Version bump, keep logs of build, check and test

7 files changed, 112 insertions, 4 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
index 700385ef..0cf899b7 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -19,3 +19,6 @@ vignettes/*.synctex.gz
 ^vignettes/*_files$
 ^figure/*
 ^Rplots.pdf$
+test.log
+check.log
+build.log
diff --git a/.gitignore b/.gitignore
index 105ccc7b..8768f592 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,3 +22,4 @@ vignettes/figure/
 vignettes/*_cache/
 vignettes/*_files/
 mkin.Rcheck
+install.log
diff --git a/DESCRIPTION b/DESCRIPTION
index 56f3fe15..7004f0da 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: mkin
 Type: Package
 Title: Routines for Fitting Kinetic Models with One or More State
   Variables to Chemical Degradation Data
-Version: 0.9-38
+Version: 0.9-39
 Date: 2015-06-23
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"),
diff --git a/GNUmakefile b/GNUmakefile
index 9caa84f7..57a6ca15 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -40,7 +40,7 @@ README.md: README.Rmd
 
 $(TGZ): $(pkgfiles) vignettes/*.html vignettes/*.pdf
 	cd ..;\
-		"$(RBIN)/R" CMD build $(PKGSRC)
+		"$(RBIN)/R" CMD build $(PKGSRC) 2>&1 | tee $(PKGNAME)/build.log
 
 $(TGZVNR): $(pkgfiles)
 	cd ..;\
@@ -59,7 +59,7 @@ install-no-vignettes: build-no-vignettes
 	"$(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)
@@ -78,7 +78,7 @@ clean:
 
 test: install-no-vignettes
 	cd tests;\
-		"$(RBIN)/Rscript" testthat.R
+		"$(RBIN)/Rscript" testthat.R 2>&1 | tee ../test.log
 
 vignettes/%.pdf: vignettes/header.tex vignettes/references.bib vignettes/%.Rnw
 	"$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/$*.Rnw', dir = 'vignettes')"
diff --git a/build.log b/build.log
new file mode 100644
index 00000000..2b07aa3f
--- /dev/null
+++ b/build.log
@@ -0,0 +1,10 @@
+* checking for file ‘mkin/DESCRIPTION’ ... OK
+* preparing ‘mkin’:
+* checking DESCRIPTION meta-information ... OK
+* installing the package to build vignettes
+* 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_0.9-39.tar.gz’
+
diff --git a/check.log b/check.log
new file mode 100644
index 00000000..593d6c53
--- /dev/null
+++ b/check.log
@@ -0,0 +1,81 @@
+* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
+* using R version 3.2.1 (2015-06-18)
+* 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 ‘0.9-39’
+* package encoding: UTF-8
+* checking CRAN incoming feasibility ... NOTE
+Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
+
+Days since last update: 0
+* checking package namespace information ... OK
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘mkin’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking use of S3 registration ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd line widths ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking sizes of PDF files under ‘inst/doc’ ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* 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
+   ‘compiled_models.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
+
+Status: 1 NOTE
+See
+  ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
+for details.
+
+
diff --git a/test.log b/test.log
new file mode 100644
index 00000000..a3222cea
--- /dev/null
+++ b/test.log
@@ -0,0 +1,13 @@
+Lade nötiges Paket: methods
+Lade nötiges Paket: minpack.lm
+Lade nötiges Paket: rootSolve
+Lade nötiges Paket: inline
+Calculation of FOCUS chi2 error levels : ..
+Results for FOCUS D established in expertise for UBA (Ranke 2014) : ......
+The t-test for significant difference from zero : ..
+Model predictions with mkinpredict : ...
+Fitting of parent only models : .....................
+Complex test case from Schaefer et al. (2007) Piacenza paper : ..
+Results for synthetic data established in expertise for UBA (Ranke 2014) : ....
+
+Woot!