diff options
Diffstat (limited to 'log')
| -rw-r--r-- | log/check.log | 23 | ||||
| -rw-r--r-- | log/test.log | 58 |
2 files changed, 37 insertions, 44 deletions
diff --git a/log/check.log b/log/check.log index f7a0d87e..9f05935f 100644 --- a/log/check.log +++ b/log/check.log @@ -1,5 +1,5 @@ * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.2.2 (2022-10-31) +* using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-tests --as-cran’ @@ -10,9 +10,7 @@ * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking package namespace information ... OK -* checking package dependencies ...Warning: unable to access index for repository https://cran.rstudio.com/src/contrib: - cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES' - 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 @@ -23,8 +21,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking whether package ‘mkin’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK -* checking for future file timestamps ... NOTE -unable to verify current time +* checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK @@ -44,7 +41,7 @@ unable to verify current time * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [14s/14s] OK +* checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -61,21 +58,17 @@ unable to verify current time * checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [18s/18s] OK +* checking examples ... [11s/11s] 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 ... [11s/11s] OK +* checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK -* skipping checking HTML version of manual: 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/jranke/git/mkin/mkin.Rcheck/00check.log’ -for details. - +Status: OK diff --git a/log/test.log b/log/test.log index d3939c0f..de28f836 100644 --- a/log/test.log +++ b/log/test.log @@ -1,53 +1,53 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [2.8s] +✔ | 5 | Analytical solutions for coupled models [1.6s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 12 | Confidence intervals and p-values [0.9s] -✔ | 1 12 | Dimethenamid data from 2018 [30.7s] +✔ | 12 | Confidence intervals and p-values [0.4s] +✔ | 1 12 | Dimethenamid data from 2018 [12.0s] ──────────────────────────────────────────────────────────────────────────────── -Skip ('test_dmta.R:99:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data +Skip ('test_dmta.R:99'): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [6.9s] +✔ | 14 | Error model fitting [2.3s] ✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.5s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.7s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] -✔ | 1 | Fitting the logistic model [0.2s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [42.7s] -✔ | 1 11 | Nonlinear mixed-effects models [13.3s] +✔ | 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 11 | Nonlinear mixed-effects models [5.9s] ──────────────────────────────────────────────────────────────────────────────── -Skip ('test_mixed.R:78:3'): saemix results are reproducible for biphasic fits +Skip ('test_mixed.R:78'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve ──────────────────────────────────────────────────────────────────────────────── ✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls [0.6s] -✔ | 3 | mkinfit features [0.6s] -✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 12 | Multistart method for saem.mmkin models [73.3s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.0s] -✔ | 9 | Nonlinear mixed-effects models with nlme [1107.1s] -✔ | 15 | Plotting [13.3s] +✔ | 10 | Special cases of mkinfit calls [0.5s] +✔ | 3 | mkinfit features [0.5s] +✔ | 8 | mkinmod model generation and printing +✔ | 3 | Model predictions with mkinpredict [0.1s] +✔ | 12 | Multistart method for saem.mmkin models [21.7s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [3.7s] +✔ | 15 | Plotting [4.9s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [74.8s] +✔ | 1 36 | saemix parent models [32.6s] ──────────────────────────────────────────────────────────────────────────────── -Skip ('test_saemix_parent.R:143:3'): We can also use mkin solution methods for saem +Skip ('test_saemix_parent.R:143'): 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 [1.5s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.5s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.3s] +✔ | 10 | Fitting the SFORB model [1.7s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 5 | Summary [0.1s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.8s] -✔ | 9 | Hypothesis tests [6.1s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [1.8s] +✔ | 5 | Summary +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s] +✔ | 9 | Hypothesis tests [3.0s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 1386.7 s +Duration: 114.8 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) |