diff options
Diffstat (limited to 'log')
| -rw-r--r-- | log/build.log | 2 | ||||
| -rw-r--r-- | log/check.log | 20 | ||||
| -rw-r--r-- | log/test.log | 76 |
3 files changed, 44 insertions, 54 deletions
diff --git a/log/build.log b/log/build.log index 717128fd..11086361 100644 --- a/log/build.log +++ b/log/build.log @@ -7,4 +7,6 @@ * checking for empty or unneeded directories Removed empty directory ‘mkin/vignettes/web_only’ * building ‘mkin_1.2.5.tar.gz’ +Warning: invalid uid value replaced by that for user 'nobody' +Warning: invalid gid value replaced by that for user 'nobody' diff --git a/log/check.log b/log/check.log index fedb0bd9..64457e57 100644 --- a/log/check.log +++ b/log/check.log @@ -1,17 +1,17 @@ -* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ +* 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 ‘1.2.5’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... [3s/12s] 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 ... [15s/15s] OK +* checking R code for possible problems ... [14s/15s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -62,22 +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 ... [18s/18s] 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 ... [17s/17s] OK +* checking re-building of vignette outputs ... [17s/18s] OK * checking PDF version of manual ... OK * checking HTML version of manual ... NOTE -Skipping checking math rendering: package 'V8' unavailable +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: 1 NOTE See - ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ + ‘/home/agsad.admin.ch/f80868656/projects/mkin/mkin.Rcheck/00check.log’ for details. diff --git a/log/test.log b/log/test.log index 2f1b6949..3bca2e6a 100644 --- a/log/test.log +++ b/log/test.log @@ -4,59 +4,47 @@ ✔ | 5 | Analytical solutions for coupled models [2.9s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [5.7s] -✔ | 12 | Confidence intervals and p-values [1.0s] -✔ | 1 12 | Dimethenamid data from 2018 [33.1s] -──────────────────────────────────────────────────────────────────────────────── -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 [7.5s] +✔ | 6 | Use of precompiled symbols in mkinpredict [6.6s] +✔ | 12 | Confidence intervals and p-values [1.1s] +✔ | 1 12 | Dimethenamid data from 2018 [32.2s] +✔ | 14 | Error model fitting [5.4s] ✔ | 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 [43.6s] -✔ | 2 16 | Nonlinear mixed-effects models [364.4s] -──────────────────────────────────────────────────────────────────────────────── -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 [46.9s] +✔ | 2 16 | Nonlinear mixed-effects models [399.6s] ✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls [0.4s] -✔ | 3 | mkinfit features [0.7s] -✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 12 | Multistart method for saem.mmkin models [80.2s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.0s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.1s] +✔ | 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 [50.1s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.8s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.3s] ✔ | 15 | Plotting [10.9s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [77.0s] -──────────────────────────────────────────────────────────────────────────────── -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 -──────────────────────────────────────────────────────────────────────────────── +✔ | 1 36 | saemix parent models [68.4s] ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.2s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.5s] +✔ | 10 | Fitting the SFORB model [3.8s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.8s] -✔ | 9 | Hypothesis tests [6.7s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s] +✔ | 5 | Summary +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.9s] +✔ | 9 | Hypothesis tests [6.4s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [1.4s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 656.7 s +Duration: 655.6 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 ] |