We get about 25% performance gain

with the custom lsoda call, avoiding repeated getNativeSymbolInfo calls.
It's just that we should not be calling foreign functions from different
packages, because the may change without notice. Using
getNativeSymbolInfo for "call_lsoda" avoids the CRAN note, and a similar
call could probably be used for "unlock_solver", avoiding the NOTE in
checks for cran, but we should not do this in a CRAN package.

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)