diff options
Diffstat (limited to 'log')
| -rw-r--r-- | log/build.log | 2 | ||||
| -rw-r--r-- | log/check.log | 23 | ||||
| -rw-r--r-- | log/test.log | 34 |
3 files changed, 35 insertions, 24 deletions
diff --git a/log/build.log b/log/build.log index c4f9b8a2..245bd205 100644 --- a/log/build.log +++ b/log/build.log @@ -5,5 +5,5 @@ * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories -* building ‘mkin_1.2.0.tar.gz’ +* building ‘mkin_1.3.0.tar.gz’ diff --git a/log/check.log b/log/check.log index 3fea2ec6..e7d4d327 100644 --- a/log/check.log +++ b/log/check.log @@ -5,7 +5,7 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.2.0’ +* this is package ‘mkin’ version ‘1.3.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ @@ -37,11 +37,18 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * 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 dependencies in R code ... NOTE +Package in Depends field not imported from: ‘deSolve’ + These packages need to be imported from (in the NAMESPACE file) + for when this namespace is loaded but not attached. * 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 foreign function calls ... NOTE +Foreign function call to a different package: + .C("unlock_solver", ..., PACKAGE = "deSolve") +See chapter ‘System and foreign language interfaces’ in the ‘Writing R +Extensions’ manual. +* checking R code for possible problems ... [17s/17s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -57,7 +64,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [15s/15s] OK +* checking examples ... [20s/20s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK @@ -69,5 +76,9 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’ * checking for detritus in the temp directory ... OK * DONE -Status: OK +Status: 2 NOTEs +See + ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ +for details. + diff --git a/log/test.log b/log/test.log index 7005ac37..10c0aa76 100644 --- a/log/test.log +++ b/log/test.log @@ -1,22 +1,22 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.2s] +✔ | 5 | Analytical solutions for coupled models [2.9s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.0s] -✔ | 1 12 | Dimethenamid data from 2018 [32.4s] +✔ | 1 12 | Dimethenamid data from 2018 [29.5s] ──────────────────────────────────────────────────────────────────────────────── -Skip ('test_dmta.R:98'): 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 [4.9s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] +✔ | 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 [24.2s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [24.7s] ✔ | 1 12 | Nonlinear mixed-effects models [0.3s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:74'): saemix results are reproducible for biphasic fits @@ -26,28 +26,28 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 10 | Special cases of mkinfit calls [0.5s] ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 7 | Multistart method for saem.mmkin models [36.9s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.6s] -✔ | 16 | Plotting [9.8s] +✔ | 3 | Model predictions with mkinpredict [0.4s] +✔ | 7 | Multistart method for saem.mmkin models [36.8s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s] +✔ | 16 | Plotting [10.0s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [66.3s] +✔ | 1 36 | saemix parent models [66.1s] ──────────────────────────────────────────────────────────────────────────────── 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 [1.4s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.1s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.7s] +✔ | 10 | Fitting the SFORB model [3.4s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] -✔ | 9 | Hypothesis tests [8.0s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.6s] +✔ | 9 | Hypothesis tests [6.1s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 211.7 s +Duration: 206.2 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) |