[adegenet-commits] r1129 - in pkg: . R

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2013-05-15 12:57:43 +0200 (Wed, 15 May 2013)
New Revision: 1129

Removed:
   pkg/TODO
Modified:
   pkg/R/glPlot.R
Log:
fixed a NOTE due to glPlot; removed useless TODO file

Modified: pkg/R/glPlot.R
===================================================================
--- pkg/R/glPlot.R	2013-05-14 21:54:19 UTC (rev 1128)
+++ pkg/R/glPlot.R	2013-05-15 10:57:43 UTC (rev 1129)
@@ -31,6 +31,9 @@
 
 
 
+## hack to remove the NOTE in R CMD check about:
+## "plot,genlight: no visible binding for global variable ‘y’"
+if(getRversion() >= "2.15.1")  utils::globalVariables("y")
 
 ## plot method
 setMethod("plot", signature(x="genlight", y="ANY"), function(x, y=NULL, col=NULL, legend=TRUE,

Deleted: pkg/TODO
===================================================================
--- pkg/TODO	2013-05-14 21:54:19 UTC (rev 1128)
+++ pkg/TODO	2013-05-15 10:57:43 UTC (rev 1129)
@@ -1,82 +0,0 @@
-#######################
-#
-# adegenet TODO list
-#
-#######################
-#
-# please list here all intended modifications
-# and all detected bugs
-#
-# please add a "-- done" or "-- fixed" tag when
-# you achieved something
-# '*' indicates stuff to do
-# 'o' indicates done stuff
-# '*o*' indicates partly done stuff
-#
-# Inside a given section, priority goes decreasing.
-#
-# Delete fixed things each new release.
-#
-# T.J. 2008
-#
-######################
-
-
-
-# FOR NEXT STABLE VERSION
-=========================
-=========================
-
-# CODE ISSUES:
-==============
-* fix request 1.2-2.04 (implement adjusted heretozygosity in summary)
-
-
-# DOCUMENTATION ISSUES:
-=======================
-* explain new changes inside the tutorial (handling of AFLP/RAPD...)
-
-
-# NEW IMPLEMENTATIONS:
-=====================
-
-o allow genind2df to export alleles on separate columns -- done
-
-
-# TESTING:
-==========
-
-
-# LOW PRIORITY / MINOR ISSUES
-===========================
-===========================
-* in spca, when nfposi=0, the returned object actually contains what corresponds to nfposi=1. Comes from multispati in ade4. To correct in ade4.
-* use spcaIllus to illustrate global.rtest and local.rtest
-* Implement a method to merge different markers for the same individuals
-*o* Build accessors for:
-- marker names -- done <locNames> (TJ)
-- indiv names
-- pop names/factor -- done <pop> (TJ) 
-- spatial coords
-- nb of loci -- done <nLoc> (TJ) 
-* Return a spatial object from monmonier (class sp?)
-* implement classical Fst sensu Weir 1996 ? Or wait for EP to do it...
-* Implement different levels of ploidy in:
-- hybridize - done (TJ)
-- read.structure
-
-
-
-# LONG TERM
-==========================
-==========================
-* import from pegas
-* import from geneticsBase -- wait for geneSet to be stable
-* export to geneticsBase -- same thing
-* see where code needs tuning, and use C/C++
-* implement global.rtest and local.rtest for genind/genpop objects
-* Check the formulae provided for Reynolds (consistent with Felsenstein's
-formulae, not straightforward reading the original article)
-* Implement wrappers for spatial function (Moran's I, Mantel's correlogram, etc.).
-
-