Release/1.4.0

[kylebaron]

mrgsolve 1.4.0

• evtools is a new plugin providing API for dynamic dosing from within the model; functions and classes are in the evt namespace (#1149).

• regimen is a new class located in the evt namespace via the evtools plugin; regimen objects can execute doses in a regular regimen (#1156).

• mread() and mcode() no longer print a message before the required waiting period on model recompile (#1145).

• ev_rep() output rownames are cleaned up before returning (#1158).

• C++ model code blocks (GLOBAL, PREAMBLE, MAIN/PK, ODE/DES, TABLE/ERROR) are now checked for <object>.<attribute> syntax; if found, symbols on both sides of the dot become reserved words when loading and compiling that model; specifically, an error will be generated if either side of the dot (<object> or <attribute>) is found in parameter names, compartment names, ETA labels, or EPS labels (#1159).

• ETA values are always simulated from OMEGA, even when the user requests they get scraped from data or idata via etasrc argument to mrgsim(); this ensures EPS are reproducible for model runs where etasrc = "omega" (default, ETA are simulated) or, for example, where etaasrc = "data.all" (scrape ETA from the data set) (#1163).

Bugs Fixed

• Fixed a bug where modeled doses scheduled to happen now were ignored if the time attribute was set to a value prior to the current simulation time (#1152).

• Fixed a bug in how doses were computed using the until argument to ev() (#1154).

[kylebaron]

macbuilder r-devel

``` * using log directory ‘/Volumes/PkgBuild/work/1707334594-6e909bb41aaf0adb/packages/big-sur-arm64/results/4.4/mrgsolve.Rcheck’ * using R Under development (unstable) (2024-01-29 r85841) * 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 ‘1.4.0’ * 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 ... [19s/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 6.9Mb sub-directories of 1Mb or more: libs 5.0Mb * 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 R 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/6s] OK Running ‘testthat.R’ [6s/6s] * checking PDF version of manual ... [5s/5s] OK * DONE Status: 1 NOTE * using check arguments '--no-clean-on-error ' * elapsed time (check, wall clock): 0:56 ```

[kylebaron]

macbuilder r-patched

OK

``` * using log directory ‘/Volumes/PkgBuild/work/1707334858-07482cd35103e30d/packages/big-sur-arm64/results/4.3/mrgsolve.Rcheck’ * using R version 4.3.0 Patched (2023-05-18 r84451) * using platform: aarch64-apple-darwin20 (64-bit) * 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 ‘1.4.0’ * 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 ... [19s/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 6.9Mb sub-directories of 1Mb or more: libs 5.0Mb * 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 R 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 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 ... [2s/3s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [6s/6s] OK Running ‘testthat.R’ [6s/6s] * checking PDF version of manual ... [5s/5s] OK * DONE Status: 1 NOTE * using check arguments '--no-clean-on-error ' * elapsed time (check, wall clock): 1:02 ```

[kylebaron]

winbuilder r-devel

``` * using log directory 'd:/RCompile/CRANguest/R-devel/mrgsolve.Rcheck' * using R Under development (unstable) (2024-02-06 r85870 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * 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 '1.4.0' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [11s] Note_to_CRAN_maintainers Maintainer: 'Kyle T Baron ' * 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) 12.3.0' * 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 R 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 ... [17s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [20s] OK Running 'testthat.R' [20s] * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... [19s] OK * DONE Status: OK ```

[kylebaron]

Metworx

``` tests/testthat ✔ | F W S OK | Context ✔ | 54 | test-annot ✔ | 4 | test-as_data_set ✔ | 39 | test-as_list_mrgmod ✔ | 4 | test-cache ✔ | 16 | test-carry_out_recover ✔ | 9 | test-carry-out ✔ | 48 | test-data_set ✔ | 11 | test-deslist ✔ | 21 | test-dplyr-generics ✔ | 20 | test-env ✔ | 3 | test-ev_assign ✔ | 7 | test-ev_days ✔ | 16 | test-ev_rx ✔ | 80 | test-ev ✔ | 49 | test-evd ✔ | 9 | test-evid4 ✔ | 3 | test-fixed-cmtn ✔ | 3 | test-funset ✔ | 3 | test-idata_set ✔ | 14 | test-infusion ✔ | 6 | test-init ✔ | 36 | test-inventory-too ✔ | 7 | test-inventory ✔ | 6 | test-iv-po ✔ | 7 | test-knobs ✔ | 42 | test-matlist ✔ | 20 | test-matrix ✔ | 3 | test-modlib ✔ | 132 | test-modspec ✔ | 4 | test-mread ✔ | 41 | test-mrgindata ✔ | 19 | test-mrgmod ✔ | 3 | test-mrgsim_q ✔ | 59 | test-mrgsim ✔ | 4 | test-mrgsims ✔ | 80 | test-nmxml ✔ | 4 | test-numericlist ✔ | 9 | test-obsonly-obsaug ✔ | 4 | test-opts ✔ | 28 | test-param ✔ | 5 | test-rcpp_globals ✔ | 6 | test-realize ✔ | 2 | test-records ✔ | 12 | test-recsort ✔ | 12 | test-relabel ✔ | 7 | test-rename ✔ | 5 | test-rng ✔ | 9 | test-S4 ✔ | 17 | test-ss ✔ | 8 | test-tad ✔ | 9 | test-tgrid ✔ | 44 | test-update ✔ | 54 | test-utils ✔ | 3 | test-workflow ══ Results ════════════════════════════════════════════════════════════════════════════════════════════════════════════════ Duration: 11.7 s [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1120 ] inst/maintenance/unit ✔ | F W S OK | Context ✔ | 13 | test-alag ✔ | 6 | audit ✔ | 3 | test-bioav ✔ | 18 | test-capture [1.3s] ✔ | 38 | test-D-R-F ✔ | 20 | tran-inputs ✔ | 1 | test-fail ✔ | 15 | test-initials ✔ | 2 | test-loadso ✔ | 4 | test-mevent ✔ | 34 | misc-syntax [1.3s] ✔ | 1 1 | test-modlib models ✔ | 35 | test-mread [1.2s] ✔ | 58 | nm-vars ✔ | 8 | test-nocb [1.7s] ✔ | 12 | test-on-off ✔ | 6 | One compartment model tests ✔ | 6 | Two compartment model tests ✔ | 3 | Multiple dosing - 1 cmt ✔ | 3 | Multiple dosing - 2 cmt ✔ | 21 | Compare PKMODEL with equivalent ODEs [2.3s] ✔ | 3 | PLUGIN: Rcpp [2.4s] ✔ | 3 | PLUGIN: simeta ✔ | 18 | test-pred ✔ | 12 | test-request ✔ | 12 | Testing various request settings [2.2s] ✔ | 3 36 | test-simeta.R [1.4s] ✔ | 2 | test-solver ✔ | 10 | test-stop-id ✔ | 5 | test-tad-cmt ✔ | 11 | test-update-unit ✔ | 8 | Set F via F_CMT ✔ | 37 | Set ALAG via ALAG_CMT [1.4s] ══ Results ════════════════════════════════════════════════════════════════════════════════════════════════════════════════ Duration: 27.5 s ── Skipped tests (4) ────────────────────────────────────────────────────────────────────────────────────────────────────── • resim(n) is deprecated (3): test-simeta.R:97:3, test-simeta.R:136:3, test-simeta.R:143:3 • skipping modlib builds (1): test-modlib.R:34:3 [ FAIL 0 | WARN 0 | SKIP 4 | PASS 464 ] make[1]: Leaving directory '/data/home/kyleb/git/metrumresearchgroup/mrgsolve' rm -rf tests/testthat/mrgsolve-so-* kyleb@metworx:~/git/metrumresearchgroup/mrgsolve$ make test-cpp Rscript -e 'testthat::test_dir("inst/maintenance/unit-cpp")' ✔ | F W S OK | Context ✔ | 21 | test-cpp [5.9s] ✔ | 12 | evtools-regimen [1.3s] ✔ | 14 | evtools ══ Results ════════════════════════════════════════════════════════════════════════════════════════════════════════════════ Duration: 8.3 s [ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ] ``` ``` * using log directory ‘/data/home/kyleb/git/metrumresearchgroup/mrgsolve/mrgsolve.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-manual’ * checking for file ‘mrgsolve/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mrgsolve’ version ‘1.4.0’ * 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 ... OK * checking installed package size ... NOTE installed size is 9.5Mb sub-directories of 1Mb or more: libs 7.3Mb * 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 R 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 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 ... OK * checking Rd files ... 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 ... 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 ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... OK Running ‘testthat.R’ * DONE Status: 1 NOTE ```

[kyleam]

mpn.scorecard (via score-r-pkg script) looks as expected (on 062b996).

[kylebaron]

Thanks, @kyleam; fixed and merged.

[kylebaron]