From 7447f43f0ebd79ad4f89c670a819402c9339de3c Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 17 Nov 2016 22:50:44 +0100
Subject: Satisfy CRAN checks, also on R-devel

- Use https for canonical R URLs
- Update CAKE URL to one giving a valid SSL certificate
---
 .Rbuildignore            |  3 ++-
 README.md                |  8 +++---
 inst/staticdocs/index.r  | 63 ------------------------------------------------
 vignettes/references.bib |  6 ++---
 4 files changed, 9 insertions(+), 71 deletions(-)
 delete mode 100644 inst/staticdocs/index.r

diff --git a/.Rbuildignore b/.Rbuildignore
index 5ac1f320..b037b763 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -6,7 +6,7 @@
 ^README.html$
 ^mkin.Rcheck
 ^inst/web/*
-^inst/staticdocs/*
+^docs/*
 ^vignettes/.build.timestamp$
 ^vignettes/*_cache$
 ^vignettes/*_files$
@@ -23,3 +23,4 @@
 ^vignettes/figure
 ^vignettes/FOCUS_Z.tex$
 ^vignettes/mkin.tex$
+^_pkgdown.yml$
diff --git a/README.md b/README.md
index 4372be93..66258aed 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # mkin
 
-[![](http://www.r-pkg.org/badges/version/mkin)](http://cran.r-project.org/package=mkin)
+[![](http://www.r-pkg.org/badges/version/mkin)](https://cran.r-project.org/package=mkin)
 
 The R package **mkin** provides calculation routines for the analysis of
 chemical degradation data, including <b>m</b>ulticompartment <b>kin</b>etics as
@@ -10,7 +10,7 @@ if several compartments are involved.
 ## Installation
 
 You can install the latest released version from 
-[CRAN](http://cran.r-project.org/package=mkin) from within R:
+[CRAN](https://cran.r-project.org/package=mkin) from within R:
 
 ```r
 install.packages("mkin")
@@ -121,7 +121,7 @@ BayerCropScience, which is based on the MatLab runtime environment.
 The companion package 
 [kinfit](http://kinfit.r-forge.r-project.org/kinfit_static/index.html) (now deprecated) was 
 [started in 2008](https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=2) and 
-[first published](http://cran.r-project.org/src/contrib/Archive/kinfit/) on
+[first published](https://cran.r-project.org/src/contrib/Archive/kinfit/) on
 CRAN on 01 May 2010.
 
 The first `mkin` code was 
@@ -140,7 +140,7 @@ Somewhat in parallel, Syngenta has sponsored the development of an `mkin` and
 KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is
 more limited in the model formulation, but puts more weight on usability.
 CAKE is available for download from the [CAKE
-website](http://projects.tessella.com/cake), where you can also
+website](http://showcase.tessella.com/products/cake), where you can also
 find a zip archive of the R scripts derived from `mkin`, published under the GPL
 license.
 
diff --git a/inst/staticdocs/index.r b/inst/staticdocs/index.r
deleted file mode 100644
index 2a976f70..00000000
--- a/inst/staticdocs/index.r
+++ /dev/null
@@ -1,63 +0,0 @@
-sd_section(
-  "Main functions",
-  "Essential functionality",
-  c("mkinmod", "mkinfit", "mmkin")
-)
-sd_section(
-  "Show results",
-  "Functions working on mkinfit objects",
-  c("plot.mkinfit",
-    "summary.mkinfit",
-    "mkinresplot",
-    "mkinparplot",
-    "endpoints", 
-    "mkinerrmin")
-)
-sd_section(
-  "Work with mmkin objects",
-  "Functions working with aggregated results",
-  c("[.mmkin", 
-    "plot.mmkin")
-)
-sd_section(
-  "Datasets and known results",
-  "",
-  c("FOCUS_2006_datasets",
-    "FOCUS_2006_SFO_ref_A_to_F",
-    "FOCUS_2006_FOMC_ref_A_to_F",
-    "FOCUS_2006_HS_ref_A_to_F",
-    "FOCUS_2006_DFOP_ref_A_to_B",
-    "mccall81_245T",
-    "schaefer07_complex_case",
-    "synthetic_data_for_UBA_2014"
-  )
-)
-sd_section(
-  "Helper functions",
-  "",
-  c("mkin_wide_to_long", 
-    "mkin_long_to_wide",
-    "mkinsub",
-    "mkinds", "print.mkinds",
-    "print.mkinmod",
-    "mkinpredict",
-    "transform_odeparms",
-    "ilr",
-    "geometric_mean")
-)
-sd_section(
-  "Analytical solutions",
-  "Parent only model solutions",
-  c("SFO.solution", 
-    "FOMC.solution",
-    "DFOP.solution",
-    "SFORB.solution",
-    "HS.solution",
-    "IORE.solution"
-  )
-)
-sd_section(
-  "Deprecated functions",
-  "Functions that have been superseeded",
-  c("mkinplot")
-)
diff --git a/vignettes/references.bib b/vignettes/references.bib
index da51602f..b465f828 100644
--- a/vignettes/references.bib
+++ b/vignettes/references.bib
@@ -47,7 +47,7 @@
   address = {Vienna, Austria},
   year = {2016},
   note = {{ISBN} 3-900051-07-0},
-  url = {http://www.R-project.org}
+  url = {https://www.R-project.org}
 }
 
 @MANUAL{pkg:kinfit,
@@ -55,14 +55,14 @@
 	degradation data},
   author = {J. Ranke},
   year = {2015},
-  url = {http://CRAN.R-project.org/package=kinfit}
+  url = {https://CRAN.R-project.org/package=kinfit}
 }
 
 @MANUAL{pkg:mkin,
   title = {`mkin`: {K}inetic evaluation of chemical degradation data},
   author = {J. Ranke},
   year = {2016},
-  url = {http://CRAN.R-project.org/package=mkin}
+  url = {https://CRAN.R-project.org/package=mkin}
 }
 
 @Inproceedings{   schaefer2007,
-- 
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