From b17dc3ee5f4fda17fcbc659730cb81e447510121 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 22 Mar 2023 22:34:30 +0100
Subject: Fix typo in mkinerrmin
Thanks to Sebastian Meyer for spotting it.
---
log/check.log | 22 ++++++++++++++--------
log/test.log | 53 +++++++++++++++++++++++++++--------------------------
2 files changed, 41 insertions(+), 34 deletions(-)
(limited to 'log')
diff --git a/log/check.log b/log/check.log
index 967b51d0..b44bc1b4 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,14 +1,16 @@
* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.2.2 Patched (2022-11-10 r83330)
+* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 ‘1.3.0’
+* this is package ‘mkin’ version ‘1.2.3’
* package encoding: UTF-8
-* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
+* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
+
+The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
@@ -41,7 +43,7 @@ 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/14s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
@@ -58,17 +60,21 @@ 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 ... [10s/10s] OK
+* checking examples ... [18s/18s] 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 ... [12s/12s] OK
* checking PDF version of manual ... OK
-* checking HTML version of manual ... OK
+* skipping checking HTML version of manual: 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/jranke/git/mkin/mkin.Rcheck/00check.log’
+for details.
+
diff --git a/log/test.log b/log/test.log
index 42ed75e4..d4fb85a2 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,53 +1,54 @@
+ℹ Loading mkin
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [1.4s]
+✔ | 5 | Analytical solutions for coupled models [2.8s]
✔ | 5 | Calculation of Akaike weights
✔ | 3 | Export dataset for reading into CAKE
-✔ | 12 | Confidence intervals and p-values [0.4s]
-✔ | 1 12 | Dimethenamid data from 2018 [11.6s]
+✔ | 12 | Confidence intervals and p-values [1.0s]
+✔ | 1 12 | Dimethenamid data from 2018 [31.3s]
────────────────────────────────────────────────────────────────────────────────
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 [2.3s]
+✔ | 14 | Error model fitting [6.9s]
✔ | 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 [18.5s]
-✔ | 1 11 | Nonlinear mixed-effects models [5.9s]
+✔ | 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 [13.1s]
────────────────────────────────────────────────────────────────────────────────
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 [0.4s]
-✔ | 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 [21.1s]
-✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [3.4s]
-✔ | 15 | Plotting [4.4s]
+✔ | 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 [74.1s]
+✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.9s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [8.5s]
+✔ | 15 | Plotting [11.4s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 1 36 | saemix parent models [29.4s]
+✔ | 1 36 | saemix parent models [73.9s]
────────────────────────────────────────────────────────────────────────────────
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 [0.5s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.1s]
✔ | 11 | Processing of residue series
-✔ | 10 | Fitting the SFORB model [1.6s]
+✔ | 10 | Fitting the SFORB model [3.1s]
✔ | 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]
+✔ | 5 | Summary [0.1s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.7s]
+✔ | 9 | Hypothesis tests [6.0s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [1.9s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 108.9 s
+Duration: 285.4 s
── Skipped tests ──────────────────────────────────────────────────────────────
• Fitting this ODE model with saemix takes about 15 minutes on my system (1)
--
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