diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-05-02 17:07:55 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-05-02 17:51:07 +0200 |
| commit | a4ca3451f1b5c37d10c6a41cb18a99b1631e8aa2 (patch) | |
| tree | ec29538cd4517617a1dfa1bd164d927da22e918c /vignettes/web_only | |
| parent | ce9399d08a05fffe8b003386c445f5ceab25dde5 (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.Rmd | 4 | ||||
| -rw-r--r-- | vignettes/web_only/benchmarks.html | 60 | ||||
| -rw-r--r-- | vignettes/web_only/mkin_benchmarks.rda | bin | 0 -> 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 <- 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") { @@ -1636,9 +1642,10 @@ if (mkin_version > "0.9.48.1") { }</code></pre> <pre class="r"><code># Parent only t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D)))[["elapsed"]] -t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D), error_model = "tc"))[["elapsed"]] - -# One metabolite +t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D), error_model = "tc"))[["elapsed"]]</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 <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))</code></pre> @@ -1653,9 +1660,8 @@ SFO_SFO <- mkinmod( <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre class="r"><code>t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[["elapsed"]]</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 = "~/git/mkin/inst/benchmark_data/mkin_benchmarks.rda")</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 = "~/git/mkin/vignettes/mkin_benchmarks.rda")</code></pre> </div> diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda Binary files differnew file mode 100644 index 00000000..388a7886 --- /dev/null +++ b/vignettes/web_only/mkin_benchmarks.rda |