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