% Check from R:
%  news(db = tools:::.build_news_db_from_package_NEWS_Rd("~/R/Pkgs/Matrix/inst/NEWS.Rd"))
\name{NEWS}
\title{News for \R Package \pkg{Matrix}}% MM: look into ../svn-log-from.all
\encoding{UTF-8}
%% NB: The date (yyyy-mm-dd) is the "Packaged:" date in ../DESCRIPTION

%%_NOT YET__FIXME_ : needs *MORE THAN* cholmod_l_dense_to_sparse() in
%%----------------   our dense_to_Csparse() in ../src/dense.c (see there)
%%
%% \item \code{as(<large-matrix>, "sparseMatrix")} no longer fails
%%  when \code{prod(dim(.))} is larger than \eqn{2^{31} - 1}.
%

\section{Changes in version 1.4-1 (2022-03-21 r3446)}{
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{diag(x)} methods now mostly also keep \code{names} from
      \code{dimnames(x)} by default and obey \code{names=*} more generally.
    }
  }
  \subsection{New Features}{
    \itemize{
      \item New virtual class \code{packedMatrix} containing packed (dense)
      symmetric and triangular matrices.  Methods for subscripting,
      including \code{diag()}, notably keeping names by default and for
      \code{t()} which are memory efficient, i.e., do not work via
      unpacking, thanks to Mikael Jagan.

      \item New \code{dmperm()} implementing a Dulmage-Mendelsohn
      decomposition, thanks to the persistency of Mauricio Vargas (@uc.cl).

      \item Export more low-level conversion utilities:
      \code{.n2dgT}, \code{.m2ngCn}, \code{.m2ngTn}.

      \item Provide some matrix multiplication methods for \code{"RsparseMatrix"}.
    }
  }
  \subsection{Misc}{
    \itemize{
      \item Our C sources now use \code{R_Calloc()}, \code{R_Free()}
      etc, instead of the shorter versions with 'R_'. Consequently, we
      get closer to \code{STRICT_R_HEADERS}.
      Also, include \code{<float.h>} for \code{DBL_EPSILON}.

      \item \code{PROTECT()} 3 more; as from \samp{rchk} for Matrix 1.4-0.

      \item Slightly better patch notably for Windows,
      for \file{src/SuiteSparse_config/SuiteSparse_config.h}

      \item Fix to continue working for \R 3.5.0 and newer, providing
      \code{tryInvokeRestart()} for older versions of \R, thanking
      Michael Chirico for the heads up.

      \item Modified \code{AZERO()} to work with \code{R_xlen_t} and new
      \code{AZEROs()} for \code{size_t}; other tweaks to evade
      \code{-Wconversion} warnings.
    }
  }
}

\section{Changes in version 1.4-0 (2021-12-08 r3419)}{
  \subsection{Bug Fixes}{
    \itemize{
      \item Update many \file{src/*.c} preventing integer overflow in
      \dQuote{pointer} and index computations for large (dense) matrices;
      prompted by Dario Strbenac's post to R-devel.% June 7, "dgTMatrix Segmentation Fault"

      \item \code{sparse.model.matrix(.., contrasts.arg = <.. ddiMatrix ..>)}
      now works correctly, fixing R-forge Matrix bug #6673 by Davor Josipovic.

      \item \code{sparse.model.matrix(..)} now also works in cases the
      contrast matrix has become a \code{"denseMatrix"}; e.g., in a case
      using \code{poly(.)} in the formula; now works correctly, fixing
      R-forge Matrix bug #6657 and useful suggestions by Nick Hanewinckel.

      \item Fixed the internal \code{attr.all_Mat()} auxiliary for
      \code{all.equal()}, notably for the case when exactly one of the
      matrices is a base \code{matrix}.

      \item Fixed long-standing bug in the \code{rbind2()} method for
      logical dense matrices, specifically \code{"lgeMatrix"}, thanks to
      the notice by Aaron Lun.

      \item fix leak in C-level \code{Csparse_to_dense()} thanks to Bill
      Dunlap in \R's \PR{18204} and \code{install_lu()}
      called from \code{solve(<dgCMatrix>)} in \PR{18206}.

      \item fix leak in crossprod(<dsTMatrix>), thanks to report and patch
      in \PR{18205} by Bill Dunlap.

      \item \code{band(M, k1, k2)} now also works when \code{k1 * k2} is
      larger than 2^31-1, the maximal integer, fixing R-forge Matrix bug
      6743 by Ariel Paulson.  Further, it works when \code{M} is a sparse
      \code{"symmetricMatrix"} but the band is not symmetric, \code{k1 != -k2}.

      \item fix leak in C-level code for \code{cbind(m1,m2)} or
      \code{rbind(*)} when \code{m1} is \code{"n.Csparse"} and \code{m2} is
      not, thanks to Bill Dunlap's diagnosis and patch in \R's \PR{18210}.

      \item \code{sparseVector(i=integer(), length=2^33)} now does show/print,
      after fixing a bug in the \code{head()} method for \emph{empty}
      sparseVectors.  Reported by David Cortes as Matrix bug #6745.

      \item inverting or solving \code{dsCMatrix} no longer catches C level
      warnings too early which would not free, but rather leak memory;
      thanks to Bill Dunlap's analysis and patch in \R's \PR{18214}.
      Additionally, such warnings and error are \code{message()}d when
      \code{getOption("Matrix.verbose")} is \code{ >= 1}.

      \item \file{test-tools-1.R}: \code{Sys.memGB()} can no longer use
      \code{memory.limit()} on Windows; no returns \code{NA.value = 2.10201}
      in such cases.

      \item \code{ss <-  <sparseVector>[i]} gave an invalid sparseVector
      \code{ss} as \code{ss@i} was not necessarily sorted; thanks to a
      report by Quran Wu.

      \item \code{as(<dsyMatrix>, "generalMatrix")} and similar, sometimes
      did \emph{not} use (C-level) \code{symmetric_Dimnames()} etc; report
      (to \R's \PR{18250} by  Mikael Jagan); fixed all on C level.  As a
      consequence, you will now see \emph{more} preserved dimnames after
      matrix transformations or operations which involved symmetric matrices.

      \item \code{as(<ddiMatrix>, "matrix")} no longer loses dimnames,
      thanks to Mikael Jagan's report as Matrix bug #6751.
    }
  }
  \subsection{Misc}{
    \itemize{
      \item No longer include \file{Rdefines.h} as it is somewhat deprecated.
    }
  }
}

\section{Changes in version 1.3-4 (2021-05-24 r3392)}{
  \subsection{Misc}{
    \itemize{
      \item Update \code{matrix(<data>, n,m)} in \file{tests/*} to work with
      \command{R-devel CMD check --as-cran}
    }
  }
}

\section{Changes in version 1.3-3 (2021-05-01 r3390)}{
  \subsection{Deprecated and Defunct}{
    \itemize{
      \item \code{cBind()} and \code{rBind()} are now defunct:
      simply use \code{cbind()} and \code{rbind()} instead.
    }
  }
  \subsection{Dependency}{
    \itemize{
      \item For now revert to \code{R (>= 3.5.0)} dependency to accomodate
      users on older R installations.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item Fixed a thinko (in 1.3-2): Now direct coercion from
      \code{"ddiMatrix"} to \code{"dgCMatrix"}, and hence, e.g.,
      \code{as(Matrix(1, sparse=TRUE), "dgCMatrix") now works.}

      \item Fixed error message in <dtrMatrix> multiplication.

      \item Fixed long-standing bug in \code{R[,j] <- v} when \code{R} is "Rsparse*",
      R-forge Matrix bug #6709 by David Cortes.

      \item \file{./include/cholmod.h} and \file{./include/Matrix_stubs.h}
      needed updating from SparseSuite update; R-forge Matrix bug #6714 by
      Kasper Kristensen (TMB pkg).

      \item \code{as.matrix()} and \code{as.array()} now work for
      \code{"sparseVector"}s as expected; see Matrix bug #6708.

      \item \code{M[,]} (and similar) now work as in base \R; ; R-forge Matrix bug #6720 by
      David Cortes.

      \item \code{-S} now works also when \code{S} has no `factors` slot.
      It signalled an error, e.g., for sparse triangular matrices \code{S};
      R-forge Matrix bug #6656, reported by Chun Fung (Jackson) Kwok.

      \item \code{M*2} and similar no longer keep cached factorizations (in
      `factors` slot), but drop them via internal new \code{.empty.factors()}.
      R-forge Matrix bug #6606, reported by Tomas Lumley.

      \item removed the nowhere used (and unexported but still active)
      class union \code{"Mnumeric"} which actually trickled into many base
      classes properties.  Notably would it break validity of \code{factor}
      with a proposed change in validity checking, as factors were also
      \code{"Mnumeric"} but did not fulfill its validity method.
      Similarly removed (disabled) unused class union \code{"numericVector"}.

      \item removed a few duplicated \code{.alias{.}} from \file{man/*.Rd}.
    }
  }
  \subsection{Misc}{
    \itemize{
      \item translation updates (of outlines only); finally added Italian
      (by Daniele Medri) to svn; updated French (by Philippe Grosjean),
      forgotten (R part of) Korean.
      New Lithuanian translations by Gabriele Stupuriene & Rimantas Zakauskas.

      \item In internal \code{diagOdiag()} method, no longer use
      \code{matrix(x, n,n)} when \code{x} is longer than n*n.

      \item Update tests/*.R to future \code{matrix(x, n,k)} warning in more
      mismatch cases.

      \item Eliminating the need for \file{ftp://*}, add the very small
      \code{jgl009} MatrixMarket example to our \file{external/} files.
    }
  }
}

\section{Changes in version 1.3-2 (2021-01-05 r3362)}{
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{rankMatrix()} tweaks for the singular values based methods,
      notably \code{method = "maybeGrad"}.

      \item \code{as(new("dtCMatrix", diag="U"), "matrix")} now works, as
      C-level \code{diagU2N()} now also works for 0-dimensional triangular
      matrices; this also fixes a subsetting (\dQuote{indexing}) bug of
      such 0-dimensional matrices, thanks to a report by Aaron Lun.

      \item logical subsetting of 0-dim. (diagonal/triangular) matrices
      fixes.

      \item The new \code{FCONE} macros added for newer Fortran/C compiler
      combinations are now defined back compatibly with R >= 3.6.0.

      \item \code{chol(<diagonal dt[CRT]Matrix>)} now works.

      \item \file{rchk}: fix potentially un\code{PROTECT}ed vars in
      \file{src/dsyMatrix.c}
    }
  }
}

\section{Changes in version 1.3-1 (2020-12-23 r3352)}{
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{rankMatrix(<dense>, method="qr.R")} no longer assumes
      non-negative diagonal entries of the \eqn{R} matrix.
    }
  }
}

\section{Changes in version 1.3-0 (2020-12-15 r3351)}{
  \subsection{Significant User-Visible Change}{
    \itemize{
      \item \code{Matrix(*, doDiag=TRUE)} where \code{doDiag=TRUE} has
      always been the \emph{default} is now obeyed also in the sparse
      case, as all \code{"diagonalMatrix"} are also \code{"sparseMatrix"}.

      \code{Matrix(0, 3,3)} returns a \code{"ddiMatrix"} instead of a
      \code{"dsCMatrix"} previously.  The latter is still returned from
      \code{Matrix(0, 3,3, doDiag=FALSE)}, and e.g., \code{.symDiagonal(3,pi)}.

      Also a triangular matrix, e.g., \code{"dtrMatrix"} is detected now in
      cases with \code{NA}s.

      This is both a bug fix \emph{and} an API change which breaks code
      that assumes \code{Matrix(.)} to return a \code{"CsparseMatrix"} in
      cases where it now returns a \code{"diagonalMatrix"} (which does
      extend \code{"sparseMatrix"}).
    }
  }
  \subsection{New Features}{
    \itemize{
      \item Subassignment to \code{"diagonalMatrix"} now returns
      sparse \code{"triangularMatrix"} more often; also (sparse)
      \code{"symmetricMatrix"}.

      \item \code{nearPD()} gets new option: If \code{base.matrix = TRUE},
      the resulting \code{mat} component is a \pkg{base} \code{matrix}, as
      often used desired when \code{nearPD()} is used outside the
      \pkg{Matrix} package context.

      \item Factored out new \code{qr2rankMatrix()} utility from
      \code{rankMatrix()}.

      \item New \code{BunchKaufman(<matrix>)} method.

      \item Added \code{wrld_1deg} sparse matrix example to
      \emph{distributed} version of \pkg{Matrix} (no longer excluding it
      via \file{.Rbuildignore}).

      \item New (simple) \code{mat2triplet()} function to be used instead
      of \code{summary(<sparseMatrix>)} in code.

      \item Internal \code{.diag2tT()} gains new option \code{drop0 = TRUE}
      and hence now by default drops zero diagonal entries.  Consequently,
      e.g., \code{as(<diagonalMatrix>, "CsparseMatrix")} now drops such
      zeros, too.

      \item Updated the crucial underlying C libraries from SuiteSparse,
      from 4.2.1 to 5.7.1 (from 2020-02-20), visible in \code{.SuiteSparse_version()} .

      \item \code{sparseMatrix()} gets new argument \code{repr = "C"},
      superseding the (now deprecated) \code{giveCsparse = TRUE}.  Allows
      to return \code{"RsparseMatrix"} matrices.

      Similarly, \code{rsparsematrix()}, \code{fac2sparse()} and \code{fac2Sparse()}
      get the new \code{repr} argument and their \code{giveCsparse} is
      deprecated, sometimes only informally for now.% no deprecation warning yet

      \item \code{sparse.model.matrix()} gets option \code{sep = ""}, with,
      e.g., \code{sep = ":"} allowing to get easier column names; from
      R-forge Matrix (non-)bug #6581, by Vitalie Spinu.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{rankMatrix(<sparse>, method="qr")} now returns \code{NA}
      (or \code{NaN}) instead of signalling an error in the case the sparse
      \eqn{Q R} decomposition gave \code{NA}s in \code{diag(R)}.

      \item Coercion (\code{as(., .)}) from e.g., \code{"lsyMatrix"} to
      \code{"CsparseMatrix"} silently made asymmetric dimnames symmetric,
      as did the \emph{internal} \code{forceCspSymmetric(*, dimNames)}
      which may be called from \code{forceSymmetric()}.

      \item Adapt code to new Fortran requirements of passing length of
      character arguments, thanks to Brian Ripley.

      \item (R-forge Matrix bug #6659, reported by Georg Kindermann):
      \code{<sparseVector>[i] <- val} bug fixed.

      \item (R-forge Matrix bug #6666, reported by Ezra Tucker):
      \code{which(<ldiMatrix>, array.ind=TRUE)} thinko fixed.

      \item For R-devel Dec 4, 2020: adapt all.equal() check of sparse
      matrix images (which contain panel functions with environments ..).

      \item tried fixing warning \emph{'cholmod_factorize_p' accessing 16
	bytes in a region of size 8 [-Wstringop-overflow=]} in
      \file{src/dsCMatrix.c} (in two places); seen by pre-release-gcc11 compilation.
    }
  }
}

%
\section{Changes in version 1.2-18 (2019-11-26, manually picked from svn)}{
  \subsection{Bug Fixes}{
    \itemize{
      \item Fix last(?) \code{PROTECT()} warning found by \command{rchk} in
      \file{src/dense.c}'s \code{ddense_skewpart()}.

      \item \code{as(m, "dgTMatrix")} does not lose \code{dimnames} anymore
      when \code{m} is a (traditional) \code{matrix}.

      \item \code{M[logical(0), ]} now has dimension \eqn{0 x k} for sparse
      \code{M} as for base matrices.

      \item \code{log(M, base)} (the 2-argument version of \code{log()})
      wrongly gave the result for \code{base = exp(1)}, i.e., the 1-argument default.

      \item \file{test-tools-Matrix.R}: \code{Qidentical()} no longer assumes
      \code{class(<matrix>)} to be of length 1.

      \item \file{test-tools-1.R}: provide bug-fixed \code{canCoerce()} in
      old R versions.
    }
  }
}

\section{Changes in version 1.2-17 (2019-03-20, svn r3294)}{
  \subsection{New Features}{
    \itemize{
      \item (none)
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item Fix new \code{PROTECT()} warnings (bugs?) found by \command{rchk}.

      \item Provide \code{isFALSE()} for \R < 3.5.0 as now need it for
      sparseMatrix printing.
    }
  }
}

\section{Changes in version 1.2-16 (2019-03-04, svn r3291)}{
  \subsection{New Features}{
    \itemize{
      \item regression tests depending on \code{sample()} now are future
      proof reproducible, via \code{RNGversion(.)}.

      \item give information about #{rows} and #{columns} that are
      suppressed in print()ing if the matrix is larger than `max.print`.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{data(<Matrix-data>)} no longer attaches \pkg{Matrix} to
      the search path.

      \item \code{"Ops"} group methods, i.e., "Arith", "Compare" & "Logic",
      now should all work with 0-extent matrices as well, thanks to bug
      reports by Aaron Lun, University of Cambridge.

      \item when printing and formatting sparse matrices, see \code{formatSpMatrix()},
       the \code{maxp} option, e.g., from \code{getOption("max.print")}, is
      \dQuote{rounded up} to 100, as very small values are very rarely appropriate.
    }
  }
}

\section{Changes in version 1.2-15 (2018-08-20, svn r3283)}{
  \subsection{New Features}{
    \itemize{
      \item \code{image()} gets new optional argument \code{border.color}.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{image(Matrix(0, n,m))} now works.
    }
  }
}


\section{Changes in version 1.2-14 (2018-04-08, svn r3278)}{
  \subsection{New Features}{
    \itemize{
      \item German translation updates.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item one more \code{PROTECT()}.
    }
  }
}

\section{Changes in version 1.2-13 (2018-03-25, svn r3275)}{
  \subsection{New Features}{
    \itemize{
      \item Faster \code{as(<matrix>, "sparseMatrix")} and coercion
	\code{"dgCMatrix"}, \code{"ngCMatrix"}, etc, via new direct C
	\code{matrix_to_Csparse()} which does \emph{not} go via
	\code{"dgeMatrix"}.  This also works for large matrices
	\code{m}, i.e., when \code{length(m) >= .Machine$integer.max}.

	Also provide low-level \R functions \code{.m2dgC()},
	\code{.m2lgC()}, and \code{.m2ngC()} for these.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{cbind(NULL,<Matrix>)} no longer return \code{NULL};
      analogously for \code{rbind()}, \code{rbind2()}, \code{cbind2()},
      fixing very long standing typo in the corresponsing \code{cbind2()}
      and \code{rbind2()} methods.

      \item The deprecation warning (once per session) for
      \code{cBind()} and \code{rBind()} finally works (fixing a simple thinko).

      \item \code{cbind()} and \code{rbind()} for largish sparse
      matrices no longer gives an error because of integer overflow
      (in the default case where \code{sparse} is not been specified
      hence is chosen by a \code{nnzero()} based heuristic).

      \item \code{.symDiagonal(5, 5:1)} and \code{.trDiagonal(x = 4:1)}
      now work as expected.

      \item \code{Sp[i]} now is much more efficient for large sparse
      matrices \code{Sp}, notably when the result is short.

      \item \code{<sparseVector>[ <negative integer> ]} now also gives
      the correct answer when the result is \dQuote{empty}, i.e., all
      zero or false.

      \item large \code{"dspMatrix"} and \code{"dtpMatrix"} objects can
      now be constructed via \code{new(*, Dim = *, x = *)} also when
      \code{length(x)} is larger than 2^31 (as the C internal
      validation method no longer suffers from integer overflow).

      \item More \samp{PROTECT()}ing to be \dQuote{rather safe than
	sorry} thanks to Tomas Kalibera's check tools.
    }
  }
}

\section{Changes in version 1.2-12 (2017-11-10, svn r3239)}{
  \subsection{New Features}{
    \itemize{
      \item \code{crossprod(x,y)} and \code{kronecker(x,y)} have become
      considerably more efficient for large \code{"indMatrix"} objects
      \code{x, y}, thanks to private nudging by Boris Vaillant.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item (R-forge Matrix bug #6185): \code{c < 0} now also works for
      derived sparse Matrices (which only \emph{contain} Matrix
      classes); via improving hidden \code{MatrixClass()}.   Part of
      such derived matrices only work in R >= 3.5.0.

      \item using \code{Authors@R} in \file{../DESCRIPTION} to list all
      contributors.

      \item \code{solve(-m)} no longer should use a cached Cholesky
      factorization (of \code{m}).
    }
  }
}

\section{Changes in version 1.2-11 (2017-08-10, svn r3225)}{
  \subsection{New Features}{
    \itemize{
      \item S4 method dispatch no longer emits ambiguity
      notes (by default) for everybody, apart from the package
      maintainer.  You can reactivate them by
      \code{options(Matrix.ambiguityNotes = TRUE)}
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{rankMatrix(<matrix of all 0>)} now gives zero for all
      methods, as it should be.

      \item no longer calling \code{length(NULL) <- <positive>} which
      has been deprecated in R-devel since July.

      \item \code{qr.coef(<sparseQR>, y)} now finally has correct (row)
      names (from pivot back permutation).

      \item \code{.trDiagonal()} utility is now exported.
    }
  }
}

\section{Changes in version 1.2-10 (2017-04-19, svn r3216)}{
  \subsection{Bug Fixes}{
    \itemize{
      \item quite a collection of new \code{PROTECT(.)}'s thanks to
      Tomas Kalibera's \sQuote{rprotect} analysis.
    }
  }
}

\section{Changes in version 1.2-9 (2017-03-08, svn r3211)}{
  \subsection{New Features}{
    \itemize{
      \item \code{"Ops"} between "table", "xtabs", and our matrices now work.
      \item \code{as(matrix(diag(3), 3, dimnames=rep(list(c("A","b","c")),2)),
 	"diagonalMatrix")@x} is no longer named.
      \item \code{norm(x, "2")} now works as well (and equivalently to \code{base::norm}).
      \item \code{sparseVector()} now also works without \code{x} argument.
      \item \code{c.sparseVector()} method for \code{c()} of
      sparseVectors (and available as regular function on purpose).
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{as(Diagonal(3), "denseMatrix")} no longer returns a
      non-dense \code{"ddiMatrix"}.

      \item \code{S[sel,] <- value} and similar no longer segfault, but
      give a \code{"not (yet?) supported"} error
      for sparse matrices \code{S} and logical \code{sel} when
      \code{sel} contains \code{NA}s.

      The same error (instead of a low-level one) is signalled for
      \emph{indexing} (with NA-containing logical \code{sel}), i.e.,
      \code{S[sel,]}.
      %% from in ../TODO :
      %% \item \code{S[sel,]}, \code{S[,sel] <- value} and similar now also work for
      %% sparse matrices \code{S} and logical \code{sel} when \code{sel} contains \code{NA}s.

      \item \code{which(x, arr.ind=TRUE, *)} (when \code{x} is a
      \code{"lMatrix"} or \code{"nMatrix"}) now works the same as
      \code{base::which}, obeying an optional \code{useNames} argument
      which defaults to \code{TRUE}.  Previously, the resulting
      two-column matrix typically had empty \code{dimnames}.
    }
  }
}

\section{Changes in version 1.2-8 (2017-01-16, svn r3201)}{
  \subsection{New Features}{
    \itemize{
      \item 0-length matrix \code{"Ops"} (binary operations) are now
      compatible to R-devel (to be \R 3.4.0).
      \item C-API: \code{SuiteSparse_long} is now defined as
      \code{int64_t} on all platforms, and we now include (C99) \file{inttypes.h}
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{x[.] <- value} now also works for
      \code{"sparseVector"}'s, both as \code{x} and as \code{value}.
      \item \code{x[FALSE] <- value} now also works for \code{"sparseVector"}'s.

      \item \code{rep(x, *)} now works for \code{"sparseVector"}s and
      sparse and dense \code{"Matrix"}-classed matrices \code{x}.

      \item \code{solve(<sparse_LU>)} no gives an error in some cases of
      singular matrices, where before the C code accessed illegal memory locations.
    }
  }
}


\section{Changes in version 1.2-7.1 (2016-08-29, svn r3187)}{
  \itemize{ \item in C code, protect _POSIX_C_SOURCE by #ifdef __GLIBC__ }
}
\section{Changes in version 1.2-7 (2016-08-27, svn r3185)}{
  \subsection{New Features}{
    \itemize{
      \item \code{cBind()} and \code{rBind()} have been almost silently
      deprecated in \R \code{>= 3.2.0} and now give a warning,
      \dQuote{once per session} only.

      \item \code{bandSparse(*, k=k, *)} now returns matrices inheriting from
      \code{"triangularMatrix"} when obvious from the diagonal indices \code{k}.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{KhatriRao(X,Y)} now also works when \code{X} or
      \code{Y} is completely zero.
    }
  }
}

\section{Changes in version 1.2-6 (2016-04-27, svn r3175)}{
  \subsection{Bug Fixes}{
    \itemize{
      \item The 0-dim. Matrix multiplication fix in 1.2-5 did trigger
      wrong warnings in other diagonal matrix multiplications.
    }
  }
}

\section{Changes in version 1.2-5 (2016-04-14, svn r3170)}{
  \subsection{New Features}{
    \itemize{
      \item \code{isSymmetric(m)} now also works for \code{"indMatrix"} \code{m}.
      \item \code{isSymmetric(m)} is faster for large dense asymmetric matrices.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item Matrix multiplications (\code{A \%*\% B}) now work correctly
      when one of the matrices is diagonal and the other has a zero dimension.
    }
  }
}

\section{Changes in version 1.2-4 (2016-02-29, svn r3162)}{
  \subsection{New Features}{
    \itemize{
      \item \code{sparseMatrix()} gets new argument \code{triangular}
      and a smarter default for \code{dims} when \code{symmetric} or
      \code{triangular} is true.
      \item \code{as(<sparse>, "denseMatrix")} now works in more cases
      when \code{prod(dim(.))} is larger than \eqn{2^{31} - 1}.
      Hence, e.g., \code{!S} now works for much larger sparse matrices
      \code{S}.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item creating very large dense matrices, e.g., by
      \code{as(<sparseM.>, "matrix")} would segfault (in case it could
      allocate enough storage).
    }
  }
}

\section{Changes in version 1.2-3 (2015-11-19, svn r3155)}{
  \subsection{New Features}{
    \itemize{
      \item \code{MatrixClass()} is exported now.
      \item More exports of semi-internal functions (for speed, named
      \code{".<foo>"}, i.e., inofficial API), such as \code{.solve.dgC.lu()}.
      \item more Korean translations
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item Packages \emph{linking} to \pkg{Matrix} (\code{LinkingTo:}
      in \file{DESCRIPTION}) now find
      \samp{alloca} properly defined in \file{Matrix.h} even for non-GNU
      compilation environments such as on Solaris or AIX.

      \item extended "n?CMatrix" classes (e.g., from \code{setClass(.,
	contains="ngCMatrix")}) now can be coerced via \code{as(.)} to
      \code{"d.CMatrix"}.

      \item The printing of largish sparse matrices is improved, notably
      in the case where columns are suppressed, via new \code{fitWidth =
	TRUE} option in \code{printSpMatrix2()}. %%% FIXME __ EXAMPLES __

      \item \code{cbind2()} and \code{rbind2()} no longer fail to
      determine \code{sparse} when it is unspecified and hence
      \code{NA}, fixing R-forge bug #6259.
    }
  }
}

\section{Changes in version 1.2-2 (2015-07-03, svn r3131)}{
  \subsection{New Features}{
    \itemize{
      \item Explicitly import from \dQuote{base} packages such as \code{"stats"}.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item Our \code{colSums(x)}, \code{rowMeans(y)}, \dots, methods
      now \dQuote{keep names}, i.e., if the result is a numeric vector,
      and the matrix \code{x} has column or row names, these become the
      \code{names(.)} of the result, fixing R-forge bug #6018.
    }
  }
}

\section{Changes in version 1.2-1 (2015-05-30, svn r3127)}{
  \subsection{New Features}{
    \itemize{
      \item \code{"Matrix"} now has an \code{initialization()} method
      coercing 0-length dimnames components to \code{NULL} and other
      non-\code{NULL} dimnames to \code{character}.  Before, e.g.,
      numeric dimnames components partially worked, even though it has
      always been documented that non-\code{NULL} dimnames should be
      \code{character}.
      \item For \code{symmetricMatrix} objects which have symmetrical
      dimnames by definition, it is allowed to only set one half of the
      \code{dimnames} to save storage, e.g., \code{list(NULL, nms)} is
      \emph{semantically} equivalent to \code{list(nms, nms)}.

      \item \code{as.vector(<sparseVector>)} etc, now work, too.
      \item \code{lu(\emph{<sparseMatrix>})} now keeps \code{dimnames}.
      \item better \file{NEWS.Rd} (which pleases Kurt and \command{tidy} ;-)
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{S[] <- T} and \code{S[] <- spV} now work (in more cases)
      for sparse matrices S, T and sparseVector \code{spV}.
      \item Huge dense matrix multiplication did lead to segfaults, see
      R-help, \dQuote{does segfault mean (always) a bug?}, May 5, 2015.
      Fixed by using C's Alloca() only in smallish cases.
      \item Optional arguments in \code{image()}, e.g., \code{main=
	<..>)} now also work for \code{lgCMatrix}, \code{nMatrix} etc;
      thanks to a 4.5 years old report by Mstislav Elagin.
      \item \code{dimnames(A) <- val} now resets the \code{factors} slot
      to empty, as the factorizations now keep dimnames more often.
      \item \code{crossprod(<matrix>, Diagonal(<n>))} works again (and
      these are tested more systematically).
      \item Matrix products (\code{\%*\%}, \code{crossprod}, and
      \code{tcrossprod}) for \code{"dtrMatrix"} are correct in all
      cases, including keeping dimnames.
      \item \code{Matrix(d)} (and other coercions to \code{"Matrix"})
      now correctly keeps \code{dimnames} also when \code{d} is a
      traditional \emph{diagonal} \code{"matrix"}.
    }
  }
}

\section{Changes in version 1.2-0 (2015-04-03, svn r3096)}{
  \subsection{New Features}{
    \itemize{
      \item New \code{\%&\%} for \dQuote{boolean arithmetic} matrix product.
      \item New argument \code{boolArith = NA} in \code{crossprod()} and
      \code{tcrossprod()}.  \code{boolArith = TRUE} now forces boolean
      arithmetic, where \code{boolArith = FALSE} forces numeric one.

      Several of these products are more efficient thanks to new C
      functionality based on our new \code{chm_transpose_dense()}, and
      others based on \code{geMatrix_crossprod},
      \code{geMatrix_matrix_mm}, etc.

      \item Most dense matrix products, also for non-\code{dgeMatrix},
      including \code{"l..Matrix"} and \code{"n..Matrix"} ones are now
      directly handled by new \code{.Call()}s.

      \item \code{"dMatrix"} (numeric) and \code{"lMatrix"} (logical)
      matrices can now be coerced to \code{"nMatrix"} (non-zero pattern
      or \dQuote{boolean}) even when they contain \code{NA}s, which then
      become \code{TRUE}s.

      \item More thorough checking of \code{cbind2()} and
      \code{rbind2()} methods, notably as they are called from \code{cbind()}
      and \code{rbind()} from \R version 3.2.0 on.

      \code{rbind2(<dense>, <dense>)} is faster, being based on new C code.

      \item symmetric Matrices (i.e., inheriting from
      \code{"symmetricMatrix"}) are allowed to have \code{dimnames} of
      the form \code{list(NULL, <names>)} \emph{and} now print correctly
      and get correctly coerced to general matrices.

      \item \code{indMatrix} object (\dQuote{index matrices}) no longer
      need to be \dQuote{skinny}.

      \item \code{rsparseMatrix()} now accepts \code{rand.x = NULL} and
      then creates a random \emph{patter\bold{n}} matrix
      (\code{"nsparseMatrix"}).

      \item \code{anyDuplicatedT()} and \code{uniqTsparse()} low level
      utilities are exported now.

      \item Partial Korean translations of messages.
    }
  }
  \subsection{Deprecation}{
    \itemize{
      \item For \eqn{R \ge 3.2.0}, \code{cBind()} and \code{rBind()}
      are deprecated, as they are no longer needed since \code{cbind()}
      and \code{rbind()} do work automatically.
    }
  }

  \subsection{Bug Fixes}{
    \itemize{
      \item Fix some \code{rbind2()} methods.
      \item \code{t()} now transposes the dimnames even for symmetric
      matrices.
      \item \code{diag(M) <- val} did not always recycle \code{val} to
      full length, e.g., when \code{M} was a \code{"dtrMatrix"}.
      \item \code{crossprod(<indMatrix>)} was wrong in cases where the
      matrix had all-zero columns.
      \item Matrix products (\code{\%*\%}, \code{crossprod}, and
      \code{tcrossprod}) with one sparse and one dense argument now
      return \emph{numeric} (a \code{"dMatrix"}) when they should, i.e.,
      unless the new setting \code{boolArith = TRUE} is applied.
    }
  }
}

\section{Changes in version 1.1-5 (2015-01-18, svn r3037)}{
  \subsection{New Features}{
    \itemize{
      \item More use of \code{anyNA()} (for speedup).
      \item Matrix products (\code{\%*\%}, \code{crossprod},
      \code{tcrossprod}) now behave compatibly to \R 3.2.0, i.e., more
      lenient in matching dimensions for matrix - vector products.
      \item \code{isTriangular()} gets new optional argument \code{upper = NA}.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{crossprod()} and \code{tcrossprod()} fixes for
      several <diagonal> o <sparse> combinations.
      \item \code{rowMeans(<dgeMatrix>, na.rm=TRUE)} was wrong sometimes.
      \item fix and speedup of coercions (\code{as(., .)}) from and to
      symmetric or triangular matrices.
      \item \code{invPerm()} coercion to integer
      \item \code{dimnames( solve(.,.) )} fix [r3036]
      \item \code{tril()} and \code{triu()} now return correct \code{uplo}.
      \item \code{names(dimnames(.))} now preserved, e.g. in
      \code{symmpart()} or subsetting (\code{A[i,j]}).
    }
  }
}

\section{Changes in version 1.1-4 (2014-06-14, svn r2994)}{
  \subsection{New Features}{
    \itemize{
      \item new \code{rsparsematrix()} for random sparse Matrices.
      \item improved warnings, notably for unused arguments previously
      swallowed into \code{...}.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{crossprod(<vec>, <dsyMatrix>)} fixed.
      \item \code{crossprod()} and \code{kronecker()} fixes for some
      <indMatrix> cases.
    }
  }
}

\section{Changes in version 1.1-3 (2014-03-30, svn r2982)}{
  \subsection{New Features}{
    \itemize{
      \item \code{\%*\%} and \code{crossprod()} now also work with
      \code{sparseVector}s.
      \item speedup of \code{crossprod(v, <sparseM>)}, thanks to nudge
      by Niels Richard Hansen.
      \item new help page for all such matrix products
      (\file{../man/matrix-products.Rd}).
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{image()} now gets correct \code{ylim} again.
      \item More consistent matrix products.
    }
  }
}

\section{Changes in version 1.1-2-2 (2014-03-04, svn r2966)}{
  \subsection{Bug Fixes}{
    \itemize{
      \item correct adaption to \R 3.1.0
      \item using \code{tolerance} (and not \sQuote{tol}) in \code{all.equal()}
    }
  }
}

\section{Changes in version 1.1-2 (2014-01-28, svn r2962)}{
  \subsection{New Features}{
    \itemize{
      \item export fast power-user coercion utilities
      \code{.dsy2mat()}, \code{.dxC2mat()}, \code{.T2Cmat()}, \code{..2dge()}.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item matrix products now (mostly) work with \code{sparseVector}s;
      and correctly in some more cases.
    }
  }
}

\section{Changes in version 1.1-1.1 (2013-12-30, svn r2957)}{
    \itemize{
      \item Testing code's \code{assertWarning()} adapted for \eqn{R \le 3.0.1}.
      \item \code{Depends: R >= 2.15.2} eases checking.
    }
}

\section{Changes in version 1.1-1 (2013-12-28)}{
  \subsection{New Features}{
    \itemize{
      \item \code{image(.., xlim, ylim)}: nicer defaults %% ../R/dgTMatrix.R
      for the axis limits, and \code{ylim} is sorted decreasingly; not
      strictly back-compatible but should never harm.
      \item \code{rankMatrix(*, method="qr")} now using \code{tol}
      \item \code{T2graph()} and \code{graph2T()} export old functionality explicitly.
      Tweaks in conversions between \code{"graph"} and
      \code{"sparseMatrix"} objects.  Notably, \code{as(<graph>,
	<Matrix>)} now more often returns a (0/1 pattern) "n..Matrix".
      \item \code{sparseMatrix()}: new \code{use.last.ij} argument.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{KhatriRao()}: fix rownames (X <-> Y)
      \item \code{qr.coef()}, \code{qr.fitted}, and \code{qr.resid} now
      also work with \emph{sparse} RHS \code{y}.
      \item sparse matrix \dQuote{sub assignments}, e.g., \code{M[ii] <- v},
      speedup and fixes.
      \item bug fixes also in \code{M[negative indices] <- value} and
      \code{<sparseMatrix>[cbind(i,j)]}.
    }
  }
}

\section{Changes in version 1.1-0 (2013-10-21, svn r2930)}{
  \subsection{New Features}{
    \itemize{
      \item \code{fac2sparse} and \code{fac2Sparse} now exported, with a
      new \code{giveCsparse} option.
      \item Update to latest \command{SuiteSparse} C library by Tim Davis,
      U. Florida.
      \item ensuing \dQuote{C API changes}
      \item new \code{.SuiteSparse_version()} function
      \item Many \sQuote{Imports:} instead of \sQuote{Depends:}.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item fixed long lasting undetected \code{solve(<dsCMatrix>, *)}
      bug.
      \item Our \code{all.equal()} methods no longer sometimes return
      \code{c("TRUE", "....difference..")}.
      \item \code{rankMatrix(<matrix>)}: fix the internal \code{x.dense}
      definition.
    }
  }
}

\section{Changes in version 1.0-14 (2013-09-12, svn r2907)}{
  \subsection{Bug Fixes}{
    \itemize{
      \item Revert some wrong changes to \code{solve(<sparse>, *)} from
      1.0-13 (\dQuote{stop gap fix} for \R 3.0.2).
    }
  }
}

\section{Changes in version 1.0-13 (2013-09-10, svn r2904)}{
  \subsection{New Features}{
    \itemize{
      \item New (efficient) \code{KhatriRao()} function by Michael Cysouw
      \item New \code{"indMatrix"} class of \dQuote{index matrices}, a
      generalization of \code{"pMatrix"}, the permutation matrices, many
      methods generalized from pMatrix to indMatrix.  All (initial)
      functionality contributed by Fabian Scheibl, Univ.\sspace{} Munich.
      \item Export and document \code{isDiagonal()} and
      \code{isTriangular()} as they are useful outside of \pkg{Matrix}.
      \item \code{rankMatrix(M, method="qr")} no longer needs
      \code{sval} which makes it considerably more useful for large
      sparse \code{M}.
      \item Start providing \code{anyNA} methods for \eqn{R >= 3.1.0}.
      \item \code{solve(<sparse> a, <sparse> b)}: if \code{a} is
      symmetric, now compute \emph{sparse} result.
      \item \code{nearPD()} gets new option \code{conv.norm.type = "I"}.
      \item \code{determinant(<dpoMatrix>)} now uses \code{chol()}, and
      hence also an existing (\sQuote{cached}) Cholesky factor.
      \item 3 new \code{C -> R} utilities (including hidden \R function
      \code{.set.factors()} for caching also from \R, not just in C).
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{M[] <- v} for unitriangular \code{M} now correct.
      \item \code{lu(.)} no longer sometimes returns unsorted columns.
    }
  }
}
%% TODO: fill in from here <<<<<<<<<<<<<<<<<<<
%% ----  using ../ChangeLog and notably my ../svn-log-from.all
\section{Changes in version 1.0-12 (2013-03-26, svn r2872)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}


\section{Changes in version 1.0-11 (2013-02-02)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item \code{as(<csr>, "dgCMatrix")} (from package \CRANpkg{SparseM})
      now works again.
      \item .
    }
  }
}

\section{Changes in version 1.0-10 (2012-10-22)}{
  \subsection{New Features}{
    \itemize{
      \item \code{.sparseDiagonal()}: new \code{unitri} argument, and
      more flexibility;
      \item new \code{solve(<dsCMatrix>, <missing>)} via efficient C code.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}

\section{Changes in version 1.0-9 (2012-09-05)}{
  \subsection{New Features}{
    \itemize{
      \item new \code{sparseVector()} constructor function.
      \item \code{is.finite()} \code{is.infinite()} now work for our
      matrices and "*sparseVector" objects.
      \item \code{diag(.) <- V} now preserves symmetricity,
      triangularity and even uni-triangularity sometimes.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item Quite a few fixes for \code{Ops} (arithmetic, logic, etc)
      group methods.
      \item Ditto for \code{diagonalMatrix} methods.
    }
  }
}

\section{Changes in version 1.0-6 (2012-03-16, publ. 2012-06-18)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}

\section{Changes in version 1.0-5 (2012-03-15)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}

\section{Changes in version 1.0-4 (2012-02-21)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}

\section{Changes in version 1.0-3 (2012-01-13)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}

\section{Changes in version 1.0-2 (2011-11-19)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}

\section{Changes in version 1.0-1 (2011-10-18)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}

\section{Changes in version 1.0-0 (2011-10-04)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}

\section{Changes in version 0.9996875-3 (2011-08-13)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}

\section{Changes in version 0.9996875-2 (2011-08-09)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}

\section{Changes in version 0.9996875-1 (2011-08-08)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }

  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}

\section{Changes in version 0.999375-50 (2011-04-08)}{
  \subsection{New Features}{
    \itemize{
      \item .
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}


% How can I add vertical space ?

% \preformatted{} is not allowed, nor is \cr





%--------------- start of DB+MM history: ------------------------

\section{Changes in version 0.95-1 (2005-02-18, svn r561)}{
  \subsection{Authorship}{
    \itemize{
      \item During Doug Bates' sabbatical in Zurich,
      Martin Maechler becomes co-author of the \pkg{Matrix} package.
    }
  }
  \subsection{New Features}{
    \itemize{
      \item Beginning of class reorganization with a more systematic
      naming scheme.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item More (correct) coercions \code{as(<from>, <to>)}.
    }
  }
}

\section{Changes in version 0.9-1 (2005-01-24, svn r451)}{
  \subsection{New Features}{
    \itemize{
      \item lme4 / lmer specific R code moved out to \CRANpkg{lme4} package.
    }
  }
  \subsection{Bug Fixes}{
    \itemize{
      \item .
    }
  }
}




% How can I add vertical space ?  ( \preformatted{} is not allowed, nor is \cr )


%--------------- pre-pre-history: ------------------------

\section{Changes in version 0.8-2 (2004-04-06, svn r51)}{
  \subsection{Authorship}{
    \itemize{
      \item Doug Bates (only)
    }
  }
  \subsection{New Features}{
    \itemize{
      \item Sparse matrices, classes and methods, partly via
      \item Interface to LDL, TAUCS, Metis and UMFPACK C libraries
    }
  }
}

% How can I add vertical space ? .................................


\section{Version 0.2-4}{
\subsection{..., 0.3-1, 0.3-n (n=3,5,...,26): 22 more CRAN releases}{
  \itemize{ \item ............................................. } }}

% How can I add vertical space ?
% \preformatted{} is not allowed, nor is \cr



\section{Version 0.2-1 (2000-07-15)}{
  The first CRAN release of the \pkg{Matrix} package,
  titled \dQuote{A Matrix library for R} authored by
  Douglas Bates (maintainer, principal author) and Saikat DebRoy.
  \subsection{Features}{
    \itemize{
      \item \code{Matrix()} constructor for \R objects of class \code{Matrix}.
      \item \code{Matrix.class()} returning informal subclasses such as
      \code{"Hermitian"}, \code{"LowerTriangular"}
      \item \code{is.Orthonormal()}, \code{is.Hermitian()} ,
      \code{is.UpperTriangular()} functions.
      \item \code{SVD()}, \code{lu()}, and \code{schur()} decomposition
      generics with \code{"Matrix"} methods.
      \item \code{rcond()}, \code{norm()}, \code{det()};
      \code{expand()} and \code{facmul()}.

      \item C++ interface to LAPACK
    }
  }
}