Reorganise data generation

- Use inst/data_generation for R code generating data as in some of my other packages
- data/*.RData files were checked using https://github.com/jranke/dotfiles/blob/main/bin/rda_diff
  contents were not changed
- Remove ChangeLog, the history is in the git logs
- Update docs and some links contained therein
- use \doi{} markup
- Move logs to log directory

2 files changed, 87 insertions, 0 deletions

diff --git a/log/build.log b/log/build.log
new file mode 100644
index 0000000..63a1cd1
--- /dev/null
+++ b/log/build.log
@@ -0,0 +1,7 @@
+* checking for file ‘./DESCRIPTION’ ... OK
+* preparing ‘pfm’:
+* checking DESCRIPTION meta-information ... OK
+* checking for LF line-endings in source and make files and shell scripts
+* checking for empty or unneeded directories
+* building ‘pfm_0.6.1.tar.gz’
+
diff --git a/log/check.log b/log/check.log
new file mode 100644
index 0000000..b08d8dc
--- /dev/null
+++ b/log/check.log
@@ -0,0 +1,80 @@
+* using log directory ‘/home/agsad.admin.ch/f80868656/projects/pfm/pfm.Rcheck’
+* using R version 4.3.2 (2023-10-31)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.3 LTS
+* using session charset: UTF-8
+* using options ‘--no-tests --as-cran’
+* checking for file ‘pfm/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘pfm’ version ‘0.6.1’
+* package encoding: UTF-8
+* checking CRAN incoming feasibility ... NOTE
+Maintainer: ‘Johannes Ranke <johannes.ranke@agroscope.admin.ch>’
+
+Size of tarball: 8487405 bytes
+* 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 ‘pfm’ can be installed ... OK
+* checking installed package size ... NOTE
+  installed size is 10.2Mb
+  sub-directories of 1Mb or more:
+    testdata   9.9Mb
+* checking package directory ... OK
+* checking for future file timestamps ... 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 LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... SKIPPED
+* checking PDF version of manual ... OK
+* checking HTML version of manual ... NOTE
+Skipping checking HTML validation: no command 'tidy' found
+* checking for non-standard things in the check directory ... OK
+* checking for detritus in the temp directory ... OK
+* DONE
+
+Status: 3 NOTEs
+See
+  ‘/home/agsad.admin.ch/f80868656/projects/pfm/pfm.Rcheck/00check.log’
+for details.
+
+