Refactor mkinfit, infrastructure work

mkinfit objects now include an ll() function to calculate the
log-likelihood. Part of the code was refactored, hopefully making it
easier to read and maintain. IRLS is currently the default algorithm for
the error model "obs", for no particular reason. This may be subject
to change when I get around to investigate.

Slow tests are now in a separate subdirectory and will probably
only be run by my own Makefile target.

Formatting of test logs is improved.

Roundtripping error model parameters works with a precision of 10% when
we use lots of replicates in the synthetic data (see slow tests). This
is not new in this commit, but as I think it is reasonable this
closes #7.

1 files changed, 8 insertions, 23 deletions

diff --git a/check.log b/check.log
index b7cccd35..d2a6122d 100644
--- a/check.log
+++ b/check.log
@@ -24,27 +24,9 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking for future file timestamps ... OK
 * checking ‘build’ directory ... OK
 * checking DESCRIPTION meta-information ... OK
-* checking top-level files ... WARNING
-Conversion of ‘README.md’ failed:
-[WARNING] This document format requires a nonempty <title> element.
-  Please specify either ‘title’ or ‘pagetitle’ in the metadata.
-  Falling back to ‘README’
-Could not fetch https://www.r-pkg.org/badges/version/mkin
-HttpExceptionRequest Request {
-  host                 = "www.r-pkg.org"
-  port                 = 443
-  secure               = True
-  requestHeaders       = []
-  path                 = "/badges/version/mkin"
-  queryString          = ""
-  method               = "GET"
-  proxy                = Nothing
-  rawBody              = False
-  redirectCount        = 10
-  responseTimeout      = ResponseTimeoutDefault
-  requestVersion       = HTTP/1.1
-}
- ConnectionTimeout
+* checking top-level files ... NOTE
+Non-standard file/directory found at top level:
+  ‘tests_slow.log’
 * checking for left-over files ... OK
 * checking index information ... OK
 * checking package subdirectories ... OK
@@ -76,7 +58,10 @@ HttpExceptionRequest Request {
 * checking data for ASCII and uncompressed saves ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... OK
+* checking examples ... NOTE
+Examples with CPU or elapsed time > 5s
+                             user system elapsed
+synthetic_data_for_UBA_2014 9.778  0.239  10.019
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
@@ -85,7 +70,7 @@ HttpExceptionRequest Request {
 * checking PDF version of manual ... OK
 * DONE
 
-Status: 1 WARNING
+Status: 2 NOTEs
 See
   ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
 for details.