CHANGES in rexpokit VERSION 0.26.6.15


NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o Fixed this CRAN note: 
    Check: for unstated dependencies in ‘demo’
      Result: NOTE 
        '::' or ':::' import not declared from: ‘Matrix’
        'library' or 'require' call not declared from: ‘Matrix’
    
    


CHANGES in rexpokit VERSION 0.26.6.14


NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o Fixed LTO warning noted here:
      www.stats.ox.ac.uk/pub/bdr/LTO/rexpokit.out
      It was an issue with zswapy:
      input "m" is complex, explicitly converted to 
      integer tempm, tempm=INT(m) to avoid possible change of type. This
      fixes this LTO warning: lapack.f:1261:72: warning: 
      type of 'zswapy' does not match original declaration -Wlto-type-mismatch
      1261 zswapy(tempkm1,tempx,tempzx,1,b(1),1)
      blas_mod.f:961:24: note: 'zswapy' was previously declared here
      961 zswapy (n,m,zx,incx,zy,incy)
      ...which I replicated on Mac OS X Monterey 12.5 with a fresh install of gcc 13.2 
         following these directions at gcc.gnu.org wiki InstallingGCC

      



CHANGES in rexpokit VERSION 0.26.6.13


NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o Predefined inputs for a zswapy usage to avoid LTO error


CHANGES in rexpokit VERSION 0.26.6.12


NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o Updated dates and version number across all files
    o Removed mistaken "SysData" field from the DESCRIPTION file



CHANGES in rexpokit VERSION 0.26.6.11


NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o Minor changes to fix "Found the following file with non-portable usage of KIND:"
      Warnings on: r-devel-linux-x86_64-debian-clang
                   r-devel-linux-x86_64-debian-gcc
                   r-devel-linux-x86_64-fedora-clang
                   r-devel-linux-x86_64-fedora-gcc
                   r-devel-windows-x86_64


CHANGES in rexpokit VERSION 0.26.6.10


NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o Removed broken link to Foster 2001, Zen of likelihood unleashed, at
      http://filogeografia.dna.ac/PDFs/phylo/Foster_01_EasyIntro_MLPhylo.pdf



CHANGES in rexpokit VERSION 0.26.6.9


NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o Fixed type mismatch errors noted by Brian Ripley for: 
      GNU extension not supported by the flang compiler
    o Fixed some old/broken links.
    o Changed personList() to c() in 00_rexpokit-package.Rd



CHANGES in rexpokit VERSION 0.26.6.7


NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o Fixed type mismatch errors noted by Brian Ripley with gfortran/gcc10 beta. 
      




CHANGES in rexpokit VERSION 0.26.6.6


NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o Fixed type mismatch errors noted by Brian Ripley with gfortran/gcc10 beta. 
      These concerned e.g. 
      
      "Type mismatch between actual argument at (1) and actual 
      argument at (2) (REAL(4)/INTEGER(4))" 
      
      ...for zswapy in lapack.f, and
      
      "Rank mismatch between actual argument at (1) and actual argument
      at (2) (scalar and rank-1)"
      
      ...for DSCALX. These are warnings generated by gfortran / gcc10, 
      which constitute errors on latest CRAN check.  They are reproduced
      reproduced by installing gcc10 from macports, then making variable 
      definitions explicit so that types match.
      
      E.g., where u(:) (a rank-1 vector) disagrees with wsp(ip) (a scalar),
      make a double precision u1, and say u1 = u(1) and replace u(:).
      
      All tests pass with this change. Changes marked with 2019-11-04_NJM.


NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o Fixed type mismatch errors noted by Brian Ripley. These concerned 
      e.g. ZSWAPX taking scalar "u" in one usage, and "wsp(ip)" (an 
      array with a single entry) in another usage. This apparently now 
      creates warnings of e.g. "Warning: Rank mismatch between actual 
      argument at (1) and actual argument at (2) (scalar and rank-1)" 
      in gfortran in GCC10.0 (still in beta). Easy fix with e.g. 
      wspip = REAL(wsp(ip)).



CHANGES in rexpokit VERSION 0.26.6.4

NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o In .f files, reproduced and fixed these errors:
      
      "type of "zswapy" does not match 
        original declaration [-Wlto-type-mismatch]"
    
    o The details took some doing to figure out, see 
      rexpokit/inst/notes/2019-07-02_fix_LTO_errors_rexpokit.txt




CHANGES in rexpokit VERSION 0.26.6.3

NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o In lapack.f, converted ZSWAP to ZSWAPX (for 5-argument inputs)
      and ZSWAPY (for 6-argument inputs), in attempt to fix LTO
      warnings about not matching original declaration, e.g.:
        type of "zswapy" does not match 
        original declaration [-Wlto-type-mismatch]
        call zswapy(k-1,b(k),a(1,k),1,b(1),1)
        lapack/blas_mod.f:961: note: "zswapy" was previously declared here
        subroutine  zswapy (n,m,zx,incx,zy,incy)




CHANGES in rexpokit VERSION 0.26.6.2

NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o Fixed old .Rd documentation file mistakenly not updated previously




CHANGES in rexpokit VERSION 0.26.6.1

NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o In tests/expm.R, expm changed to rexpokit::expm to avoid ambiguous defn
    o Passes check with R-3.6.0 with "--enable-lto=check"


CHANGES in rexpokit VERSION 0.26.6

NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o In FORTRAN code, fixed one final warning on CRAN precheck Windows/Debian compiler:
      complex(kind=8) alpha(ndeg), theta(ndeg), tmpc ->
      complex(kind=8) alpha(2*ndeg), theta(2*ndeg), tmpc
      ...this avoids issues with array overruns when the legacy code is
         checked on gfortran-8 (alpha and theta were size 7, should be 14)
    o Returning CRAN maintainer to Nick Matzke nickmatzke.ncse@gmail.com



CHANGES in rexpokit VERSION 0.26.5

NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o In FORTRAN code, edits to comply with on CRAN precheck Windows/Debian compiler
      with "-fpic  -g -O2 -Wall -pedantic -mtune=native -c" flags
    o All changes involved explicitly specifying KIND, or commenting out
      unused code/variables (due to print statements previously commented
      out for previous CRAN compliance)



CHANGES in rexpokit VERSION 0.26.4

NEW FEATURES
    
    o None

BUG FIXES

    o None
    
OTHER CHANGES
    
    o In FORTRAN code, changed REALPART->REAL, IMAGPART->AIMAG, DCONJG->CONJG
      to comply with flang compiler
    o Changed jstor link to journal website, to avoid a note due to redirect:
      Cleve Moler and Charles Van Loan (2003)
      Nineteen Dubious Ways to Compute the Exponential of a Matrix, Twenty-Five Years Later
      SIAM Rev., 45(1), 3-49.
      https://epubs.siam.org/doi/10.1137/S00361445024180



CHANGES in rexpokit VERSION 0.26.3

NEW FEATURES
    
    o None

BUG FIXES

   	o None

OTHER CHANGES
    
    o None; CRAN kept author, but updated Maintainer to "Orphaned" due to flang 
      compiler issue.



CHANGES in rexpokit VERSION 0.26.3

NEW FEATURES
    
    o None

BUG FIXES

   	o None

OTHER CHANGES
    
    o Changing integer to double for length of workspace (lwsp in EXPOKIT source); works
   	  for very large problems...




CHANGES in rexpokit VERSION 0.26.1

NEW FEATURES
    
    o None

BUG FIXES

   	o Minor fix to DESCRIPTION issues noted on submission of 0.26


OTHER CHANGES
    
    o None


CHANGES in rexpokit VERSION 0.26

NEW FEATURES
    
    o None

BUG FIXES

   	o Numerous changes were made to FORTRAN source to solve CRAN check
   	  warnings or installation issues on e.g. Windows machines
   	  (https://win-builder.r-project.org). Typically these were obsolescence
      issues with legacy F77 code. Typically the solution was to convert to
      F90 standard. Summary below.
   	o Fix to a CRAN-identified NOTE: "Packages in Depends field not imported from:
	    'Rcpp'  'SparseM' 'methods'."  Solution: removed methods and SparseM from 
	    Depends, moved Rcpp to Imports in NAMESPACE file
    o Commented out -W flag in Makevars, in order to remove "Non-portable 
      flags in variable 'PKG_FFLAGS'" warning
    o Summary of modernization edits to FORTRAN:
    o complex*16 -> complex(kind=8)
    o CHARACTER*6 -> CHARACTER(LEN=6)
    o double complex -> complex(kind=8)
    o absx = dabs(dreal(zx(i))) -> absx = DABS(REALPART(Zx(i)))
    o absx = dabs(dimag(zx(i))) -> absx = DABS(IMAGPART(Zx(i)))
    o Removed all "statement functions", replaced with basic math in-line
    o Variable declarations for dreal, dimag, dzum, dzumi, dzumr now unnecessary and
      commented out
    o Replaced "Computed GO TO" statements loops re-coded using On-Line 
      Fortran F77 - F90 Converter: https://www.fortran.uk/plusfortonline.php
    o Problems like "Index '2' of dimension 1 of array 'dx' above upper bound of 1"
      solved with changing dx(1) -> dx(n), dy(1) -> dy(n)
    o cabs1 "statement function" replaced with several in-line calculations
    o All example matrix exponentiations checked after FORTRAN edits
    o Generated "init.c" using package_native_routine_registration_skeleton() in 
      order to register native routines. 
      (Following instructions at: 
      https://stat.ethz.ch/pipermail/r-devel/2017-February/073755.html)
    o init.c content was integrated into pre-existing "wrappers.cpp", adding
      "R_CMethodDef CEntries[]" and "R_init_rexpokit" entries


OTHER CHANGES
    
    o Changed Maintainer email (Nicholas J. Matzke, matzke@berkeley.edu -> 
      Nicholas J. Matzke, nickmatzke.ncse@gmail.com); this is a permanent email.
      All functions changed as well.
    o Added maxent function to avoid BioGeoBEARS dependency on FD
    o Minor edits to documentation
    o Made examples not depend on SparseM
    o updated CITATION file to refer to first publication on BioGeoBEARS/rexpokit: 
      Matzke, Nicholas J. (2013). Probabilistic historical biogeography: 
      new models for founder-event speciation, imperfect detection, and fossils allow 
      improved accuracy and model-testing. Frontiers of Biogeography, 5(4), 242-248. 
      http://escholarship.org/uc/item/44j7n141


CHANGES in rexpokit VERSION 0.25 (2014-05-17, GitHub version)

NEW FEATURES
    
    o (Drew Schmidt) rewrote compiled code wrappers to improve performance (~10-40%).
    o Fixed Fortran flags.
    o Added demos.

OTHER CHANGES
    
    o Added Drew Schmidt, Univ. Tennessee Knoxville, as a coauthor
    o Minor changes to documentation to avoid links outside of package (to diversitree and expoRkit)
    o Wrote local alternative for as.matrix.coo to remove dependency on SparseM package



CHANGES in rexpokit VERSION 0.24.1

NEW FEATURES

    o removed live links to the ctarma package, which has been archived (ctarma was
      not a dependency, it was just linked from the documentation for explanatory
      purposes)
    o fixed line-length issue in various places in the documentation
    o added NEWS file

BUG FIXES

    o none

OTHER CHANGES

    o none
    