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authorJohannes Ranke <jranke@uni-bremen.de>2015-07-20 23:30:42 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-07-20 23:30:42 +0200
commit9e38e562349da58edfad8e1745315735d6b60307 (patch)
tree3ace2b0c853a73b494fa6b3a0297ed0db34cf40f
parent84700ea7677160d96e13f74ddb74fdababec322a (diff)
Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge
-rw-r--r--build.log7
-rw-r--r--check.log12
-rw-r--r--test.R10
-rw-r--r--vignettes/FOCUS_D.html10
-rw-r--r--vignettes/FOCUS_L.html64
-rw-r--r--vignettes/FOCUS_Z.pdfbin226064 -> 225027 bytes
-rw-r--r--vignettes/mkin.pdfbin160258 -> 160258 bytes
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
Binary files differ
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index d5183527..710a9534 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

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