diff options
Diffstat (limited to 'log')
| -rw-r--r-- | log/build.log | 2 | ||||
| -rw-r--r-- | log/check.log | 29 | ||||
| -rw-r--r-- | log/test.log | 78 |
3 files changed, 51 insertions, 58 deletions
diff --git a/log/build.log b/log/build.log index 30c5e432..717128fd 100644 --- a/log/build.log +++ b/log/build.log @@ -6,5 +6,5 @@ * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Removed empty directory ‘mkin/vignettes/web_only’ -* building ‘mkin_1.2.4.tar.gz’ +* building ‘mkin_1.2.5.tar.gz’ diff --git a/log/check.log b/log/check.log index 970fbc7a..64457e57 100644 --- a/log/check.log +++ b/log/check.log @@ -1,17 +1,17 @@ -* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.3.0 Patched (2023-05-18 r84448) +* using log directory ‘/home/agsad.admin.ch/f80868656/projects/mkin/mkin.Rcheck’ +* using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by - 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) + 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 * 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 ‘1.2.4’ +* this is package ‘mkin’ version ‘1.2.5’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... [2s/10s] Note_to_CRAN_maintainers +* checking CRAN incoming feasibility ... [5s/26s] 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 ... OK +* checking R code for possible problems ... [14s/15s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -62,17 +62,22 @@ 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 ... OK +* checking examples ... [20s/22s] 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 ... OK +* checking re-building of vignette outputs ... [17s/18s] OK * checking PDF version of manual ... OK -* checking HTML version of manual ... OK +* checking HTML version of manual ... NOTE +Skipping checking HTML validation: no command 'tidy' found * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE -Status: OK +Status: 1 NOTE +See + ‘/home/agsad.admin.ch/f80868656/projects/mkin/mkin.Rcheck/00check.log’ +for details. + diff --git a/log/test.log b/log/test.log index b1b4ae31..c872cb1d 100644 --- a/log/test.log +++ b/log/test.log @@ -1,62 +1,50 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [1.5s] +✔ | 5 | Analytical solutions for coupled models [3.1s] ✔ | 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 [12.5s] -──────────────────────────────────────────────────────────────────────────────── -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 15 minutes on my system -──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [2.3s] +✔ | 6 | Use of precompiled symbols in mkinpredict [5.3s] +✔ | 12 | Confidence intervals and p-values +✔ | 1 12 | Dimethenamid data from 2018 [31.5s] +✔ | 14 | Error model fitting [5.6s] ✔ | 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 [18.9s] -✔ | 2 16 | Nonlinear mixed-effects models [148.4s] -──────────────────────────────────────────────────────────────────────────────── -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 -──────────────────────────────────────────────────────────────────────────────── +✔ | 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 [43.1s] +✔ | 2 16 | Nonlinear mixed-effects models [441.3s] ✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls [0.3s] -✔ | 3 | mkinfit features [0.5s] +✔ | 10 | Special cases of mkinfit calls +✔ | 3 | mkinfit features ✔ | 8 | mkinmod model generation and printing -✔ | 3 | Model predictions with mkinpredict [0.1s] -✔ | 12 | Multistart method for saem.mmkin models [23.3s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] -✔ | 9 | Nonlinear mixed-effects models with nlme [3.5s] -✔ | 15 | Plotting [4.5s] +✔ | 3 | Model predictions with mkinpredict +✔ | 12 | Multistart method for saem.mmkin models [71.6s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.7s] +✔ | 9 | Nonlinear mixed-effects models with nlme [10.1s] +✔ | 15 | Plotting [12.1s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [30.7s] -──────────────────────────────────────────────────────────────────────────────── -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] +✔ | 1 36 | saemix parent models [81.8s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [1.7s] +✔ | 10 | Fitting the SFORB model [3.8s] ✔ | 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] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s] +✔ | 9 | Hypothesis tests [7.3s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [1.5s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 259.6 s +Duration: 731.0 s -── Skipped tests ────────────────────────────────────────────────────────────── -• Fitting this ODE model with saemix takes about 15 minutes on my 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) +── Skipped tests (4) ─────────────────────────────────────────────────────────── +• Fitting this ODE model with saemix takes about 15 minutes on my 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 281 ] |