Re-save data files (now smaller); now Depends: R (>=2.10)
Change some qtl:::[func] to qtl::[func]
refineM.R and refineM2.R had some lines with "stats:::C <- Cdqrls"

  - Should be "stats:::C_Cdqrls"; underscore turned into arrow
use lm.fit rather than .Call(stats:::C_Cdqrls)
Turn a bunch of qtl:::[func] calls into qtl::[func]

 - those functions now exported from qtl; funqtl depends on qtl >= 1.31-5
plotlod: use full argument names in a couple of function calls
addintM and stepwiseqtlM: removed references to covar which was never used
Fix a bunch of problems in the help files
Fix some problems in R code
Fix problem in scanoneF if there's just one phenotype
Bug in scanoneM and scanoneM2: only looping over a portion of the pseudomarkers
example in getY.Rd: example had some stuff that seemed to be unrelated
Fix bugs in scanoneM and scanoneM2
refineqtlF example: need to first run calc.genoprob
Help files for scanoneM and scanoneM2 had extra stuff in the examples
Remove par(mar=...) from plot2lod
Merge pull request #1 from kbroman/master

A whole bunch of changes