing deprecated 'namespace' arg * man/RcppEigen.package.skeleton.Rd: Removed 'namespace' for current R * inst/skeleton/rcppeigen_hello_world.cpp: Rewritten / extended similar to the RcppArmadillo variant; now contains four functions exported by Rcpp Attributes * inst/skeleton/Makevars: Updated for Rcpp 0.11.0, also noted C++11 option via setting of 'USE_CXX1X=' with R 3.1.0 or later * inst/skeleton/Makevars.win: Ditto 2014-01-26 Dirk Eddelbuettel * DESCRIPTION: New minor version 3.2.0.2 2014-01-22 Dirk Eddelbuettel * NAMESPACE: Added importFrom(Rcpp, evalCpp) needed for next Rcpp 2014-01-12 Dirk Eddelbuettel * R/SHLIB.maker: Commented-out, file to be removed 2013-12-19 Dirk Eddelbuettel * DESCRIPTION: Updated Description to mention MPL-2 license for Eigen * inst/unitTests/runit.solutions.R: RUnit file converted from testthat * inst/unitTests/runit.transform.R: Idem * inst/unitTests/runit.wrap.R: Idem * DESCRIPTION: Remove Suggests: of testthat 2013-12-18 Dirk Eddelbuettel * DESCRIPTION: New minor version 3.2.0.1 * DESCRIPTION: New maintainer * DESCRIPTION: Added Copyright: reference to new COPYRIGHTS file * DESCRIPTION: Added reference to new LICENSE file * inst/COPYRIGHTS: Added, based on existing debian/copyright file * LICENSE: Added to state MPL-2 for Eigen, GPL (>=2) for RcppEigen * inst/include/Eigen/src/SparseLU/SparseLU.h: Applied Solaris patch * inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h: Idem * inst/include/RcppEigenForward.h: Idem 2013-12-04 Dirk Eddelbuettel * debian/*: Added after emails with Doug * .Rbuildignore: Added debian/ 2013-11-13 Douglas Bates * DESCRIPTION: New version, release date and dependencies * inst/include/Eigen: Update to release 3.2.0 of Eigen 2013-02-03 Dirk Eddelbuettel * DESCRIPTION: New minor version 0.3.1.2.1 for upload to CRAN and JSS * NEWS.org: Updated 2013-01-26 Dirk Eddelbuettel * vignettes/jss835/: Regroup all related files in this directory * .Rbuildignore: Ignore vignettes/jss835 2013-01-14 Dirk Eddelbuettel * inst/CITATION: Added as provided by JSS editor * man/fastLm.Rd: Added reference to JSS paper * man/RcppEigen-package.Rd: Idem 2012-11-29 Douglas Bates * DESCRIPTION: New version * inst/include/Eigen, inst/include/unsupported: Update to version 3.1.2 of Eigen. 2012-11-29 Romain Francois * include/RcppEigenWrap.h: compatibility issue with Rcpp 0.10.1 2012-08-14 Dirk Eddelbuettel * R/flags.R: Add two (unexported) functions CxxFlags() and RcppEigenCxxFlags() for use in Makefiles etc 2012-07-30 Douglas Bates * inst/include/RcppEigenWrap.h, inst/unitTests/runit.RcppEigen.R: Another suggestion from Gael Guennebaud to allow row vectors to be wrapped. 2012-07-28 Douglas Bates * inst/include/RcppEigenWrap.h, inst/unitTests/runit.RcppEigen.R: More fixes to RcppEigenWrap.h and adjustment of tests accordingly. The changes allow RowMajor matrices to be wrapped (thanks to Gael Guennebaud) but cannot handle RowVector types. There will need to be more template metaprogramming done to redirect the case of RowVector, which cannot be changed to a ColMajor form. * src/Makevars: Because of changes in R, -DNDEBUG is automatic. One must override it with -UNDEBUG in the local ~/.R/Makevars to activate the debugging code. * inst/doc/code.R: New version of wrap code provides correct answer to the badtrans example * DESCRIPTION: Bump the date. 2012-07-27 Douglas Bates * inst/include/Eigen/*: Changed to released version of Eigen-3.1.0 using the MPL2 license. 2012-07-19 Dirk Eddelbuettel * R/fastLm.R: correct residual standard error display * R/fastLm.R: improved test for intercept once more with a tip of the hat to Doug 2012-07-17 Dirk Eddelbuettel * R/fastLm.R: Corrections for R^2 in no-intercept case 2012-06-26 Douglas Bates * DESCRIPTION, R/unit.test.R, inst/include/Eigen/*: Massive changes related to upgrade to Eigen-3.1.0 2012-03-13 Douglas Bates * inst/include/RcppEigenWrap.h: Change the wrap methods to avoid creating Rcpp::Dimension objects (which are implicitly created by the Rcpp::Matrix constructor). * inst/tests/test-solutions.R: Clean up. I defined the results then reevaluated them. 2012-03-08 Douglas Bates * inst/include/RcppEigenForward.h: Remove an include of RcppEigenConfig.h which is no longer needed. * ChangeLog, NEWS, NEWS.org: Update Changelog and NEWS which is generated from an org-mode file NEWS.org * inst/include/RcppEigenConfig.h, inst/include/unsupported/Eigen/MoreVectorization, inst/include/unsupported/Eigen/src/MoreVectorization/CMakeLists.txt: Delete the unsupported/Eigen/src/MoreVectorization module which we don't need * inst/include/unsupported/Eigen/src/MoreVectorization/MathFunctions.h: Delete the unsupported/Eigen/src/MoreVectorization module which we don't need * inst/tests/test-solutions.R, inst/tests/test-transform.R, inst/tests/test-wrap.R: Add testthat test files, temporarily disabled for R CMD check because of an unknown conflict * DESCRIPTION, R/unit.test.R, inst/include/Eigen/Cholesky, ..., src/Makevars: Massive changes in upgrade to Eigen-3.1.0-alpha2 2012-03-03 Douglas Bates * inst/include/RcppEigenWrap.h: Correct a typo. 2012-02-28 Douglas Bates * inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: Add as templates for ArrayXd and ArrayXXd 2012-02-03 Douglas Bates * inst/include/RcppEigenWrap.h, inst/unitTests/runit.sparse.R: Allow import of compressed row sparse matrices. Add test of same. 2012-01-18 Douglas Bates * inst/include/RcppEigenWrap.h: Allow for wrapping sparse row-major matrices. 2011-12-31 Douglas Bates * inst/include/RcppEigenCholmod.h: Minor typo in a comment 2011-12-23 Dirk Eddelbuettel * inst/unitTests/runTests.R: unit tests output 'fallback' directory changed to '..' and files are now in top-level of $pkg.Rcheck/ 2011-11-14 Douglas Bates * vignettes/RcppEigen-intro-nojss.Rnw: Many, many changes by Dirk and by Doug over the last two weeks to create a JSS paper and updated package. Too many changes to list. 2011-10-26 Douglas Bates * inst/doc/Rcpp.bib, inst/doc/RcppEigen-Intro.Rnw, inst/doc/RcppEigen-Intro.pdf: Add an introductory vignette. * src/fastLm.cpp, src/fastLm.h: Use a method for XtX but returning a MatrixXd, not a view. * inst/doc/RcppEigen-Intro.Rnw: Describe the SymmEig method correctly. * src/fastLm.cpp, src/fastLm.h: Use a macro for XtX temporarily. Clean up code. * inst/include/RcppEigenCholmod.h, inst/include/RcppEigenStubs.h: Update to Matrix_1.0.2 versions * inst/include/Eigen, inst/include/unsupported: update to eigen 3.0.3 * src/RcppEigen.cpp: Add externally callable functions for Eigen version and SSE instruction sets in use. * inst/examples/lmBenchmark.R: Suppress messages and provide additional information about Eigen version and SSE instructions in use. * R/fastLm.R: Allow optional arguments to be passed to printCoefmat; adapt to new returned structure. 2011-09-16 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Avoid compiler warnings about comparing signed and unsigned values. 2011-09-13 Douglas Bates * src/Makevars: Force the -DNDEBUG flag to satisfy R CMD check in R-2.14.0 and higher 2011-09-12 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Remove the solvetype specification for the solve method (but type is retained for solveInPlace). 2011-09-11 Douglas Bates * inst/include/RcppEigenForward.h: Remove forward declaration of non-existent templated function. 2011-09-02 Douglas Bates * DESCRIPTION, inst/include/Eigen/src/Core/util/Meta.h: New release. ifdef the use of "long long" using RCPP_HAS_LONG_LONG_TYPES (thanks, Dirk) 2011-08-31 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Delete my addition of a CholmodAutoLLt mode, which is not needed (I misunderstood something previously). 2011-08-28 Douglas Bates * many files in inst/include/Eigen and inst/include/unsupported: Upgrade to Eigen release 3.0.2 2011-08-12 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: By-passing the const reference 2011-08-11 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Add a solveInPlace method to try to avoid memory problems. 2011-08-10 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Attempted fix of problem of freeing Map'ed memory in the Cholmod solve. 2011-07-31 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Trying to fix the memory problems from the CholmodDecomposition solve methods - apparently unsuccessfully. 2011-07-29 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Add LLtAuto method (which doesn't seem to work), more extractors and a factorize_p method for a const_CHM_SP argument. * inst/include/RcppEigenCholmod.h: Add a declaration of log determinant squared function. * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h, inst/unitTests/runit.sparse.R: Allow rectangular matrix in CholmodDecomposition's factorize method. Test rectangular version of KNex example. 2011-07-28 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Added a solveType member - there will be better ways of doing this * inst/include/RcppEigenForward.h: Include the stubs unconditionally * inst/include/RcppEigenStubs.cpp: * inst/include/RcppEigenStubs.h: Inlined the function definitions so it is a header file now * inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h: Extended CholmodDecomposition analyzePattern and factorize to support rectangular matrices. Added factorize_p method, primarily for the factorization of A'A + I. * DESCRIPTION, NAMESPACE, R/SHLIB.R, R/inline.R, inst/include/RcppEigen.h, inst/include/RcppEigenConfig.h, inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h, inst/include/unsupported/Eigen/SparseExtra, inst/include/unsupported/Eigen/src/SparseExtra/CholmodSupport.h, inst/skeleton/Makevars, inst/unitTests/runit.sparse.R: Add support for Cholmod functions linked through the Matrix package. Tests for same. Wrap of an Eigen::SparseMatrix now returns an S4 dgCMatrix object. * inst/include/RcppEigenCholmod.h, inst/include/RcppEigenStubs.cpp: Create stubs and the Cholmod header. (To Do: make the stubs inline functions in a header file.) 2011-07-27 Douglas Bates * inst/unitTests/runit.sparse.R: Separate the tests for sparse matrices. 2011-07-26 Douglas Bates * inst/include/unsupported/Eigen/src/SparseExtra/SimplicialCholesky.h: Added matrixLDL method 2011-07-18 Douglas Bates * src/fastLm.cpp: clean up code, taking advantage of the more general wrap methods 2011-07-15 Douglas Bates * inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h, inst/unitTests/runit.RcppEigen.R: added as methods for Eigen::SparseMatrix and Eigen::MappedSparseMatrix classes and tests of same 2011-07-13 Douglas Bates * DESCRIPTION, inst/include/RcppEigenWrap.h, inst/unitTests/runit.RcppEigen.R: Dispatch on wrap to vector according to T::ColsAtCompileTime; modify tests to avoid the .eval() methods; bump Rcpp version dependence 2011-07-13 Romain Francois * inst/include/RcppEigenWrap.h: dispatch sparse/dense and generalizes dealing with sparse objects * inst/include/RcppEigenWrap.h: comment non generic implementations * inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: comment non generic implementations * inst/include/RcppEigenWrap.h: deal with dimensions in eigen_wrap_is_plain * inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: first steps into dealing with Eigen expressions 2011-07-10 Douglas Bates * inst/include/PlainObjectBaseAddon.h: Added some begin and end methods to PlainObjectBase template through the extension mechanism. Should make these legitimate iterators to simplify some wrap methods (need a value_type member). * inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h, inst/unitTests/runit.RcppEigen.R: Added as methods for mapped vectors and mapped matrices (still some code duplication) and tests of same. 2011-07-09 Dirk Eddelbuettel * inst/unitTests/runit.RcppEigen.R: s/Armadillo/Eigen/ in a few places 2011-07-09 Douglas Bates * inst/unitTests/runit.RcppEigen.R: Added tests of wrap and as. Need to create an as method for mapped arrays. 2011-07-08 Douglas Bates * DESCRIPTION: Prepare for a new release. * inst/include/RcppEigen.h, inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: Add wrap methods for mapped Eigen objects; Initial support for as<> with some Eigen classes. * inst/include/unsupported/Eigen/src/SparseExtra/SimplicialCholesky.h: Commit interim version of the SimplicialLLT and SimplicialLDLT classes that will appear in Eigen 3.0.2 2011-06-30 Douglas Bates * src/fastLm.cpp: Code simplification suggested by Gael Guennebaud 2011-06-29 Dirk Eddelbuettel * DESCRIPTION: make Maintainers equal to Authors (but keep our joint email address) 2011-06-29 Douglas Bates * inst/include/RcppEigenWrap.h: Syntax errors corrected. 2011-06-28 Douglas Bates * inst/examples/lmBenchmark.R: Print the results from do_bench() so echo=TRUE is not needed when sourcing; add a suppressSVD argument to do_bench(). 2011-06-27 Douglas Bates * inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: Add a wrap method (compiles but currently untested) for Eigen::SparseMatrix * src/fastLm.cpp: Include sample code for the Moore-Penrose inverse. There are better ways of doing this but I can't work out the syntax. 2011-06-25 Douglas Bates * inst/examples, inst/examples/lmBenchmark.R: Add lm benchmark example * src/fastLm.cpp: tighten code a bit 2011-06-23 Douglas Bates * src/fastLm.cpp: Don't try to extract names that aren't there. * man/fastLm.Rd: Add a simple example. * src/fastLm.cpp, src/fastLm.h: Add the SymmEig lm method. Preliminary support for setting a tolerance for the rank calculation. * src/RcppEigen.cpp: Use the correct macros for eigen_version. * man/fastLm.Rd, tests/simple.R: Add examples and test cases for simple crossprod and tcrossprod functions * inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: bypass the incomplete exporter functions to support as<> 2011-06-21 Douglas Bates * src/fastLm.cpp, src/fastLm.h: Add an SVD method for fastLm * DESCRIPTION: Minor fix in punctuation. * R/fastLm.R, inst/unitTests/runit.fastLm.R, man/fastLm.Rd, src/fastLm.cpp, src/fastLm.h: Refactoring of the fastLm code to allow algorithms to be added easily. Adjust docs and R code accordingly. 2011-06-17 Douglas Bates * inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h: Add wrap instantiations for ArrayXd, ArrayXXd classes in Eigen 2011-06-15 Douglas Bates * DESCRIPTION, R/RcppEigen.package.skeleton.R, R/SHLIB.R, R/fastLm.R, R/inline.R, R/unit.test.R, inst/doc/RcppEigen-unitTests.Rnw, inst/include/RcppEigen.h, inst/include/RcppEigenConfig.h, inst/include/RcppEigenForward.h, inst/include/RcppEigenWrap.h, inst/unitTests/runit.fastLm.R, man/fastLm.Rd, src/RcppEigen.cpp, src/fastLm.cpp: Change references to Armadillo into Eigen; author order in copyright statements. 2011-06-15 Dirk Eddelbuettel * tests/doRUnit.R: oops: s/Armadillo/Eigen/ 2011-06-15 Douglas Bates * src/fastLm.cpp: Initial (not very good) implementation of "fastLmSVD", which isn't really that fast. * man/fastLm.Rd: Minor clarification. 2011-06-15 Douglas Bates * cleanup, inst/doc/*: Documentation based on unit tests. * R/SHLIB.R, R/inline.R, R/unit.test.R: Add support for inline package * inst/include/RcppEigen.h: Add support for sparse Cholesky and LU * inst/include/unsupported, inst/include/unsupported/*: Add support for sparse Cholesky and LU * man/RcppEigen-package.Rd: Add reference to web page * NAMESPACE, R/RcppEigen.package.skeleton.R, inst/skeleton/*, man/RcppEigen.package.skeleton.Rd: Add RcppEigen.package.skeleton and support files. * DESCRIPTION: Remove Conrad's text about Armadillo, as suggested by Dirk 2011-06-15 Dirk Eddelbuettel * inst/unitTests/runit.fastLm.R: better way to load trees dataset * man/fastLm.Rd: better way to load trees dataset * inst/unitTests/runit.fastLm.R, man/fastLm.Rd: added unit tests for fastLm{Bench,Chol1,Chol2} * ChangeLog, inst/unitTests, inst/unitTests/runTests.R, inst/unitTests/runit.fastLm.R, tests, tests/doRUnit.R: added initial unit tests 2011-06-14 Dirk Eddelbuettel * inst/unitTests/*: Added initial unit tests * tests/doRUnit.R: Added hook to run RUnit tests 2011-06-14 Douglas Bates * src/fastLm.cpp: Cosmetic fixes. * DESCRIPTION: New version. * man/fastLm.Rd: Change order of fastLmPure arguments in the example. Dirk said I would miss one of these. :-) * R/fastLm.R, man/fastLm.Rd, src/fastLm.cpp: Change order of fastLmPure arguments and the various fastLm* C++ functions. Add fastLmChol1 and fastLmChol2. 2011-06-13 Douglas Bates * ChangeLog: Add ChangeLog * src/fastLm.cpp: Handle the rank-deficient case. * inst/include/Eigen/src/LU/arch/Inverse_SSE.h: Use an _m128d type instead of long long int for the mask. * R/fastLm.R: Associate names with coefficients. Clean up fastLm. Forward the object through summary. * inst/include/Eigen/src/Core/util/Meta.h: Suppress use of long long