NEWS
rexpokit 0.26.6.14 (2023-11-22)
NEW FEATURES
BUG FIXES
OTHER CHANGES
- 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
rexpokit 0.26.6.13
NEW FEATURES
BUG FIXES
OTHER CHANGES
- Predefined inputs for a zswapy usage to avoid LTO error
rexpokit 0.26.6.12 (2023-10-30)
NEW FEATURES
BUG FIXES
OTHER CHANGES
- Updated dates and version number across all files
- Removed mistaken "SysData" field from the DESCRIPTION file
rexpokit 0.26.6.11
NEW FEATURES
BUG FIXES
OTHER CHANGES
- 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
rexpokit 0.26.6.10
NEW FEATURES
BUG FIXES
OTHER CHANGES
- Removed broken link to Foster 2001, Zen of likelihood unleashed, at
http://filogeografia.dna.ac/PDFs/phylo/Foster_01_EasyIntro_MLPhylo.pdf
rexpokit 0.26.6.9 (2023-06-21)
NEW FEATURES
BUG FIXES
OTHER CHANGES
- Fixed type mismatch errors noted by Brian Ripley for:
GNU extension not supported by the flang compiler
- Fixed some old/broken links.
- Changed personList() to c() in 00_rexpokit-package.Rd
rexpokit 0.26.6.7 (2020-07-04)
NEW FEATURES
BUG FIXES
OTHER CHANGES
- Fixed type mismatch errors noted by Brian Ripley with gfortran/gcc10 beta.
rexpokit 0.26.6.6 (2019-11-04)
NEW FEATURES
BUG FIXES
OTHER CHANGES
- 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.
- 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)).
rexpokit 0.26.6.4 (2019-07-02)
NEW FEATURES
BUG FIXES
OTHER CHANGES
- In .f files, reproduced and fixed these errors:
"type of "zswapy" does not match
original declaration [-Wlto-type-mismatch]"
- The details took some doing to figure out, see
rexpokit/inst/notes/2019-07-02_fix_LTO_errors_rexpokit.txt
rexpokit 0.26.6.3
NEW FEATURES
BUG FIXES
OTHER CHANGES
- 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)
rexpokit 0.26.6.2 (2019-06-27)
NEW FEATURES
BUG FIXES
OTHER CHANGES
- Fixed old .Rd documentation file mistakenly not updated previously
rexpokit 0.26.6.1
NEW FEATURES
BUG FIXES
OTHER CHANGES
- In tests/expm.R, expm changed to rexpokit::expm to avoid ambiguous defn
- Passes check with R-3.6.0 with "--enable-lto=check"
rexpokit 0.26.6 (2018-10-02)
NEW FEATURES
BUG FIXES
OTHER CHANGES
- 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)
- Returning CRAN maintainer to Nick Matzke [email protected]
rexpokit 0.26.5
NEW FEATURES
BUG FIXES
OTHER CHANGES
- In FORTRAN code, edits to comply with on CRAN precheck Windows/Debian compiler
with "-fpic -g -O2 -Wall -pedantic -mtune=native -c" flags
- All changes involved explicitly specifying KIND, or commenting out
unused code/variables (due to print statements previously commented
out for previous CRAN compliance)
rexpokit 0.26.4
NEW FEATURES
BUG FIXES
OTHER CHANGES
- In FORTRAN code, changed REALPART->REAL, IMAGPART->AIMAG, DCONJG->CONJG
to comply with flang compiler
- 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
rexpokit 0.26.3 (2018-05-06)
NEW FEATURES
BUG FIXES
OTHER CHANGES
- None; CRAN kept author, but updated Maintainer to "Orphaned" due to flang
compiler issue.
- Changing integer to double for length of workspace (lwsp in EXPOKIT source); works
for very large problems...
rexpokit 0.26.1 (2017-08-15)
NEW FEATURES
BUG FIXES
- Minor fix to DESCRIPTION issues noted on submission of 0.26
OTHER CHANGES
rexpokit 0.26
NEW FEATURES
BUG FIXES
- 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.
- 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
- Commented out -W flag in Makevars, in order to remove "Non-portable
flags in variable 'PKG_FFLAGS'" warning
- Summary of modernization edits to FORTRAN:
- complex*16 -> complex(kind=8)
- CHARACTER*6 -> CHARACTER(LEN=6)
- double complex -> complex(kind=8)
- absx = dabs(dreal(zx(i))) -> absx = DABS(REALPART(Zx(i)))
- absx = dabs(dimag(zx(i))) -> absx = DABS(IMAGPART(Zx(i)))
- Removed all "statement functions", replaced with basic math in-line
- Variable declarations for dreal, dimag, dzum, dzumi, dzumr now unnecessary and
commented out
- Replaced "Computed GO TO" statements loops re-coded using On-Line
Fortran F77 - F90 Converter: https://www.fortran.uk/plusfortonline.php
- 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)
- cabs1 "statement function" replaced with several in-line calculations
- All example matrix exponentiations checked after FORTRAN edits
- 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)
- init.c content was integrated into pre-existing "wrappers.cpp", adding
"R_CMethodDef CEntries[]" and "R_init_rexpokit" entries
OTHER CHANGES
- Changed Maintainer email (Nicholas J. Matzke, [email protected] ->
Nicholas J. Matzke, [email protected]); this is a permanent email.
All functions changed as well.
- Added maxent function to avoid BioGeoBEARS dependency on FD
- Minor edits to documentation
- Made examples not depend on SparseM
- 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
rexpokit 0.25
NEW FEATURES
- (Drew Schmidt) rewrote compiled code wrappers to improve performance (~10-40%).
- Fixed Fortran flags.
- Added demos.
OTHER CHANGES
- Added Drew Schmidt, Univ. Tennessee Knoxville, as a coauthor
- Minor changes to documentation to avoid links outside of package (to diversitree and expoRkit)
- Wrote local alternative for as.matrix.coo to remove dependency on SparseM package
rexpokit 0.24.1 (2013-07-15)
NEW FEATURES
- 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)
- fixed line-length issue in various places in the documentation
- added NEWS file
BUG FIXES
OTHER CHANGES