From d337a9665d9261d18734d81edc8fe4b569635e71 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 18 May 2015 16:58:44 +0200
Subject: Make checking faster, testing is done by tests

---
 DESCRIPTION                   |  2 +-
 GNUmakefile                   |  2 +-
 man/mkinfit.Rd                | 19 ++++++-------------
 man/synthetic_data_for_UBA.Rd |  2 ++
 man/transform_odeparms.Rd     |  2 ++
 5 files changed, 12 insertions(+), 15 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 295eaac6..59b653f4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Routines for Fitting Kinetic Models with One or More State
   Variables to Chemical Degradation Data
 Version: 0.9-36
-Date: 2015-05-15
+Date: 2015-05-18
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"),
              person("Katrin", "Lindenberger", role = "ctb"),
diff --git a/GNUmakefile b/GNUmakefile
index 30576682..613c124c 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -60,7 +60,7 @@ check: build
 
 check-no-vignettes: build-no-vignettes
 	mv $(TGZVNR) $(TGZ)
-	"$(RBIN)/R" CMD check --as-cran --no-tests $(TGZ)
+	"$(RBIN)/R" CMD check --as-cran --no-tests --no-build-vignettes --no-vignettes $(TGZ)
 	mv $(TGZ) $(TGZVNR)
 
 clean: 
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index 34e5bbae..2d8d3726 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -243,20 +243,14 @@ SFO_SFO <- mkinmod(
 # Fit the model to the FOCUS example dataset D using defaults
 system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, 
                            solution_type = "eigen"))
-system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, 
-                           solution_type = "deSolve", use_compiled = FALSE))
-system.time(fit.deSolve.compiled <- mkinfit(SFO_SFO, FOCUS_2006_D, 
-                           solution_type = "deSolve", use_compiled = TRUE))
-# The performance benefit of using the compiled version is immense compared
-# with deSolve without compilation, and about a factor of two compared with the
-# eigenvalue based solution
 coef(fit)
-coef(fit.deSolve)
-coef(fit.deSolve.compiled)
 endpoints(fit)
+\dontrun{
+system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, 
+                           solution_type = "deSolve"))
+coef(fit.deSolve)
 endpoints(fit.deSolve)
-# Check compiled model versions against other solutions
-
+}
 
 # Use stepwise fitting, using optimised parameters from parent only fit, FOMC
 \dontrun{
@@ -282,6 +276,7 @@ fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSol
 # Use starting parameters from parent only SFORB fit (not really needed in this case)
 fit.SFORB = mkinfit(SFORB, FOCUS_2006_D)
 fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode)
+}
 
 \dontrun{
 # Weighted fits, including IRLS
@@ -309,7 +304,5 @@ f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man",
                        reweight.method = "obs")
 summary(f.w.man.irls)
 }
-
 }
-\keyword{ models }
 \keyword{ optimize }
diff --git a/man/synthetic_data_for_UBA.Rd b/man/synthetic_data_for_UBA.Rd
index 5d924afd..468e3731 100644
--- a/man/synthetic_data_for_UBA.Rd
+++ b/man/synthetic_data_for_UBA.Rd
@@ -41,6 +41,7 @@
   measurement error in analytical chemistry. Technometrics 37(2), 176-184.
 }
 \examples{
+\dontrun{
 m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
                            M1 = list(type = "SFO", to = "M2"),
                            M2 = list(type = "SFO"), use_of_ff = "max")
@@ -62,4 +63,5 @@ m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),
 
 mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)
 }
+}
 \keyword{datasets}
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index ba93af7d..1385a896 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -76,6 +76,7 @@ names(transformed) <- rownames(fit$start_transformed)
 transform_odeparms(initials, SFO_SFO)
 backtransform_odeparms(transformed, SFO_SFO)
 
+\dontrun{
 # The case of formation fractions
 SFO_SFO.ff <- mkinmod(
   parent = list(type = "SFO", to = "m1", sink = TRUE),
@@ -98,4 +99,5 @@ SFO_SFO.ff.2 <- mkinmod(
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D)
 summary(fit.ff.2, data = FALSE)
 }
+}
 \keyword{ manip }
-- 
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