From a4ca3451f1b5c37d10c6a41cb18a99b1631e8aa2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 2 May 2019 17:07:55 +0200 Subject: Prepare for CRAN release - Skip long running tests on CRAN as well to avoid timeout on winbuilder - Don't install benchmark results in the package, they are only needed in the git repository - Don't run example in man/add_err.Rd as it takes > 10 s on winbuilder - Rebuild docs --- docs/articles/FOCUS_D.html | 6 ++--- docs/articles/FOCUS_L.html | 42 ++++++++++++++--------------- docs/articles/web_only/benchmarks.html | 26 +++++++++--------- docs/articles/web_only/compiled_models.html | 10 +++---- 4 files changed, 42 insertions(+), 42 deletions(-) (limited to 'docs/articles') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 0ae6a391..4b82dd03 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -168,8 +168,8 @@ 
summary(fit)
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 12:40:29 2019 
-## Date of summary: Thu May  2 12:40:29 2019 
+## Date of fit:     Thu May  2 17:42:41 2019 
+## Date of summary: Thu May  2 17:42:41 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -177,7 +177,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 396 model solutions performed in 1.048 s
+## Fitted using 396 model solutions performed in 1.055 s
 ## 
 ## Error model:
 ## Constant variance 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index b05963ae..05980b97 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -114,15 +114,15 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 12:40:31 2019 
-## Date of summary: Thu May  2 12:40:31 2019 
+## Date of fit:     Thu May  2 17:42:43 2019 
+## Date of summary: Thu May  2 17:42:43 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.289 s
+## Fitted using 133 model solutions performed in 0.286 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -215,8 +215,8 @@
 ## finite result is doubtful
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 12:40:33 2019 
-## Date of summary: Thu May  2 12:40:33 2019 
+## Date of fit:     Thu May  2 17:42:45 2019 
+## Date of summary: Thu May  2 17:42:45 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -228,7 +228,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 599 model solutions performed in 1.277 s
+## Fitted using 599 model solutions performed in 1.253 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -319,15 +319,15 @@
 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 12:40:34 2019 
-## Date of summary: Thu May  2 12:40:34 2019 
+## Date of fit:     Thu May  2 17:42:46 2019 
+## Date of summary: Thu May  2 17:42:46 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 240 model solutions performed in 0.506 s
+## Fitted using 240 model solutions performed in 0.485 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -394,8 +394,8 @@
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 12:40:35 2019 
-## Date of summary: Thu May  2 12:40:35 2019 
+## Date of fit:     Thu May  2 17:42:47 2019 
+## Date of summary: Thu May  2 17:42:47 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -404,7 +404,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 587 model solutions performed in 1.273 s
+## Fitted using 587 model solutions performed in 1.22 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -493,8 +493,8 @@
 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 12:40:37 2019 
-## Date of summary: Thu May  2 12:40:37 2019 
+## Date of fit:     Thu May  2 17:42:49 2019 
+## Date of summary: Thu May  2 17:42:49 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -503,7 +503,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 372 model solutions performed in 0.777 s
+## Fitted using 372 model solutions performed in 0.769 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -598,15 +598,15 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 12:40:38 2019 
-## Date of summary: Thu May  2 12:40:38 2019 
+## Date of fit:     Thu May  2 17:42:50 2019 
+## Date of summary: Thu May  2 17:42:50 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 146 model solutions performed in 0.298 s
+## Fitted using 146 model solutions performed in 0.293 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -662,15 +662,15 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 12:40:38 2019 
-## Date of summary: Thu May  2 12:40:38 2019 
+## Date of fit:     Thu May  2 17:42:50 2019 
+## Date of summary: Thu May  2 17:42:50 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.458 s
+## Fitted using 224 model solutions performed in 0.453 s
 ## 
 ## Error model:
 ## Constant variance 
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 2cafe5c9..0653517a 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -105,7 +105,7 @@
 operating_system <- Sys.info()[["sysname"]]
 mkin_version <- as.character(packageVersion("mkin"))
 system_string <- paste0(operating_system, ", ", cpu_model, ", mkin version ", mkin_version)
-load("~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda")
+load("~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")
 mkin_benchmarks[system_string, c("CPU", "OS", "mkin")] <- c(cpu_model, operating_system, mkin_version)
 
 if (mkin_version > "0.9.48.1") {
@@ -198,68 +198,68 @@
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.853
 ##                                                                         t2
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 19.968
 ##                                                                        t3
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.320
 ##                                                                         t4
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  8.461
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 14.542
 ##                                                                        t5
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.786
 ##                                                                        t6
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.524
 ##                                                                        t7
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.224
 ##                                                                        t8
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.02
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.696
 ##                                                                         t9
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  8.171
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  7.618
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.763
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.776
 ##                                                                       t10
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.432
 ##                                                                        t11
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  5.636
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.574
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.365
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  5.626

-
save(mkin_benchmarks, file = "~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda")

+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  5.599

+
save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")

 
   
 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index ee279f51..3174a067 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -163,9 +163,9 @@
 ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
 ## = TRUE): Observations with value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.178    1.000     3.176        0
-## 1 deSolve, not compiled            3  28.700    9.031    28.685        0
-## 2      Eigenvalue based            3   4.401    1.385     4.398        0
+## 3     deSolve, compiled            3   3.199    1.000     3.198        0
+## 1 deSolve, not compiled            3  28.591    8.937    28.578        0
+## 2      Eigenvalue based            3   4.405    1.377     4.403        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -214,8 +214,8 @@
 ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
 ## value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.549    1.000     4.547        0
-## 1 deSolve, not compiled            3  49.752   10.937    49.729        0
+## 2     deSolve, compiled            3   4.553    1.000     4.551        0
+## 1 deSolve, not compiled            3  49.844   10.948    49.822        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

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