Merge branch 'develop' into patch-4

base/utils/R/read.output.R

@@ -31,7 +31,7 @@
 ##'   variables in output file..
 ##' @param dataframe Logical: if TRUE, will return output in a
 ##'   `data.frame` format with a posix column. Useful for
-##'   [PEcAn.benchmark::align.data()] and plotting.
+##'   [PEcAn.benchmark::align_data()] and plotting.
 ##' @param pft.name character string, name of the plant functional
 ##'   type (PFT) to read PFT-specific output. If `NULL` no
 ##'   PFT-specific output will be read even the variable has PFT as a

modules/photosynthesis/code/Sunny.preliminary.code/C3 photomodel.r → modules/photosynthesis/code/Sunny.preliminary.code/C3_photomodel.r

@@ -1,6 +1,6 @@
 library(R2WinBUGS)
 library(BRugs)
-dat=read.csv("C3 Species.csv",header=T)
+dat=read.csv("C3_Species.csv",header=T)
 #dat2=read.csv('c3covariates.csv',header=T)
 
 my.model  = function(){

modules/photosynthesis/tests/Rcheck_reference.log

@@ -13,12 +13,7 @@
 * checking if there is a namespace ... OK
 * checking for executable files ... OK
 * checking for hidden files and directories ... OK
-* checking for portable file names ... WARNING
-Found the following files with non-portable file names:
-  code/Sunny.preliminary.code/C3 photomodel.r
-  code/Sunny.preliminary.code/C3 Species.csv
-These are not fully portable file names.
-See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
+* checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
 * checking serialization versions ... OK
 * checking whether package ‘PEcAn.photosynthesis’ can be installed ... OK
@@ -108,4 +103,4 @@ Files in the 'vignettes' directory but no files in 'inst/doc':
 Package has no Sweave vignette sources and no VignetteBuilder field.
 * checking examples ... NONE
 * DONE
-Status: 3 WARNINGs, 4 NOTEs
+Status: 2 WARNINGs, 4 NOTEs