Documentation and Makefile improvements

- Fix the remaining links to static docs on r-forge in README
- Build mkin_*.tar.gz packages in current directory
- check and test (test.log unchanged)

8 files changed, 23 insertions, 25 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
index c491eb32..359e5879 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -25,3 +25,4 @@
 ^vignettes/FOCUS_Z.tex$
 ^vignettes/mkin.tex$
 ^_pkgdown.yml$
+^mkin_.*\.tar\.gz
diff --git a/.gitignore b/.gitignore
index 06973a0b..a2664163 100644
--- a/.gitignore
+++ b/.gitignore
@@ -21,3 +21,4 @@ vignettes/*_files/
 mkin.Rcheck
 install.log
 test.R
+mkin*.tar.gz
diff --git a/GNUmakefile b/GNUmakefile
index 1d986246..f41c2d3f 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -1,8 +1,8 @@
 PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGSRC  := $(shell basename $(PWD))
-TGZ     := ../$(PKGSRC)_$(PKGVERS).tar.gz
-TGZVNR  := ../$(PKGSRC)_$(PKGVERS)-vignettes-not-rebuilt.tar.gz
+TGZ     := $(PKGSRC)_$(PKGVERS).tar.gz
+TGZVNR  := $(PKGSRC)_$(PKGVERS)-vignettes-not-rebuilt.tar.gz
 
 # Specify the directory holding R binaries. To use an alternate R build (say a
 # pre-prelease version) use `make RBIN=/path/to/other/R/` or `export RBIN=...`
@@ -32,13 +32,10 @@ pkgfiles = \
 all: build
 
 $(TGZ): $(pkgfiles) vignettes
-	cd ..;\
-		"$(RBIN)/R" CMD build $(PKGSRC) 2>&1 | tee $(PKGNAME)/build.log
+	"$(RBIN)/R" CMD build . 2>&1 | tee build.log
 
 $(TGZVNR): $(pkgfiles) 
-	cd ..;\
-		"$(RBIN)/R" CMD build $(PKGSRC) --no-build-vignettes;\
-		cd $(PKGSRC);\
+	"$(RBIN)/R" CMD build . --no-build-vignettes;\
 	mv $(TGZ) $(TGZVNR)
                 
 build: $(TGZ)
@@ -52,7 +49,7 @@ quickinstall: build-no-vignettes
 	"$(RBIN)/R" CMD INSTALL $(TGZVNR)
 
 check: build
-	"$(RBIN)/R" CMD check --as-cran --no-tests $(TGZ)
+	"$(RBIN)/R" CMD check --as-cran --no-tests $(TGZ) 2>&1 | tee check.log
 
 quickcheck: build-no-vignettes
 	mv $(TGZVNR) $(TGZ)
@@ -117,7 +114,7 @@ drat: build
 	"$(RBIN)/Rscript" -e "drat::insertPackage('$(TGZ)', commit = TRUE)"
 
 submit:
-	@echo "\nHow about make test, make check, make winbuilder"
+	@echo "\nHow about make test, make check, make pd, make winbuilder"
 	@echo "\nIs the DESCRIPTION file up to date?"
 	@echo "\nIs the NEWS.md file up to date?"
 	@echo "\nAre you sure you want to release to CRAN?"
diff --git a/README.html b/README.html
index 72406092..a661505d 100644
--- a/README.html
+++ b/README.html
@@ -143,9 +143,9 @@ $(document).ready(function () {
 <div id="features" class="section level2">
 <h2>Features</h2>
 <ul>
-<li>Highly flexible model specification using <a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.</li>
-<li>As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example <a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html"><code>plot.mmkin</code></a>.</li>
-<li>Model solution (forward modelling) in the function <a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li>
+<li>Highly flexible model specification using <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.</li>
+<li>As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mmkin.html"><code>plot.mmkin</code></a>.</li>
+<li>Model solution (forward modelling) in the function <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li>
 <li>If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see<br />
 <a href="http://kinfit.r-forge.r-project.org/mkin_static/articles/compiled_models.html">vignette <code>compiled_models</code></a>. The autogeneration of C code was inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks to Karline Soetaert for her work on that.</li>
 <li>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice cooperation on this, especially the isometric logration transformation that is now used for the formation fractions.</li>
diff --git a/README.md b/README.md
index e7263606..c042a7d6 100644
--- a/README.md
+++ b/README.md
@@ -42,15 +42,15 @@ and at [R-Forge](http://kinfit.r-forge.r-project.org/mkin_static/index.html).
 ## Features
 
 * Highly flexible model specification using
-  [`mkinmod`](http://kinfit.r-forge.r-project.org/mkin_static/mkinmod.html),
+  [`mkinmod`](http://kinfit.r-forge.r-project.org/mkin_static/reference/mkinmod.html),
   including equilibrium reactions and using the single first-order 
   reversible binding (SFORB) model, which will automatically create
   two latent state variables for the observed variable.
 * As of version 0.9-39, fitting of several models to several datasets, optionally in 
   parallel, is supported, see for example
-  [`plot.mmkin`](http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html).
+  [`plot.mmkin`](http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mmkin.html).
 * Model solution (forward modelling) in the function
-  [`mkinpredict`](http://kinfit.r-forge.r-project.org/mkin_static/mkinpredict.html) 
+  [`mkinpredict`](http://kinfit.r-forge.r-project.org/mkin_static/reference/mkinpredict.html) 
   is performed either using the analytical solution for the case of 
   parent only degradation, an eigenvalue based solution if only simple
   first-order (SFO) or SFORB kinetics are used in the model, or
diff --git a/build.log b/build.log
index c3b0aa75..efdaa3b6 100644
--- a/build.log
+++ b/build.log
@@ -1,5 +1,10 @@
-* checking for file ‘mkin/DESCRIPTION’ ... OK
+* checking for file ‘./DESCRIPTION’ ... OK
 * preparing ‘mkin’:
 * checking DESCRIPTION meta-information ... OK
 * installing the package to build vignettes
-* creating vignettes ...
\ No newline at end of file
+* creating vignettes ... OK
+* checking for LF line-endings in source and make files
+* checking for empty or unneeded directories
+* looking to see if a ‘data/datalist’ file should be added
+* building ‘mkin_0.9.45.tar.gz’
+
diff --git a/check.log b/check.log
index 535edb19..213ee464 100644
--- a/check.log
+++ b/check.log
@@ -1,11 +1,11 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 3.2.1 (2015-06-18)
+* using R version 3.3.2 (2016-10-31)
 * 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 ‘0.9-40’
+* this is package ‘mkin’ version ‘0.9.45’
 * package encoding: UTF-8
 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
@@ -60,12 +60,6 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ...
-   ‘FOCUS_D.Rmd’ using ‘UTF-8’ ... OK
-   ‘FOCUS_L.Rmd’ using ‘UTF-8’ ... OK
-   ‘FOCUS_Z.Rnw’ using ‘UTF-8’ ... OK
-   ‘mkin.Rnw’ using ‘UTF-8’ ... OK
- OK
 * checking re-building of vignette outputs ... OK
 * checking PDF version of manual ... OK
 * DONE
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index d8bfd68c..fd313555 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf