metrumresearchgroup / mrgsolve

Simulate from ODE-based population PK/PD and QSP models in R

https://mrgsolve.org

GNU General Public License v2.0

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Release/1.3.0 #1137

Closed kylebaron closed 12 months ago

kylebaron commented 1 year ago

mrgsolve 1.3.0

The evdata object for modeled events now contains a check_unique member; when set to false, the event will be processed without checking for a matching record in the modeled event log (#1119).
The amt attribute in evdata modeled event objects is now considered when looking for duplicate records in the modeled event log (#1119).

Bugs Fixed

Fixed a bug where multiple lagged doses given at the same time but with different bioavailability were all given the bioavailability of the last dosing record (#1129, #1130).
Fixed a bug where modeled infusions given now were never turned off (#1131).
Fixed a bug where the self object (type: databox) could not be passed into functions written into header files that were included through $INCLUDE; these header files are now included immediately preceding any user code written into $GLOBAL (#1125, #1126).
Fixed a bug where modeled event log was not getting reset after simulating the first individual; this resulted in events not getting executed in subsequent individuals when matching events were executed in the first individual; this affects modeled events only, not events coming from the data set (#1117, #1118).
Fixed a bug in detecting which compartments are receiving doses (#1112, #1113).

kyleam commented 12 months ago

At some point after the 1.2.0 release, you mentioned you were considering dropping (some of the?) vignettes from .Rbuildignore (prompted by mpn.scorecard). I'm not sure if you want to bother with that for this release, but noting just in case.

kylebaron commented 12 months ago

Thanks; I was thinking about that, but wondered if it was took late to get that in and reviewed. I'll work on it today and see how it works.

kyleam commented 12 months ago

but wondered if it was took late to get that in and reviewed. I'll work on it today and see how it works.

I see you pushed some vignette-related changes and then reverted back to the original state with the latest push (4b20d545 is identical to ab5ba2d7 aside from whitespace changes), so I'm guessing it's not as simple as "tweak some .Rbuildignore entries". I'm all for leaving it be at this point then.

kylebaron commented 12 months ago

Hi @kyleam - I started down that path, but going to re-think the vignette. I'm not sure where I left this; I can review this morning, but if it looks ok to you we can release.

kyleam commented 12 months ago

but if it looks ok to you we can release.

Yes, looks great to me aside from the previously mentioned "the resulted" typo. Thanks!

kylebaron commented 12 months ago

Check - macbuilder

* using log directory ‘/Volumes/PkgBuild/work/1701701206-97c1b2d1b8bf4334/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 ‘1.3.0’
* 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): 0:57

kylebaron commented 12 months ago

Check drone

R CMD check --as-cran mrgsolve_1.3.0.tar.gz
* using log directory ‘/drone/src/mrgsolve.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘mrgsolve/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mrgsolve’ version ‘1.3.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: ‘Kyle T Baron <kyleb@metrumrg.com>’
* 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 for future file timestamps ... OK
* checking DESCRIPTION meta-information ... WARNING
Dependence on R version ‘3.6.2’ not with patchlevel 0
* 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 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 ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [18s/14s]
 OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/drone/src/mrgsolve.Rcheck/00check.log’
for details.

kylebaron commented 12 months ago

Check winbuilder

* using log directory 'd:/RCompile/CRANguest/R-devel/mrgsolve.Rcheck'
* using R Under development (unstable) (2023-12-02 r85657 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 '1.3.0'
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [12s] Note_to_CRAN_maintainers
Maintainer: 'Kyle T Baron <kyleb@metrumrg.com>'
* 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 ... [28s] 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 ... [28s] OK
  Running 'testthat.R' [28s]
* checking PDF version of manual ... [34s] OK
* checking HTML version of manual ... [22s] OK
* DONE
Status: OK

kylebaron commented 9 months ago

Screenshot 2024-02-08 at 09 27 03