diff options
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | log/build.log | 2 | ||||
| -rw-r--r-- | log/check.log | 29 | ||||
| -rw-r--r-- | log/test.log | 161 | ||||
| -rw-r--r-- | man/hierarchical_kinetics.Rd | 6 | ||||
| -rw-r--r-- | tests/testthat/test_saemix_parent.R | 2 |
6 files changed, 68 insertions, 136 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 88f4f33c..8a97fe34 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 1.2.6 -Date: 2023-10-13 +Version: 1.2.7 +Date: 2023-11-23 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "johannes.ranke@jrwb.de", diff --git a/log/build.log b/log/build.log index 6f7ac8ab..b4269860 100644 --- a/log/build.log +++ b/log/build.log @@ -7,5 +7,5 @@ * checking for empty or unneeded directories Removed empty directory ‘mkin/inst/rmarkdown/templates/hierarchical_kinetics_parent’ Removed empty directory ‘mkin/vignettes/web_only’ -* building ‘mkin_1.2.6.tar.gz’ +* building ‘mkin_1.2.7.tar.gz’ diff --git a/log/check.log b/log/check.log index 64457e57..26fdc5a0 100644 --- a/log/check.log +++ b/log/check.log @@ -1,17 +1,17 @@ -* using log directory ‘/home/agsad.admin.ch/f80868656/projects/mkin/mkin.Rcheck’ -* using R version 4.3.1 (2023-06-16) +* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ +* using R version 4.3.2 (2023-10-31) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 - GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 -* running under: Ubuntu 22.04.3 LTS + gcc (Debian 12.2.0-14) 12.2.0 + GNU Fortran (Debian 12.2.0-14) 12.2.0 +* running under: Debian GNU/Linux 12 (bookworm) * using session charset: UTF-8 * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.2.5’ +* this is package ‘mkin’ version ‘1.2.7’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... [5s/26s] Note_to_CRAN_maintainers +* checking CRAN incoming feasibility ... [2s/15s] Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking package namespace information ... OK * checking package dependencies ... OK @@ -45,7 +45,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [14s/15s] OK +* checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -62,22 +62,17 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [20s/22s] OK +* checking examples ... [10s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK -* checking re-building of vignette outputs ... [17s/18s] OK +* checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK -* checking HTML version of manual ... NOTE -Skipping checking HTML validation: no command 'tidy' found +* checking HTML 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 NOTE -See - ‘/home/agsad.admin.ch/f80868656/projects/mkin/mkin.Rcheck/00check.log’ -for details. - +Status: OK diff --git a/log/test.log b/log/test.log index 6d5bc470..a6ac83ed 100644 --- a/log/test.log +++ b/log/test.log @@ -1,117 +1,50 @@ ℹ Testing mkin -✔ | F W S OK | Context -✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [1.5s] -✔ | 5 | Calculation of Akaike weights -✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] -✔ | 12 | Confidence intervals and p-values [0.4s] -✔ | 1 12 | Dimethenamid data from 2018 [13.2s] -──────────────────────────────────────────────────────────────────────────────── -Skip ('test_dmta.R:88:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data -Reason: Fitting this ODE model with saemix takes about 5 minutes on my new system -──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [2.5s] -✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.3s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.4s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.2s] -✔ | 1 | Fitting the logistic model [0.1s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.0s] -✖ | 1 2 15 | Nonlinear mixed-effects models [149.2s] -──────────────────────────────────────────────────────────────────────────────── -Failure ('test_mixed.R:21:3'): Print methods work -Results have changed from known value recorded in 'print_dfop_saem_1.txt'. - -old[13:23] vs new[13:23] - "" - "Fitted parameters:" - " estimate lower upper" -- "parent_0 99.92 98.77 101.06" -+ "parent_0 99.96 98.82 101.11" -- "log_k1 -2.72 -2.95 -2.50" -+ "log_k1 -2.71 -2.94 -2.49" -- "log_k2 -4.14 -4.27 -4.01" -+ "log_k2 -4.14 -4.26 -4.01" -- "g_qlogis -0.35 -0.53 -0.16" -+ "g_qlogis -0.36 -0.54 -0.17" -- "a.1 0.92 0.68 1.16" -+ "a.1 0.93 0.69 1.17" - "b.1 0.05 0.04 0.06" - "SD.log_k1 0.37 0.23 0.51" -and 1 more ... - -Skip ('test_mixed.R:80:3'): saemix results are reproducible for biphasic fits -Reason: Fitting with saemix takes around 10 minutes when using deSolve - -Skip ('test_mixed.R:133:3'): SFO-SFO saemix specific analytical solution work -Reason: This is seldom used, so save some time -──────────────────────────────────────────────────────────────────────────────── -✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls [0.3s] -✔ | 3 | mkinfit features [0.5s] -✔ | 8 | mkinmod model generation and printing -✔ | 3 | Model predictions with mkinpredict [0.1s] -✖ | 3 9 | Multistart method for saem.mmkin models [23.2s] -──────────────────────────────────────────────────────────────────────────────── -Failure ('test_multistart.R:44:3'): multistart works for saem.mmkin models -Snapshot of `testcase` to 'multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed -Run `testthat::snapshot_review('multistart/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger(...) - at test_multistart.R:44:2 - 3. testthat::expect_snapshot_file(...) - -Failure ('test_multistart.R:55:3'): multistart works for saem.mmkin models -Snapshot of `testcase` to 'multistart/llhist-for-dfop-sfo-fit.svg' has changed -Run `testthat::snapshot_review('multistart/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo) - at test_multistart.R:55:2 - 3. testthat::expect_snapshot_file(...) - -Failure ('test_multistart.R:56:3'): multistart works for saem.mmkin models -Snapshot of `testcase` to 'multistart/parplot-for-dfop-sfo-fit.svg' has changed -Run `testthat::snapshot_review('multistart/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo) - at test_multistart.R:56:2 - 3. testthat::expect_snapshot_file(...) -──────────────────────────────────────────────────────────────────────────────── -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6s] -✔ | 9 | Nonlinear mixed-effects models with nlme [3.8s] -✖ | 1 14 | Plotting [4.7s] -──────────────────────────────────────────────────────────────────────────────── -Failure ('test_plot.R:55:3'): Plotting mkinfit, mmkin and mixed model objects is reproducible -Snapshot of `testcase` to 'plot/mixed-model-fit-for-nlme-object.svg' has changed -Run `testthat::snapshot_review('plot/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger(...) - at test_plot.R:55:2 - 3. testthat::expect_snapshot_file(...) -──────────────────────────────────────────────────────────────────────────────── -✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [31.4s] -──────────────────────────────────────────────────────────────────────────────── -Skip ('test_saemix_parent.R:143:3'): We can also use mkin solution methods for saem -Reason: This still takes almost 2.5 minutes although we do not solve ODEs -──────────────────────────────────────────────────────────────────────────────── -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.5s] -✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [1.7s] -✔ | 1 | Summaries of old mkinfit objects -✔ | 5 | Summary -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s] -✔ | 9 | Hypothesis tests [2.9s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s] +✔ | F W S OK | Context +✔ | 5 | AIC calculation +✔ | 5 | Analytical solutions for coupled models [1.5s] +✔ | 5 | Calculation of Akaike weights +✔ | 3 | Export dataset for reading into CAKE +✔ | 6 | Use of precompiled symbols in mkinpredict [3.3s] +✔ | 12 | Confidence intervals and p-values +✔ | 1 12 | Dimethenamid data from 2018 [13.1s] +✔ | 14 | Error model fitting [2.5s] +✔ | 5 | Time step normalisation +✔ | 4 | Calculation of FOCUS chi2 error levels +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) +✔ | 4 | Test fitting the decline of metabolites from their maximum +✔ | 1 | Fitting the logistic model +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [20.4s] +✔ | 2 16 | Nonlinear mixed-effects models [149.9s] +✔ | 3 | Test dataset classes mkinds and mkindsg +✔ | 10 | Special cases of mkinfit calls +✔ | 3 | mkinfit features +✔ | 8 | mkinmod model generation and printing +✔ | 3 | Model predictions with mkinpredict +✔ | 12 | Multistart method for saem.mmkin models [23.0s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [3.6s] +✔ | 15 | Plotting [4.8s] +✔ | 4 | Residuals extracted from mkinfit models +✔ | 1 38 | saemix parent models [35.2s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper +✔ | 11 | Processing of residue series +✔ | 10 | Fitting the SFORB model [1.6s] +✔ | 1 | Summaries of old mkinfit objects +✔ | 5 | Summary +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) +✔ | 9 | Hypothesis tests [2.8s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 262.6 s - -── Skipped tests ────────────────────────────────────────────────────────────── -• Fitting this ODE model with saemix takes about 5 minutes on my new system (1) -• Fitting with saemix takes around 10 minutes when using deSolve (1) -• This is seldom used, so save some time (1) -• This still takes almost 2.5 minutes although we do not solve ODEs (1) - -[ FAIL 5 | WARN 0 | SKIP 4 | PASS 276 ] +Duration: 268.2 s + +── Skipped tests (4) ─────────────────────────────────────────────────────────── +• Fitting this ODE model with saemix takes about 5 minutes on my new system + (1): 'test_dmta.R:88:3' +• Fitting with saemix takes around 10 minutes when using deSolve (1): + 'test_mixed.R:80:3' +• This is seldom used, so save some time (1): 'test_mixed.R:133:3' +• This still takes almost 2.5 minutes although we do not solve ODEs (1): + 'test_saemix_parent.R:143:3' + +[ FAIL 0 | WARN 0 | SKIP 4 | PASS 283 ] diff --git a/man/hierarchical_kinetics.Rd b/man/hierarchical_kinetics.Rd index bcbe1e06..8330fe68 100644 --- a/man/hierarchical_kinetics.Rd +++ b/man/hierarchical_kinetics.Rd @@ -9,7 +9,11 @@ hierarchical_kinetics(..., keep_tex = FALSE) \arguments{ \item{...}{Arguments to \code{rmarkdown::pdf_document}} -\item{keep_tex}{Keep the intermediate tex file used in the conversion to PDF} +\item{keep_tex}{Keep the intermediate tex file used in the conversion to PDF. +Note that this argument does not control whether to keep the auxiliary +files (e.g., \file{.aux}) generated by LaTeX when compiling \file{.tex} to +\file{.pdf}. To keep these files, you may set \code{options(tinytex.clean = +FALSE)}.} } \value{ R Markdown output format to pass to diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R index c80b4fa1..88b406b6 100644 --- a/tests/testthat/test_saemix_parent.R +++ b/tests/testthat/test_saemix_parent.R @@ -174,4 +174,4 @@ test_that("illparms finds a single random effect that is ill-defined", { expect_equal( as.character(illparms(m_saem_2)), "sd(log_k_parent)") -} +}) |