Finish adapting to upcoming deSolve

3 files changed, 20 insertions, 39 deletions

diff --git a/log/build.log b/log/build.log
index dbe0cd5b..db5fac76 100644
--- a/log/build.log
+++ b/log/build.log
@@ -5,5 +5,6 @@
 * creating vignettes ... OK
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
-* building ‘mkin_1.2.2.tar.gz’
+Removed empty directory ‘mkin/vignettes/web_only’
+* building ‘mkin_1.3.0.tar.gz’
 
diff --git a/log/check.log b/log/check.log
index a81475d9..967b51d0 100644
--- a/log/check.log
+++ b/log/check.log
@@ -5,30 +5,13 @@
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘mkin’ version ‘1.2.2’
+* this is package ‘mkin’ version ‘1.3.0’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... NOTE
+* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
-
-Size of tarball: 6636884 bytes
 * checking package namespace information ... OK
 * checking package dependencies ... OK
-* checking if this is a source package ... NOTE
-Found the following apparent object files/libraries:
-  vignettes/2022_wp_1/cyan_dlls/dfop_path_1.so
-  vignettes/2022_wp_1/cyan_dlls/dfop_path_2.so
-  vignettes/2022_wp_1/cyan_dlls/fomc_path_1.so
-  vignettes/2022_wp_1/cyan_dlls/fomc_path_2.so
-  vignettes/2022_wp_1/cyan_dlls/hs_path_1.so
-  vignettes/2022_wp_1/cyan_dlls/sfo_path_1.so
-  vignettes/2022_wp_1/cyan_dlls/sforb_path_1.so
-  vignettes/2022_wp_1/cyan_dlls/sforb_path_2.so
-  vignettes/2022_wp_1/dmta_dlls/m_dfop_path.so
-  vignettes/2022_wp_1/dmta_dlls/m_fomc_path.so
-  vignettes/2022_wp_1/dmta_dlls/m_hs_path.so
-  vignettes/2022_wp_1/dmta_dlls/m_sfo_path.so
-  vignettes/2022_wp_1/dmta_dlls/m_sforb_path.so
-Object files/libraries should not be included in a source package.
+* checking if this is a source package ... OK
 * checking if there is a namespace ... OK
 * checking for executable files ... OK
 * checking for hidden files and directories ... OK
@@ -72,6 +55,7 @@ Object files/libraries should not be included in a source package.
 * checking data for non-ASCII characters ... OK
 * checking LazyData ... OK
 * checking data for ASCII and uncompressed saves ... OK
+* 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
@@ -86,9 +70,5 @@ Object files/libraries should not be included in a source package.
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 2 NOTEs
-See
-  ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
-for details.
-
+Status: OK
 
diff --git a/log/test.log b/log/test.log
index dc1b6c74..42ed75e4 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,13 +1,13 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [1.6s]
+✔ |         5 | Analytical solutions for coupled models [1.4s]
 ✔ |         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 [12.4s]
+✔ |     1  12 | Dimethenamid data from 2018 [11.6s]
 ────────────────────────────────────────────────────────────────────────────────
-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 [2.3s]
@@ -16,7 +16,7 @@ Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ✔ |        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 [19.1s]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [18.5s]
 ✔ |     1  11 | Nonlinear mixed-effects models [5.9s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip ('test_mixed.R:78'): saemix results are reproducible for biphasic fits
@@ -27,27 +27,27 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |         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 [21.6s]
+✔ |        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 [3.7s]
-✔ |        15 | Plotting [4.6s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [3.4s]
+✔ |        15 | Plotting [4.4s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [30.9s]
+✔ |     1  36 | saemix parent models [29.4s]
 ────────────────────────────────────────────────────────────────────────────────
 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 [0.6s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.5s]
 ✔ |        11 | Processing of residue series
-✔ |        10 | Fitting the SFORB model [1.7s]
+✔ |        10 | Fitting the SFORB model [1.6s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.9s]
-✔ |         9 | Hypothesis tests [3.3s]
+✔ |         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]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 113.6 s
+Duration: 108.9 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)