Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge

7 files changed, 61 insertions, 42 deletions

diff --git a/build.log b/build.log
index c3b0aa75..9968573e 100644
--- a/build.log
+++ b/build.log
@@ -2,4 +2,9 @@
 * preparing ‘mkin’:
 * checking DESCRIPTION meta-information ... OK
 * installing the package to build vignettes
-* creating vignettes ...
\ No newline at end of file
+* creating vignettes ... OK
+* checking for LF line-endings in source and make files
+* checking for empty or unneeded directories
+* looking to see if a ‘data/datalist’ file should be added
+* building ‘mkin_0.9-40.tar.gz’
+
diff --git a/check.log b/check.log
index 6b81cb80..370aca69 100644
--- a/check.log
+++ b/check.log
@@ -1,6 +1,6 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 3.2.1 (2015-06-18)
-* using platform: x86_64-pc-linux-gnu (64-bit)
+* using R Under development (unstable) (2015-07-19 r68700)
+* using platform: x86_64-unknown-linux-gnu (64-bit)
 * using session charset: UTF-8
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
@@ -33,7 +33,6 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking whether the package can be unloaded cleanly ... OK
 * checking whether the namespace can be loaded with stated dependencies ... OK
 * 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 S3 generic/method consistency ... OK
@@ -66,4 +65,9 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
    ‘FOCUS_Z.Rnw’ using ‘UTF-8’ ... OK
    ‘mkin.Rnw’ using ‘UTF-8’ ... OK
  OK
-* checking re-building of vignette outputs ...
\ No newline at end of file
+* checking re-building of vignette outputs ... OK
+* checking PDF version of manual ... OK
+* DONE
+
+Status: OK
+
diff --git a/test.R b/test.R
new file mode 100644
index 00000000..5733960f
--- /dev/null
+++ b/test.R
@@ -0,0 +1,10 @@
+devtools::document("~/git/staticdocs")
+devtools::install("~/git/staticdocs")
+library(staticdocs)
+
+debug(staticdocs:::to_html.list)
+debug(staticdocs:::to_html.Rd_doc)
+debug(staticdocs:::to_html.examples)
+debug(staticdocs:::replay_html)
+debug(staticdocs:::replay_html.recordedplot)
+build_site("~/git/mkin", site_path = "~/svn/kinfit.r-forge/www/mkin_static")
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html
index f5b8f22a..800186f2 100644
--- a/vignettes/FOCUS_D.html
+++ b/vignettes/FOCUS_D.html
@@ -10,7 +10,7 @@
 
 <meta name="author" content="Johannes Ranke" />
 
-<meta name="date" content="2015-07-18" />
+<meta name="date" content="2015-07-20" />
 
 <title>Example evaluation of FOCUS Example Dataset D</title>
 
@@ -64,7 +64,7 @@ img {
 <div id="header">
 <h1 class="title">Example evaluation of FOCUS Example Dataset D</h1>
 <h4 class="author"><em>Johannes Ranke</em></h4>
-<h4 class="date"><em>2015-07-18</em></h4>
+<h4 class="date"><em>2015-07-20</em></h4>
 </div>
 
 
@@ -137,8 +137,8 @@ print(FOCUS_2006_D)</code></pre>
 <pre class="r"><code>summary(fit)</code></pre>
 <pre><code>## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Sat Jul 18 16:50:58 2015 
-## Date of summary: Sat Jul 18 16:50:59 2015 
+## Date of fit:     Mon Jul 20 14:51:06 2015 
+## Date of summary: Mon Jul 20 14:51:06 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -146,7 +146,7 @@ print(FOCUS_2006_D)</code></pre>
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.604 s
+## Fitted with method Port using 153 model solutions performed in 0.66 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 963dff0c..c84d6c83 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -10,7 +10,7 @@
 
 <meta name="author" content="Johannes Ranke" />
 
-<meta name="date" content="2015-07-18" />
+<meta name="date" content="2015-07-20" />
 
 <title>Example evaluation of FOCUS Laboratory Data L1 to L3</title>
 
@@ -65,7 +65,7 @@ img {
 <div id="header">
 <h1 class="title">Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
 <h4 class="author"><em>Johannes Ranke</em></h4>
-<h4 class="date"><em>2015-07-18</em></h4>
+<h4 class="date"><em>2015-07-20</em></h4>
 </div>
 
 <div id="TOC">
@@ -93,15 +93,15 @@ FOCUS_2006_L1_mkin &lt;- mkin_wide_to_long(FOCUS_2006_L1)</code></pre>
 summary(m.L1.SFO)</code></pre>
 <pre><code>## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Sat Jul 18 16:50:59 2015 
-## Date of summary: Sat Jul 18 16:50:59 2015 
+## Date of fit:     Mon Jul 20 14:51:06 2015 
+## Date of summary: Mon Jul 20 14:51:07 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.083 s
+## Fitted with method Port using 37 model solutions performed in 0.087 s
 ## 
 ## Weighting: none
 ## 
@@ -183,8 +183,8 @@ summary(m.L1.SFO)</code></pre>
 <pre class="r"><code>summary(m.L1.FOMC, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Sat Jul 18 16:51:00 2015 
-## Date of summary: Sat Jul 18 16:51:00 2015 
+## Date of fit:     Mon Jul 20 14:51:07 2015 
+## Date of summary: Mon Jul 20 14:51:07 2015 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -196,7 +196,7 @@ summary(m.L1.SFO)</code></pre>
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 0.414 s
+## Fitted with method Port using 188 model solutions performed in 0.43 s
 ## 
 ## Weighting: none
 ## 
@@ -263,15 +263,15 @@ FOCUS_2006_L2_mkin &lt;- mkin_wide_to_long(FOCUS_2006_L2)</code></pre>
 summary(m.L2.SFO)</code></pre>
 <pre><code>## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Sat Jul 18 16:51:00 2015 
-## Date of summary: Sat Jul 18 16:51:00 2015 
+## Date of fit:     Mon Jul 20 14:51:07 2015 
+## Date of summary: Mon Jul 20 14:51:07 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.089 s
+## Fitted with method Port using 41 model solutions performed in 0.094 s
 ## 
 ## Weighting: none
 ## 
@@ -351,15 +351,15 @@ mkinresplot(m.L2.FOMC)</code></pre>
 <pre class="r"><code>summary(m.L2.FOMC, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Sat Jul 18 16:51:01 2015 
-## Date of summary: Sat Jul 18 16:51:01 2015 
+## Date of fit:     Mon Jul 20 14:51:08 2015 
+## Date of summary: Mon Jul 20 14:51:08 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.177 s
+## Fitted with method Port using 81 model solutions performed in 0.18 s
 ## 
 ## Weighting: none
 ## 
@@ -423,8 +423,8 @@ plot(m.L2.DFOP)</code></pre>
 <pre class="r"><code>summary(m.L2.DFOP, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Sat Jul 18 16:51:03 2015 
-## Date of summary: Sat Jul 18 16:51:03 2015 
+## Date of fit:     Mon Jul 20 14:51:10 2015 
+## Date of summary: Mon Jul 20 14:51:10 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -433,7 +433,7 @@ plot(m.L2.DFOP)</code></pre>
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.791 s
+## Fitted with method Port using 336 model solutions performed in 0.793 s
 ## 
 ## Weighting: none
 ## 
@@ -500,15 +500,15 @@ plot(m.L3.SFO)</code></pre>
 <pre class="r"><code>summary(m.L3.SFO)</code></pre>
 <pre><code>## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Sat Jul 18 16:51:03 2015 
-## Date of summary: Sat Jul 18 16:51:03 2015 
+## Date of fit:     Mon Jul 20 14:51:10 2015 
+## Date of summary: Mon Jul 20 14:51:10 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.093 s
+## Fitted with method Port using 43 model solutions performed in 0.103 s
 ## 
 ## Weighting: none
 ## 
@@ -576,15 +576,15 @@ plot(m.L3.FOMC)</code></pre>
 <pre class="r"><code>summary(m.L3.FOMC, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Sat Jul 18 16:51:03 2015 
-## Date of summary: Sat Jul 18 16:51:03 2015 
+## Date of fit:     Mon Jul 20 14:51:11 2015 
+## Date of summary: Mon Jul 20 14:51:11 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 83 model solutions performed in 0.173 s
+## Fitted with method Port using 83 model solutions performed in 0.187 s
 ## 
 ## Weighting: none
 ## 
@@ -642,8 +642,8 @@ plot(m.L3.DFOP)</code></pre>
 <pre class="r"><code>summary(m.L3.DFOP, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Sat Jul 18 16:51:04 2015 
-## Date of summary: Sat Jul 18 16:51:04 2015 
+## Date of fit:     Mon Jul 20 14:51:11 2015 
+## Date of summary: Mon Jul 20 14:51:11 2015 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -652,7 +652,7 @@ plot(m.L3.DFOP)</code></pre>
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.303 s
+## Fitted with method Port using 137 model solutions performed in 0.322 s
 ## 
 ## Weighting: none
 ## 
@@ -724,15 +724,15 @@ plot(m.L4.SFO)</code></pre>
 <pre class="r"><code>summary(m.L4.SFO, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Sat Jul 18 16:51:04 2015 
-## Date of summary: Sat Jul 18 16:51:04 2015 
+## Date of fit:     Mon Jul 20 14:51:12 2015 
+## Date of summary: Mon Jul 20 14:51:12 2015 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.104 s
+## Fitted with method Port using 46 model solutions performed in 0.101 s
 ## 
 ## Weighting: none
 ## 
@@ -789,15 +789,15 @@ plot(m.L4.FOMC)</code></pre>
 <pre class="r"><code>summary(m.L4.FOMC, data = FALSE)</code></pre>
 <pre><code>## mkin version:    0.9.40 
 ## R version:       3.2.1 
-## Date of fit:     Sat Jul 18 16:51:04 2015 
-## Date of summary: Sat Jul 18 16:51:04 2015 
+## Date of fit:     Mon Jul 20 14:51:12 2015 
+## Date of summary: Mon Jul 20 14:51:12 2015 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.148 s
+## Fitted with method Port using 66 model solutions performed in 0.146 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 3745234a..580c0e4d 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index d5183527..710a9534 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf