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-rw-r--r--log/build.log2
-rw-r--r--log/check.log40
-rw-r--r--log/test.log58
-rw-r--r--log/test_dev.log116
4 files changed, 142 insertions, 74 deletions
diff --git a/log/build.log b/log/build.log
index 245bd205..dbe0cd5b 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_1.3.0.tar.gz’
+* building ‘mkin_1.2.2.tar.gz’
diff --git a/log/check.log b/log/check.log
index e7d4d327..a81475d9 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,17 +1,34 @@
* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.2.2 (2022-10-31)
+* using R version 4.2.2 Patched (2022-11-10 r83330)
* 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 ‘1.2.2’
* package encoding: UTF-8
-* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
+* checking CRAN incoming feasibility ... NOTE
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 ... 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 there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
@@ -37,18 +54,11 @@ 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 ... 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... 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 foreign function calls ... OK
+* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
@@ -64,7 +74,7 @@ Extensions’ manual.
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
-* checking examples ... [20s/20s] OK
+* checking examples ... [10s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... SKIPPED
* checking for unstated dependencies in vignettes ... OK
diff --git a/log/test.log b/log/test.log
index 10c0aa76..dc1b6c74 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,57 +1,57 @@
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [2.9s]
+✔ | 5 | Analytical solutions for coupled models [1.6s]
✔ | 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 [29.5s]
+✔ | 12 | Confidence intervals and p-values [0.4s]
+✔ | 1 12 | Dimethenamid data from 2018 [12.4s]
────────────────────────────────────────────────────────────────────────────────
-Skip ('test_dmta.R:99'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
+Skip ('test_dmta.R:98'): 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]
+✔ | 14 | Error model fitting [2.3s]
✔ | 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) [0.7s]
-✔ | 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 [24.7s]
-✔ | 1 12 | Nonlinear mixed-effects models [0.3s]
+✔ | 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 [19.1s]
+✔ | 1 11 | Nonlinear mixed-effects models [5.9s]
────────────────────────────────────────────────────────────────────────────────
-Skip ('test_mixed.R:74'): saemix results are reproducible for biphasic fits
+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 [0.5s]
-✔ | 3 | mkinfit features [0.7s]
-✔ | 8 | mkinmod model generation and printing [0.2s]
-✔ | 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]
+✔ | 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 [21.6s]
+✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [3.7s]
+✔ | 15 | Plotting [4.6s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 1 36 | saemix parent models [66.1s]
+✔ | 1 36 | saemix parent models [30.9s]
────────────────────────────────────────────────────────────────────────────────
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 [1.1s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.6s]
✔ | 11 | Processing of residue series
-✔ | 10 | Fitting the SFORB model [3.4s]
+✔ | 10 | Fitting the SFORB model [1.7s]
✔ | 1 | Summaries of old mkinfit objects
-✔ | 5 | Summary [0.2s]
-✔ | 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]
+✔ | 5 | Summary
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.9s]
+✔ | 9 | Hypothesis tests [3.3s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 206.2 s
+Duration: 113.6 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 still takes almost 2.5 minutes although we do not solve ODEs (1)
-[ FAIL 0 | WARN 0 | SKIP 3 | PASS 267 ]
+[ FAIL 0 | WARN 0 | SKIP 3 | PASS 270 ]
diff --git a/log/test_dev.log b/log/test_dev.log
index 24905a1a..370dc5af 100644
--- a/log/test_dev.log
+++ b/log/test_dev.log
@@ -1,54 +1,112 @@
-ℹ Loading mkin
-Loading required package: parallel
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [14.6s]
+✔ | 5 | Analytical solutions for coupled models [3.0s]
✔ | 5 | Calculation of Akaike weights
-✔ | 2 | Export dataset for reading into CAKE
+✔ | 3 | Export dataset for reading into CAKE
✔ | 12 | Confidence intervals and p-values [1.0s]
-⠋ | 1 | Dimethenamid data from 2018
-✔ | 1 27 | Dimethenamid data from 2018 [116.1s]
+✔ | 1 12 | Dimethenamid data from 2018 [31.6s]
────────────────────────────────────────────────────────────────────────────────
-Skip (test_dmta.R:164:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
+Skip ('test_dmta.R:98'): 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 [6.6s]
+✔ | 14 | Error model fitting [5.2s]
✔ | 5 | Time step normalisation
-✔ | 4 | Calculation of FOCUS chi2 error levels [0.8s]
-✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.5s]
-✔ | 4 | Test fitting the decline of metabolites from their maximum [0.6s]
-✔ | 1 | Fitting the logistic model [0.3s]
-⠋ | 11 | Nonlinear mixed-effects models
-✔ | 1 14 | Nonlinear mixed-effects models [1.3s]
-────────────────────────────────────────────────────────────────────────────────
-Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits
+✔ | 4 | Calculation of FOCUS chi2 error levels [0.5s]
+✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
+✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s]
+✔ | 1 | Fitting the logistic model [0.2s]
+✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [40.7s]
+✖ | 1 1 10 | Nonlinear mixed-effects models [13.2s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_mixed.R:21'): Print methods work
+Results have changed from known value recorded in 'print_dfop_saem_1.txt'.
+
+old[13:23] vs new[13:23]
+ ""
+ "Fitted parameters:"
+ " estimate lower upper"
+- "parent_0 99.92 98.77 101.06"
++ "parent_0 99.96 98.82 101.11"
+- "log_k1 -2.72 -2.95 -2.50"
++ "log_k1 -2.71 -2.94 -2.49"
+- "log_k2 -4.14 -4.27 -4.01"
++ "log_k2 -4.14 -4.26 -4.01"
+- "g_qlogis -0.35 -0.53 -0.16"
++ "g_qlogis -0.36 -0.54 -0.17"
+- "a.1 0.92 0.68 1.16"
++ "a.1 0.93 0.69 1.17"
+ "b.1 0.05 0.04 0.06"
+ "SD.log_k1 0.37 0.23 0.51"
+and 1 more ...
+
+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 [0.6s]
-✔ | 3 | mkinfit features [1.1s]
+✔ | 3 | mkinfit features [0.7s]
✔ | 8 | mkinmod model generation and printing [0.2s]
✔ | 3 | Model predictions with mkinpredict [0.3s]
-✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.1s]
-✔ | 9 | Nonlinear mixed-effects models with nlme [8.7s]
-✔ | 16 | Plotting [1.4s]
+✖ | 3 9 | Multistart method for saem.mmkin models [45.8s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_multistart.R:44'): multistart works for saem.mmkin models
+Snapshot of `testcase` to 'multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed
+Run `testthat::snapshot_review('multistart/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger(...)
+ at test_multistart.R:44:2
+ 3. testthat::expect_snapshot_file(...)
+
+Failure ('test_multistart.R:55'): multistart works for saem.mmkin models
+Snapshot of `testcase` to 'multistart/llhist-for-dfop-sfo-fit.svg' has changed
+Run `testthat::snapshot_review('multistart/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo)
+ at test_multistart.R:55:2
+ 3. testthat::expect_snapshot_file(...)
+
+Failure ('test_multistart.R:56'): multistart works for saem.mmkin models
+Snapshot of `testcase` to 'multistart/parplot-for-dfop-sfo-fit.svg' has changed
+Run `testthat::snapshot_review('multistart/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo)
+ at test_multistart.R:56:2
+ 3. testthat::expect_snapshot_file(...)
+────────────────────────────────────────────────────────────────────────────────
+✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [9.0s]
+✖ | 1 14 | Plotting [10.2s]
+────────────────────────────────────────────────────────────────────────────────
+Failure ('test_plot.R:55'): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Snapshot of `testcase` to 'plot/mixed-model-fit-for-nlme-object.svg' has changed
+Run `testthat::snapshot_review('plot/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger(...)
+ at test_plot.R:55:2
+ 3. testthat::expect_snapshot_file(...)
+────────────────────────────────────────────────────────────────────────────────
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 23 | saemix parent models [28.4s]
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [12.0s]
-✔ | 7 | Fitting the SFORB model [16.9s]
+✔ | 1 36 | saemix parent models [71.7s]
+────────────────────────────────────────────────────────────────────────────────
+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 [1.5s]
+✔ | 11 | Processing of residue series
+✔ | 10 | Fitting the SFORB model [3.5s]
✔ | 1 | Summaries of old mkinfit objects
-✔ | 4 | Summary [0.1s]
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [18.1s]
-✔ | 9 | Hypothesis tests [78.9s]
-✔ | 2 | tffm0
+✔ | 5 | Summary [0.2s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
+✔ | 9 | Hypothesis tests [7.7s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 315.9 s
+Duration: 255.0 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 still takes almost 2.5 minutes although we do not solve ODEs (1)
-[ FAIL 0 | WARN 0 | SKIP 2 | PASS 240 ]
+[ FAIL 5 | WARN 0 | SKIP 3 | PASS 265 ]

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