Release/1.5.0

[kylebaron]

mrgsolve 1.5.0

• New functions mwrite_yaml() and mwrite_cpp() can write a model object back
  to a file, accounting for all updates since the model was read from native
  mrgsolve format using mread() (Add mwrite_cpp; more verbose matrix objects in yaml #1213).

• New function mread_yaml() for reading back models written out with
  mwrite_yaml() (Add mwrite_cpp; more verbose matrix objects in yaml #1213).

• New functions in evtools plugin: evt::replace() works like evt::bolus(),
  but will replace the amount in a given compartment rather than add to it
  (Add replace() function to evtools #1203).

• The nm-vars plugin now exposes DEXP(), LOG10(), COS() and SIN()
  for use in the mrgsolve C++ code blocks (add more nm to cpp function defs #1199).

• An error is now generated when KA is equal to CL/VC while simulating from
  the one-compartment model with analytical solution invoked through
  $PKMODEL (Undefined behavior in pk1 when KA=CL/V #1179, Error when k10 is equal to ka in one-compartment closed-form model #1197).

Bugs Fixed

• A bug was fixed when certain data frame inputs were passed to as_data_set()
  (as_data_set handles uc data sets incorrectly #1115, Fix as_data_set with data.frame #1196).

[kylebaron]

Macbuilder

Status: 1 NOTE

* using log directory ‘/Volumes/PkgBuild/work/1721935390-9e96e3ba5df39c7f/packages/big-sur-arm64/results/4.4/mrgsolve.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.3.1
* using session charset: UTF-8
* checking for file ‘mrgsolve/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mrgsolve’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mrgsolve’ can be installed ... [18s/20s] OK
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking whether startup messages can be suppressed ... [0s/0s] OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [4s/4s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [6s/7s] OK
  Running ‘testthat.R’ [6s/7s]
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: 1 NOTE
* using check arguments '--no-clean-on-error '

* elapsed time (check, wall clock): 0:53

Winbuilder

There was also a compiler warning for comparison of signed and unsigned integers; going to fix that in a short PR.

UPDATE: fixed in #1218

* using log directory 'd:/RCompile/CRANguest/R-devel/mrgsolve.Rcheck'
* using R Under development (unstable) (2024-07-24 r86924 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'mrgsolve/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mrgsolve' version '1.5.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [11s] Note_to_CRAN_maintainers
Maintainer: 'Kyle T Baron <[email protected]>'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'mrgsolve' can be installed ... OK
* used C++ compiler: 'g++.exe (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [18s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [13s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [23s] OK
  Running 'testthat.R' [22s]
* checking PDF version of manual ... [17s] OK
* checking HTML version of manual ... [19s] OK
* DONE
Status: OK

[kyleam]

LGTM aside from missing PR reference.