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authorJohannes Ranke <jranke@uni-bremen.de>2019-05-02 17:07:55 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2019-05-02 17:51:07 +0200
commita4ca3451f1b5c37d10c6a41cb18a99b1631e8aa2 (patch)
treeec29538cd4517617a1dfa1bd164d927da22e918c /vignettes/web_only
parentce9399d08a05fffe8b003386c445f5ceab25dde5 (diff)
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
Diffstat (limited to 'vignettes/web_only')
-rw-r--r--vignettes/web_only/benchmarks.Rmd4
-rw-r--r--vignettes/web_only/benchmarks.html60
-rw-r--r--vignettes/web_only/mkin_benchmarks.rdabin0 -> 797 bytes
3 files changed, 35 insertions, 29 deletions
diff --git a/vignettes/web_only/benchmarks.Rmd b/vignettes/web_only/benchmarks.Rmd
index 83381717..4849635f 100644
--- a/vignettes/web_only/benchmarks.Rmd
+++ b/vignettes/web_only/benchmarks.Rmd
@@ -29,7 +29,7 @@ cpu_model <- benchmarkme::get_cpu()$model_name
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") {
@@ -86,5 +86,5 @@ mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t
mkin_benchmarks
-save(mkin_benchmarks, file = "~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda")
+save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")
```
diff --git a/vignettes/web_only/benchmarks.html b/vignettes/web_only/benchmarks.html
index b35a9695..054b4afc 100644
--- a/vignettes/web_only/benchmarks.html
+++ b/vignettes/web_only/benchmarks.html
@@ -11,7 +11,7 @@
<meta name="author" content="Johannes Ranke" />
-<meta name="date" content="2019-04-09" />
+<meta name="date" content="2019-05-02" />
<title>Benchmark timings for mkin on various systems</title>
@@ -1280,7 +1280,7 @@ window.initializeCodeFolding = function(show) {
var currentIndex = 1;
// select all R code blocks
- var rCodeBlocks = $('pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan');
+ var rCodeBlocks = $('pre.r, pre.python, pre.bash, pre.sql, pre.cpp, pre.stan, pre.julia');
rCodeBlocks.each(function() {
// create a collapsable div to wrap the code in
@@ -1387,9 +1387,7 @@ h6 {
</style>
-</head>
-<body>
<style type="text/css">
.main-container {
@@ -1421,8 +1419,6 @@ summary {
-<div class="container-fluid main-container">
-
<!-- tabsets -->
<style type="text/css">
@@ -1588,6 +1584,16 @@ div.tocify {
</style>
+
+
+</head>
+
+<body>
+
+
+<div class="container-fluid main-container">
+
+
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="col-xs-12 col-sm-4 col-md-3">
@@ -1613,8 +1619,8 @@ div.tocify {
<h1 class="title toc-ignore">Benchmark timings for mkin on various systems</h1>
-<h4 class="author"><em>Johannes Ranke</em></h4>
-<h4 class="date"><em>2019-04-09</em></h4>
+<h4 class="author">Johannes Ranke</h4>
+<h4 class="date">2019-05-02</h4>
</div>
@@ -1626,7 +1632,7 @@ div.tocify {
operating_system &lt;- Sys.info()[[&quot;sysname&quot;]]
mkin_version &lt;- as.character(packageVersion(&quot;mkin&quot;))
system_string &lt;- paste0(operating_system, &quot;, &quot;, cpu_model, &quot;, mkin version &quot;, mkin_version)
-load(&quot;~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda&quot;)
+load(&quot;~/git/mkin/vignettes/web_only/mkin_benchmarks.rda&quot;)
mkin_benchmarks[system_string, c(&quot;CPU&quot;, &quot;OS&quot;, &quot;mkin&quot;)] &lt;- c(cpu_model, operating_system, mkin_version)
if (mkin_version &gt; &quot;0.9.48.1&quot;) {
@@ -1636,9 +1642,10 @@ if (mkin_version &gt; &quot;0.9.48.1&quot;) {
}</code></pre>
<pre class="r"><code># Parent only
t1 &lt;- system.time(mmkin_bench(c(&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;, &quot;HS&quot;), list(FOCUS_2006_C, FOCUS_2006_D)))[[&quot;elapsed&quot;]]
-t2 &lt;- system.time(mmkin_bench(c(&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;, &quot;HS&quot;), list(FOCUS_2006_C, FOCUS_2006_D), error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]
-
-# One metabolite
+t2 &lt;- system.time(mmkin_bench(c(&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;, &quot;HS&quot;), list(FOCUS_2006_C, FOCUS_2006_D), error_model = &quot;tc&quot;))[[&quot;elapsed&quot;]]</code></pre>
+<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
+## false convergence (8)</code></pre>
+<pre class="r"><code># One metabolite
SFO_SFO &lt;- mkinmod(
parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;),
m1 = mkinsub(&quot;SFO&quot;))</code></pre>
@@ -1653,9 +1660,8 @@ SFO_SFO &lt;- mkinmod(
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<pre class="r"><code>t3 &lt;- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[[&quot;elapsed&quot;]]</code></pre>
<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data
-
-## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Observations with value of zero were removed from the data</code></pre>
+<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
## Observations with value of zero were removed from the data
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
@@ -1719,68 +1725,68 @@ mkin_benchmarks</code></pre>
## 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 6.712
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.023
## 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 23.082
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.409
## 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 3.595
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.283
## 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 11.975
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 14.531
## 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 4.881
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.744
## 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 1.981
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.518
## 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 3.32
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.211
## 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 3.309
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.557
## 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 6.075
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.739
## 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 2.518
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.413
## 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 4.289</code></pre>
-<pre class="r"><code>save(mkin_benchmarks, file = &quot;~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda&quot;)</code></pre>
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.588</code></pre>
+<pre class="r"><code>save(mkin_benchmarks, file = &quot;~/git/mkin/vignettes/mkin_benchmarks.rda&quot;)</code></pre>
</div>
diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda
new file mode 100644
index 00000000..388a7886
--- /dev/null
+++ b/vignettes/web_only/mkin_benchmarks.rda
Binary files differ

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