Static documentation rebuilt by pkgdown

8 files changed, 57 insertions, 32 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index f631a541..5576e5bf 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: mkin
 Type: Package
 Title: Kinetic Evaluation of Chemical Degradation Data
 Version: 0.9.49.9
-Date: 2020-03-20
+Date: 2020-03-31
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
                     email = "jranke@uni-bremen.de",
                     comment = c(ORCID = "0000-0003-4371-6538")),
@@ -17,7 +17,7 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006,
   note that no warranty is implied for correctness of results or fitness for a
   particular purpose.
 Imports: stats, graphics, methods, deSolve, R6, inline, parallel, numDeriv,
-  lmtest
+  lmtest, pkgbuild
 Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr,
   benchmarkme, tibble, stats4
 License: GPL
diff --git a/NAMESPACE b/NAMESPACE
index 26995055..6f509cd7 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -76,6 +76,7 @@ importFrom(methods,signature)
 importFrom(parallel,detectCores)
 importFrom(parallel,mclapply)
 importFrom(parallel,parLapply)
+importFrom(pkgbuild,has_compiler)
 importFrom(stats,AIC)
 importFrom(stats,BIC)
 importFrom(stats,aggregate)
diff --git a/R/mkinmod.R b/R/mkinmod.R
index cf618525..cfd40504 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -33,6 +33,7 @@
 #' @param verbose If \code{TRUE}, passed to \code{\link{cfunction}} if
 #'   applicable to give detailed information about the C function being built.
 #' @importFrom methods signature
+#' @importFrom pkgbuild has_compiler
 #' @importFrom inline cfunction
 #' @return A list of class \code{mkinmod} for use with \code{\link{mkinfit}},
 #'   containing, among others,
@@ -364,8 +365,9 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
     model$coefmat <- m
   }#}}}
 
-  # Try to create a function compiled from C code if >1 observed variable {{{
-  if (length(obs_vars) > 1) {
+  # Try to create a function compiled from C code there is more than one observed variable {{{
+  # and a compiler is available
+  if (length(obs_vars) > 1 & has_compiler()) {
 
     # Translate the R code for the derivatives to C code
     diffs.C <- paste(diffs, collapse = ";\n")
diff --git a/check.log b/check.log
index b7555c55..35ab651a 100644
--- a/check.log
+++ b/check.log
@@ -1,11 +1,11 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 3.6.2 (2019-12-12)
+* using R version 3.6.3 (2020-02-29)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘mkin’ version ‘0.9.49.8’
+* this is package ‘mkin’ version ‘0.9.49.9’
 * package encoding: UTF-8
 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
@@ -56,7 +56,10 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking data for ASCII and uncompressed saves ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... OK
+* checking examples ... NOTE
+Examples with CPU or elapsed time > 5s
+         user system elapsed
+mkinsub 2.015  4.083   0.703
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
@@ -66,5 +69,9 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: OK
+Status: 1 NOTE
+See
+  ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
+for details.
+
 
diff --git a/test.log b/test.log
index c51d06b8..2db18301 100644
--- a/test.log
+++ b/test.log
@@ -1,38 +1,53 @@
 Loading mkin
 Testing mkin
 ✔ |  OK F W S | Context
-✔ |   5       | Calculation of Akaike weights
 ✔ |   2       | Export dataset for reading into CAKE
-✔ |  10       | Confidence intervals and p-values [9.7 s]
-✔ |  14       | Error model fitting [36.9 s]
-✔ |   4       | Calculation of FOCUS chi2 error levels [2.2 s]
-✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.3 s]
-✔ |   6       | Test fitting the decline of metabolites from their maximum [0.7 s]
-✔ |   1       | Fitting the logistic model [0.9 s]
+✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.8 s]
+✔ |   4       | Calculation of FOCUS chi2 error levels [2.3 s]
+✔ |   4       | Fitting the SFORB model [1.7 s]
+✔ |   5       | Calculation of Akaike weights
+✔ |  10       | Confidence intervals and p-values [10.2 s]
+✔ |  14       | Error model fitting [40.7 s]
+✔ |   6       | Test fitting the decline of metabolites from their maximum [0.8 s]
+✔ |   1       | Fitting the logistic model [1.0 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
-✔ |  12       | Special cases of mkinfit calls [2.4 s]
+✖ |  11 1     | Special cases of mkinfit calls [2.3 s]
+────────────────────────────────────────────────────────────────────────────────
+test_mkinfit_errors.R:64: failure: We get reproducible output if quiet = FALSE
+Results have changed from known value recorded in 'DFOP_FOCUS_C_messages.txt'.
+2/165 mismatches
+x[84]: "Sum of squared residuals at call 57: 4.364077"
+y[84]: "Sum of squared residuals at call 57: 4.364078"
+
+x[105]: "85.00134 -0.7776046 -4.025878 1.248775 "
+y[105]: "85.00135 -0.7776046 -4.025878 1.248775 "
+────────────────────────────────────────────────────────────────────────────────
 ✔ |   9       | mkinmod model generation and printing [0.2 s]
 ✔ |   3       | Model predictions with mkinpredict [0.3 s]
-✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.1 s]
-✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s]
+✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.3 s]
+✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
 ✔ |   3       | Summary
-✔ |  11       | Plotting [0.6 s]
+✖ |  10 1     | Plotting [0.6 s]
+────────────────────────────────────────────────────────────────────────────────
+test_plots_summary_twa.R:118: failure: Plotting mkinfit and mmkin objects is reproducible
+Figures don't match: plot-errmod-with-sfo-lin-a-obs.svg
+
+────────────────────────────────────────────────────────────────────────────────
 ✔ |   4       | AIC calculation
 ✔ |   2       | Residuals extracted from mkinfit models
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
-✔ |   4       | Fitting the SFORB model [1.7 s]
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.6 s]
 ✔ |   1       | Summaries of old mkinfit objects
-✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.2 s]
-✔ |   7     1 | Hypothesis tests [32.3 s]
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.4 s]
+✔ |   7     1 | Hypothesis tests [33.6 s]
 ────────────────────────────────────────────────────────────────────────────────
 test_tests.R:60: skip: We can do a likelihood ratio test using an update specification
 Reason: This errors out if called by testthat while it works in a normal R session
 ────────────────────────────────────────────────────────────────────────────────
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 110.2 s
+Duration: 117.3 s
 
-OK:       138
-Failed:   0
+OK:       136
+Failed:   2
 Warnings: 0
 Skipped:  1
diff --git a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
index 2b4930ba..7ba81d7b 100644
--- a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
+++ b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
@@ -156,7 +156,7 @@
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@@ -186,7 +186,7 @@
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diff --git a/tests/testthat/DFOP_FOCUS_C_messages.txt b/tests/testthat/DFOP_FOCUS_C_messages.txt
index 78438d06..c36f11db 100644
--- a/tests/testthat/DFOP_FOCUS_C_messages.txt
+++ b/tests/testthat/DFOP_FOCUS_C_messages.txt
@@ -81,7 +81,7 @@ Sum of squared residuals at call 55: 4.364078
 85.01633 -0.7763163 -4.027611 1.248897 
 Sum of squared residuals at call 56: 4.364078
 85.01633 -0.7763164 -4.027611 1.248897 
-Sum of squared residuals at call 57: 4.364078
+Sum of squared residuals at call 57: 4.364077
 85.01633 -0.7763163 -4.027611 1.248897 
 85.01633 -0.7763163 -4.027611 1.248897 
 85.00894 -0.7777917 -4.026307 1.24772 
@@ -102,7 +102,7 @@ Sum of squared residuals at call 67: 4.362751
 85.00518 -0.7773082 -4.026004 1.248453 
 85.00134 -0.7776046 -4.025878 1.248775 
 Sum of squared residuals at call 70: 4.362721
-85.00135 -0.7776046 -4.025878 1.248775 
+85.00134 -0.7776046 -4.025878 1.248775 
 Sum of squared residuals at call 71: 4.362721
 85.00134 -0.7776046 -4.025878 1.248775 
 Sum of squared residuals at call 72: 4.362721
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index 358b50e3..a7f8edaf 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
 MeasurementUnits: % AR
 TimeUnits: days
 Comments: Created using mkin::CAKE_export
-Date: 2019-11-13
+Date: 2020-03-31
 Optimiser: IRLS
 
 [Data]