diff options
| -rw-r--r-- | .Rbuildignore | 1 | ||||
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | GNUmakefile | 15 | ||||
| -rw-r--r-- | README.html | 6 | ||||
| -rw-r--r-- | README.md | 6 | ||||
| -rw-r--r-- | build.log | 9 | ||||
| -rw-r--r-- | check.log | 10 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 239561 -> 239559 bytes |
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 @@ -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> @@ -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 @@ -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’ + @@ -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 Binary files differindex d8bfd68c..fd313555 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf |