From 851f146e866817e48a7becf25b7d76f0ad45f1fe Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 14 Sep 2018 18:24:49 +0200 Subject: Skip some more tests on CRAN Static documentation rebuilt by pkgdown --- GNUmakefile | 4 +-- docs/articles/FOCUS_L.html | 42 ++++++++++++------------- docs/articles/web_only/compiled_models.html | 10 +++--- docs/reference/Extract.mmkin.html | 12 ++++---- docs/reference/mccall81_245T.html | 12 ++++---- docs/reference/mkinfit.html | 46 ++++++++++++++-------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 2 +- docs/reference/mmkin.html | 4 +-- docs/reference/summary.mkinfit.html | 6 ++-- docs/reference/transform_odeparms.html | 24 +++++++-------- test.log | 18 +++++------ tests/testthat/test_FOCUS_chi2_error_level.R | 3 +- tests/testthat/test_parent_only.R | 4 ++- tests/testthat/test_twa.R | 6 +--- 15 files changed, 96 insertions(+), 99 deletions(-) diff --git a/GNUmakefile b/GNUmakefile index a6f0d8c6..20a9c723 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -63,8 +63,8 @@ clean: $(RM) -r vignettes/web_only/*.R $(RM) Rplots.pdf -test: quickinstall - NOT_CRAN=true "$(RBIN)/Rscript" -e 'devtools::test()' 2>&1 | tee test.log +test: install + "$(RBIN)/Rscript" -e 'devtools::test()' 2>&1 | tee test.log README.html: README.md "$(RBIN)/Rscript" -e "rmarkdown::render('README.md', output_format = 'html_document', output_options = list(mathjax = NULL))" diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 8b06f072..f1a91c04 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -110,15 +110,15 @@ summary(m.L1.SFO) 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 17:43:07 2018 
-## Date of summary: Fri Sep 14 17:43:07 2018 
+## Date of fit:     Fri Sep 14 18:22:23 2018 
+## Date of summary: Fri Sep 14 18:22:23 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.091 s
+## Fitted with method Port using 37 model solutions performed in 0.092 s
 ## 
 ## Weighting: none
 ## 
@@ -201,15 +201,15 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 17:43:09 2018 
-## Date of summary: Fri Sep 14 17:43:09 2018 
+## Date of fit:     Fri Sep 14 18:22:25 2018 
+## Date of summary: Fri Sep 14 18:22:25 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 611 model solutions performed in 1.398 s
+## Fitted with method Port using 611 model solutions performed in 1.355 s
 ## 
 ## Weighting: none
 ## 
@@ -296,15 +296,15 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 17:43:10 2018 
-## Date of summary: Fri Sep 14 17:43:10 2018 
+## Date of fit:     Fri Sep 14 18:22:25 2018 
+## Date of summary: Fri Sep 14 18:22:25 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.18 s
+## Fitted with method Port using 81 model solutions performed in 0.175 s
 ## 
 ## Weighting: none
 ## 
@@ -367,8 +367,8 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 17:43:11 2018 
-## Date of summary: Fri Sep 14 17:43:11 2018 
+## Date of fit:     Fri Sep 14 18:22:26 2018 
+## Date of summary: Fri Sep 14 18:22:26 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -377,7 +377,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.782 s
+## Fitted with method Port using 336 model solutions performed in 0.756 s
 ## 
 ## Weighting: none
 ## 
@@ -459,8 +459,8 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 17:43:12 2018 
-## Date of summary: Fri Sep 14 17:43:12 2018 
+## Date of fit:     Fri Sep 14 18:22:27 2018 
+## Date of summary: Fri Sep 14 18:22:28 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -469,7 +469,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.312 s
+## Fitted with method Port using 137 model solutions performed in 0.322 s
 ## 
 ## Weighting: none
 ## 
@@ -560,15 +560,15 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 17:43:12 2018 
-## Date of summary: Fri Sep 14 17:43:12 2018 
+## Date of fit:     Fri Sep 14 18:22:28 2018 
+## Date of summary: Fri Sep 14 18:22:28 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.106 s
+## Fitted with method Port using 46 model solutions performed in 0.101 s
 ## 
 ## Weighting: none
 ## 
@@ -620,15 +620,15 @@
 
 
## mkin version used for fitting:    0.9.47.5 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Fri Sep 14 17:43:12 2018 
-## Date of summary: Fri Sep 14 17:43:12 2018 
+## Date of fit:     Fri Sep 14 18:22:28 2018 
+## Date of summary: Fri Sep 14 18:22:28 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.15 s
+## Fitted with method Port using 66 model solutions performed in 0.16 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 0d91a50c..12c192f0 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -125,9 +125,9 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.174    1.000     2.172        0
-## 1 deSolve, not compiled            3  16.745    7.702    16.737        0
-## 2      Eigenvalue based            3   2.652    1.220     2.650        0
+## 3     deSolve, compiled            3   2.115    1.000     2.114        0
+## 1 deSolve, not compiled            3  16.235    7.676    16.228        0
+## 2      Eigenvalue based            3   2.589    1.224     2.587        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -156,8 +156,8 @@
 }

 
## Successfully compiled differential equation model from auto-generated C code.

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.012    1.000     4.010        0
-## 1 deSolve, not compiled            3  35.620    8.878    35.604        0
+## 2     deSolve, compiled            3   3.887    1.000     3.885        0
+## 1 deSolve, not compiled            3  35.492    9.131    35.474        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 8cf55860..91226e69 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -278,7 +278,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.174       0.000       0.173 
+#>       0.166       0.000       0.166 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -467,8 +467,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555bd78ed0>
-#> <environment: 0x55555bc7eda8>
+#> <bytecode: 0x55555bd812a0>
+#> <environment: 0x55555bc871e8>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -490,8 +490,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555ca99e50>
-#> <environment: 0x55555bc7eda8>
+#> <bytecode: 0x55555caa1d18>
+#> <environment: 0x55555bc871e8>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -558,7 +558,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Sep 14 17:41:26 2018"
+#> [1] "Fri Sep 14 18:20:46 2018"
 #> 
 #> $version
 #> [1] "0.9.47.5"
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 902f1224..d91431f3 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -158,8 +158,8 @@
                          anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
     summary(fit.1, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:41:38 2018 
-#> Date of summary: Fri Sep 14 17:41:38 2018 
+#> Date of fit:     Fri Sep 14 18:20:57 2018 
+#> Date of summary: Fri Sep 14 18:20:57 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -169,7 +169,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 574 model solutions performed in 3.566 s
+#> Fitted with method Port using 574 model solutions performed in 3.418 s
 #> 
 #> Weighting: none
 #> 
@@ -247,8 +247,8 @@
                    fixed_parms = "k_phenol_sink", quiet = TRUE)
     summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:41:39 2018 
-#> Date of summary: Fri Sep 14 17:41:40 2018 
+#> Date of fit:     Fri Sep 14 18:20:59 2018 
+#> Date of summary: Fri Sep 14 18:20:59 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -258,7 +258,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.577 s
+#> Fitted with method Port using 246 model solutions performed in 1.458 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 2d5ed97f..261d48fb 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -434,15 +434,15 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:41:42 2018 
-#> Date of summary: Fri Sep 14 17:41:42 2018 
+#> Date of fit:     Fri Sep 14 18:21:02 2018 
+#> Date of summary: Fri Sep 14 18:21:02 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 64 model solutions performed in 0.153 s
+#> Fitted with method Port using 64 model solutions performed in 0.143 s
 #> 
 #> Weighting: none
 #> 
@@ -511,7 +511,7 @@
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#>        User      System verstrichen 
-#>       0.946       0.000       0.947 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.918       0.000       0.919 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -586,7 +586,7 @@
 #> Model cost at call  146 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>        User      System verstrichen 
-#>       0.762       0.000       0.763 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.757       0.000       0.757 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -624,8 +624,8 @@
                       m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(f.noweight)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:41:54 2018 
-#> Date of summary: Fri Sep 14 17:41:54 2018 
+#> Date of fit:     Fri Sep 14 18:21:13 2018 
+#> Date of summary: Fri Sep 14 18:21:13 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -633,7 +633,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.874 s
+#> Fitted with method Port using 186 model solutions performed in 0.775 s
 #> 
 #> Weighting: none
 #> 
@@ -741,8 +741,8 @@
 #>   120       m1    33.31  28.78984  4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
 summary(f.irls)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:41:56 2018 
-#> Date of summary: Fri Sep 14 17:41:56 2018 
+#> Date of fit:     Fri Sep 14 18:21:15 2018 
+#> Date of summary: Fri Sep 14 18:21:15 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -750,7 +750,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 551 model solutions performed in 2.493 s
+#> Fitted with method Port using 551 model solutions performed in 2.282 s
 #> 
 #> Weighting: none
 #> 
@@ -863,8 +863,8 @@
 #>   120       m1    33.31  28.80898  4.501e+00 2.722
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
 summary(f.w.mean)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:41:57 2018 
-#> Date of summary: Fri Sep 14 17:41:57 2018 
+#> Date of fit:     Fri Sep 14 18:21:16 2018 
+#> Date of summary: Fri Sep 14 18:21:16 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -872,7 +872,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.692 s
+#> Fitted with method Port using 155 model solutions performed in 0.653 s
 #> 
 #> Weighting: mean
 #> 
@@ -981,8 +981,8 @@
                      quiet = TRUE)
 summary(f.w.value)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:41:58 2018 
-#> Date of summary: Fri Sep 14 17:41:58 2018 
+#> Date of fit:     Fri Sep 14 18:21:17 2018 
+#> Date of summary: Fri Sep 14 18:21:17 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -990,7 +990,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.749 s
+#> Fitted with method Port using 174 model solutions performed in 0.721 s
 #> 
 #> Weighting: manual
 #> 
@@ -1101,8 +1101,8 @@
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
 summary(f.w.man)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:41:59 2018 
-#> Date of summary: Fri Sep 14 17:41:59 2018 
+#> Date of fit:     Fri Sep 14 18:21:18 2018 
+#> Date of summary: Fri Sep 14 18:21:18 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1110,7 +1110,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 270 model solutions performed in 1.155 s
+#> Fitted with method Port using 270 model solutions performed in 1.215 s
 #> 
 #> Weighting: manual
 #> 
@@ -1219,8 +1219,8 @@
                        reweight.method = "obs")
 summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:42:03 2018 
-#> Date of summary: Fri Sep 14 17:42:03 2018 
+#> Date of fit:     Fri Sep 14 18:21:22 2018 
+#> Date of summary: Fri Sep 14 18:21:22 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1228,7 +1228,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 692 model solutions performed in 3.154 s
+#> Fitted with method Port using 692 model solutions performed in 3.114 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index fa2880ec..9048c1b1 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -229,7 +229,7 @@ For the definition of model types and their parameters, the equations given
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file2cf4aedfaf6.c 2> file2cf4aedfaf6.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file49ec17c0788e.c 2> file49ec17c0788e.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index fc90757d..6c30d7a8 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -331,7 +331,7 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>        0.04        0.00        0.04 

+#>       0.035       0.000       0.035 

   
   
#>        User      System verstrichen 
-#>       0.044       0.034       7.567 
time_1
#>        User      System verstrichen 
-#>      22.374       0.000      22.397 

+#>       0.059       0.027       6.918 
time_1
#>        User      System verstrichen 
+#>      21.127       0.000      21.141 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340480   0.2659520   0.7505686   0.2494314 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 01c0d330..cb6beda2 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -206,15 +206,15 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:42:54 2018 
-#> Date of summary: Fri Sep 14 17:42:54 2018 
+#> Date of fit:     Fri Sep 14 18:22:10 2018 
+#> Date of summary: Fri Sep 14 18:22:10 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.078 s
+#> Fitted with method Port using 35 model solutions performed in 0.076 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 55640a7f..db92667c 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -200,8 +200,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:43:01 2018 
-#> Date of summary: Fri Sep 14 17:43:01 2018 
+#> Date of fit:     Fri Sep 14 18:22:17 2018 
+#> Date of summary: Fri Sep 14 18:22:17 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.739 s
+#> Fitted with method Port using 153 model solutions performed in 0.701 s
 #> 
 #> Weighting: none
 #> 
@@ -276,8 +276,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
 summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:43:03 2018 
-#> Date of summary: Fri Sep 14 17:43:03 2018 
+#> Date of fit:     Fri Sep 14 18:22:19 2018 
+#> Date of summary: Fri Sep 14 18:22:19 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -285,7 +285,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 350 model solutions performed in 1.457 s
+#> Fitted with method Port using 350 model solutions performed in 1.431 s
 #> 
 #> Weighting: none
 #> 
@@ -364,8 +364,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:43:04 2018 
-#> Date of summary: Fri Sep 14 17:43:04 2018 
+#> Date of fit:     Fri Sep 14 18:22:20 2018 
+#> Date of summary: Fri Sep 14 18:22:20 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -373,7 +373,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.785 s
+#> Fitted with method Port using 186 model solutions performed in 0.778 s
 #> 
 #> Weighting: none
 #> 
@@ -448,8 +448,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 17:43:05 2018 
-#> Date of summary: Fri Sep 14 17:43:05 2018 
+#> Date of fit:     Fri Sep 14 18:22:20 2018 
+#> Date of summary: Fri Sep 14 18:22:20 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -457,7 +457,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 104 model solutions performed in 0.429 s
+#> Fitted with method Port using 104 model solutions performed in 0.417 s
 #> 
 #> Weighting: none
 #> 
diff --git a/test.log b/test.log
index 884b67c1..aab7d12b 100644
--- a/test.log
+++ b/test.log
@@ -2,22 +2,20 @@ Loading mkin
 Loading required package: testthat
 Testing mkin
 ✔ | OK F W S | Context
-
⠏ |  0       | Calculation of FOCUS chi2 error levels
⠋ |  1       | Calculation of FOCUS chi2 error levels
⠙ |  2       | Calculation of FOCUS chi2 error levels
✔ |  2       | Calculation of FOCUS chi2 error levels [2.3 s]
-
⠏ |  0       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ |  5       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [2.3 s]
-
⠏ |  0       | The t-test for significant difference from zero
⠋ |  1       | The t-test for significant difference from zero
⠙ |  2       | The t-test for significant difference from zero
✔ |  2       | The t-test for significant difference from zero [4.6 s]
-
⠏ |  0       | Iteratively reweighted least squares (IRLS) fitting
⠋ |  1       | Iteratively reweighted least squares (IRLS) fitting
⠙ |  2       | Iteratively reweighted least squares (IRLS) fitting
⠹ |  3       | Iteratively reweighted least squares (IRLS) fitting
✔ |  3       | Iteratively reweighted least squares (IRLS) fitting [37.5 s]
+
⠏ |  0       | Calculation of FOCUS chi2 error levels
⠋ |  1       | Calculation of FOCUS chi2 error levels
⠙ |  2       | Calculation of FOCUS chi2 error levels
✔ |  2       | Calculation of FOCUS chi2 error levels [2.2 s]
+
⠏ |  0       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ |  5       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ |  6       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [2.2 s]
+
⠏ |  0       | The t-test for significant difference from zero
⠋ |  1       | The t-test for significant difference from zero
⠙ |  2       | The t-test for significant difference from zero
✔ |  2       | The t-test for significant difference from zero [4.3 s]
+
⠏ |  0       | Iteratively reweighted least squares (IRLS) fitting
⠋ |  1       | Iteratively reweighted least squares (IRLS) fitting
⠙ |  2       | Iteratively reweighted least squares (IRLS) fitting
⠹ |  3       | Iteratively reweighted least squares (IRLS) fitting
✔ |  3       | Iteratively reweighted least squares (IRLS) fitting [36.3 s]
 
⠏ |  0       | Model predictions with mkinpredict
⠋ |  1       | Model predictions with mkinpredict
⠙ |  2       | Model predictions with mkinpredict
⠹ |  3       | Model predictions with mkinpredict
✔ |  3       | Model predictions with mkinpredict [0.3 s]
-
⠏ |  0       | Fitting of parent only models
⠋ |  1       | Fitting of parent only models
⠙ |  2       | Fitting of parent only models
⠹ |  3       | Fitting of parent only models
⠸ |  4       | Fitting of parent only models
⠼ |  5       | Fitting of parent only models
⠴ |  6       | Fitting of parent only models
⠦ |  7       | Fitting of parent only models
⠧ |  8       | Fitting of parent only models
⠇ |  9       | Fitting of parent only models
⠏ | 10       | Fitting of parent only models
⠋ | 11       | Fitting of parent only models
⠙ | 12       | Fitting of parent only models
⠹ | 13       | Fitting of parent only models
⠸ | 14       | Fitting of parent only models
⠼ | 15       | Fitting of parent only models
⠴ | 16       | Fitting of parent only models
⠦ | 17       | Fitting of parent only models
⠧ | 18       | Fitting of parent only models
⠇ | 19       | Fitting of parent only models
⠏ | 20       | Fitting of parent only models
⠋ | 21       | Fitting of parent only models
✔ | 21       | Fitting of parent only models [22.2 s]
+
⠏ |  0       | Fitting of parent only models
⠋ |  1       | Fitting of parent only models
⠙ |  2       | Fitting of parent only models
⠹ |  3       | Fitting of parent only models
⠸ |  4       | Fitting of parent only models
⠼ |  5       | Fitting of parent only models
⠴ |  6       | Fitting of parent only models
⠦ |  7       | Fitting of parent only models
⠧ |  8       | Fitting of parent only models
⠇ |  9       | Fitting of parent only models
⠏ | 10       | Fitting of parent only models
⠋ | 11       | Fitting of parent only models
⠙ | 12       | Fitting of parent only models
⠹ | 13       | Fitting of parent only models
⠸ | 14       | Fitting of parent only models
⠼ | 15       | Fitting of parent only models
⠴ | 16       | Fitting of parent only models
⠦ | 17       | Fitting of parent only models
⠧ | 18       | Fitting of parent only models
⠇ | 19       | Fitting of parent only models
⠏ | 20       | Fitting of parent only models
⠋ | 21       | Fitting of parent only models
✔ | 21       | Fitting of parent only models [21.8 s]
 
⠏ |  0       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠋ |  1       | Complex test case from Schaefer et al. (2007) Piacenza paper
⠙ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ |  2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.4 s]
-
⠏ |  0       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.9 s]
-
⠏ |  0       | Calculation of maximum time weighted average concentrations (TWAs)
⠋ |  1       | Calculation of maximum time weighted average concentrations (TWAs)
⠙ |  2       | Calculation of maximum time weighted average concentrations (TWAs)
⠹ |  3       | Calculation of maximum time weighted average concentrations (TWAs)
✔ |  3       | Calculation of maximum time weighted average concentrations (TWAs) [4.9 s]
+
⠏ |  0       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ |  1       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠙ |  2       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ |  3       | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠸ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ |  4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.7 s]
+
⠏ |  0       | Calculation of maximum time weighted average concentrations (TWAs)
⠋ |  1       | Calculation of maximum time weighted average concentrations (TWAs)
⠙ |  2       | Calculation of maximum time weighted average concentrations (TWAs)
⠹ |  3       | Calculation of maximum time weighted average concentrations (TWAs)
✔ |  3       | Calculation of maximum time weighted average concentrations (TWAs) [4.6 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 86.5 s
+Duration: 84.0 s
 
 OK:       46
 Failed:   0
 Warnings: 0
 Skipped:  0
-
-Nice code.
diff --git a/tests/testthat/test_FOCUS_chi2_error_level.R b/tests/testthat/test_FOCUS_chi2_error_level.R
index 2db2f4e6..1f1e2a06 100644
--- a/tests/testthat/test_FOCUS_chi2_error_level.R
+++ b/tests/testthat/test_FOCUS_chi2_error_level.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2014-15 Johannes Ranke
+# Copyright (C) 2014,2015,2018 Johannes Ranke
 # Contact: jranke@uni-bremen.de
 
 # This file is part of the R package mkin
@@ -39,6 +39,7 @@ test_that("Chi2 error levels for FOCUS D are as in mkin 0.9-33", {
 })
 
 test_that("Chi2 error levels for FOCUS E are as in mkin 0.9-33", {
+  skip_on_cran()
 
   fit <- mkinfit(SFO_SFO.ff, FOCUS_2006_E, quiet = TRUE)
 
diff --git a/tests/testthat/test_parent_only.R b/tests/testthat/test_parent_only.R
index 9a3844cf..ee0cc144 100644
--- a/tests/testthat/test_parent_only.R
+++ b/tests/testthat/test_parent_only.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2015 Johannes Ranke
+# Copyright (C) 2015,2018 Johannes Ranke
 # Contact: jranke@uni-bremen.de
 
 # This file is part of the R package mkin
@@ -89,6 +89,7 @@ test_that("Fits for FOCUS A deviate less than 0.1% from median of values from FO
 })
 
 test_that("Fits for FOCUS B deviate less than 0.1% from median of values from FOCUS report", {
+  skip_on_cran()
   fit.B.SFO <- list(mkinfit("SFO", FOCUS_2006_B, quiet = TRUE))
 
   median.B.SFO <- as.numeric(lapply(subset(FOCUS_2006_SFO_ref_A_to_F,
@@ -202,6 +203,7 @@ test_that("DFOP fits give approximately (0.001%) equal results with different so
 })
 
 test_that("SFORB fits give approximately (0.002%) equal results with different solution methods", {
+  skip_on_cran()
   fit.B.SFORB.default <- mkinfit(SFORB, FOCUS_2006_B, quiet=TRUE)$bparms.optim
 
   fits.B.SFORB <- list()
diff --git a/tests/testthat/test_twa.R b/tests/testthat/test_twa.R
index 27a76ee8..d5c0b98b 100644
--- a/tests/testthat/test_twa.R
+++ b/tests/testthat/test_twa.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2016,2017 Johannes Ranke
+# Copyright (C) 2016,2017,2018 Johannes Ranke
 # Contact: jranke@uni-bremen.de
 
 # This file is part of the R package mkin
@@ -22,10 +22,6 @@ twa_models <- c("SFO", "FOMC", "DFOP")
 fits <- mmkin(twa_models, list(FOCUS_D = FOCUS_2006_D), 
               quiet = TRUE, cores = 1)
 
-SFO_SFO <- mkinmod(parent = list(type = "SFO", to = "m1"),
-                   m1 = list(type = "SFO"), quiet = TRUE)
-fit.m1 <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-
 test_that("Time weighted average concentrations are correct", {
   outtimes_7 <- seq(0, 7, length.out = 10000)
   for (model in twa_models) {
-- 
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