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SOfireA log file (check_x86_64_linux)

Thu Apr  5 13:51:51 2018: Checking package SOfireA (SVN revision 104) ...
* using log directory ‘/srv/rf/building/build_2018-04-05-12-44/RF_PKG_CHECK/PKGS/SOfireA.Rcheck’
* using R version 3.5.0 alpha (2018-04-04 r74529)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘SOfireA/DESCRIPTION’ ... OK
* this is package ‘SOfireA’ version ‘1.1’
* checking CRAN incoming feasibility ...Warning: /srv/rf/building/build_2018-04-05-12-44/RF_PKG_CHECK/PKGS/SOfireA.Rcheck/00_pkg_src/SOfireA/man/SOfireA-package.Rd:6: unexpected '}'
Warning: /srv/rf/building/build_2018-04-05-12-44/RF_PKG_CHECK/PKGS/SOfireA.Rcheck/00_pkg_src/SOfireA/man/SOfireA-package.Rd:8: unexpected '}'
Warning: /srv/rf/building/build_2018-04-05-12-44/RF_PKG_CHECK/PKGS/SOfireA.Rcheck/00_pkg_src/SOfireA/man/SOfireA-package.Rd:18: unexpected '}'
Warning: /tmp/RtmpIMhCcZ/Rbuild99c6c30a09f/SOfireA/man/SOfireA-package.Rd:17: All text must be in a section
Warning: /tmp/RtmpIMhCcZ/Rbuild99c6c30a09f/SOfireA/man/SOfireA-package.Rd:17: All text must be in a section
 WARNING
Maintainer: ‘Matthias Forkel ’

New submission

Strong dependencies not in mainstream repositories:
  ModelDataComp

Size of tarball: 13069148 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 serialization versions ... OK
* checking whether package ‘SOfireA’ can be installed ... [9s/9s] WARNING
Found the following significant warnings:
  Warning: /tmp/RtmpIMhCcZ/Rbuild99c6c30a09f/SOfireA/man/SOfireA-package.Rd:17: All text must be in a section
See ‘/srv/rf/building/build_2018-04-05-12-44/RF_PKG_CHECK/PKGS/SOfireA.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data  12.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘SOfireA-manual.pdf’
* 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 ... WARNING
'::' or ':::' import not declared from: ‘yarrr’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/16s] NOTE
MakeFig: no visible global function definition for ‘lm’
MakeFig: no visible global function definition for ‘predict’
SofiaOpt: no visible global function definition for ‘rnorm’
SofiaOpt: no visible global function definition for ‘ldply’
Undefined global functions or variables:
  ldply lm predict rnorm
Consider adding
  importFrom("stats", "lm", "predict", "rnorm")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘SOfireA/R/Sofia.R’:
  data(firedata)
File ‘SOfireA/R/plot.Sofia.R’:
  data(firedata)
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... WARNING
prepare_Rd: SOfireA-package.Rd:6: unexpected '}'
prepare_Rd: SOfireA-package.Rd:8: unexpected '}'
prepare_Rd: SOfireA-package.Rd:18: unexpected '}'
prepare_Rd: SOfireA-package.Rd:17: All text must be in a section
prepare_Rd: SOfireA-package.Rd:17: Section \Sexpr is unrecognized and will be dropped
firedata.Rd: non-ASCII input and no declared encoding
problem found in ‘firedata.Rd’
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'SofiaOpt.Rd':
  \examples lines wider than 100 characters:
     #                    path=path, par.init=par.init, pop.size=10, max.generations=10, BFGS=FALSE, nodes=4)

Rd file 'plot.Sofia.Rd':
  \examples lines wider than 100 characters:
                                    0.13, 3, 0.53, 0, 0, 0, 0.35, -0.44, 0.36, -1.2, -4.8, -45, # for CRU.WET
                                    -0.7, 18, -1.5, 0, 0, 0, 22, 11, -17, -2.3, 0.64, 1,  # for GIMMS.FAPAR

These lines will be truncated in the PDF manual.
* 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 ... WARNING
'::' or ':::' import not declared from: ‘here’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in ‘SOfireA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SofiaOpt
> ### Title: Optimize a SOFIA model using genetic optimization
> ### Aliases: SofiaOpt
> 
> ### ** Examples
> 
> 
> # example based on artificial data
> #---------------------------------
>   
> # some example data
> n <- 500
> sm <- runif(n, 0, 100) # soil moisture
> temp <- rnorm(n, 12, 10) # temperature
> tree <- runif(n, 0, 1) # fractional tree cover
> grass <- 1 - tree # fractional grass cover
> area <- cbind(tree, grass)
> x <- cbind(sm, temp)
> 
> # create 'observations'
> sofiapar <- SofiaPar(colnames(x), colnames(area), per.group=c(TRUE, FALSE))
> sofiapar$par <- c(1, 0, 1, 20, 2, 1, 0, 0, -0.2, -0.1, 13, 10) # actual parameters
> cbind(sofiapar$name, sofiapar$par)
      [,1]           [,2]  
 [1,] "temp.max"     "1"   
 [2,] "temp.min"     "0"   
 [3,] "temp.sl"      "1"   
 [4,] "temp.x0"      "20"  
 [5,] "sm.max.grass" "2"   
 [6,] "sm.max.tree"  "1"   
 [7,] "sm.min.grass" "0"   
 [8,] "sm.min.tree"  "0"   
 [9,] "sm.sl.grass"  "-0.2"
[10,] "sm.sl.tree"   "-0.1"
[11,] "sm.x0.grass"  "13"  
[12,] "sm.x0.tree"   "10"  
> sf <- Sofia(x, area, per.group=c(TRUE, FALSE), sofiapar=sofiapar)
> plot(sf) # fitted values vs. temperature
Warning in par(op) : graphical parameter "cin" cannot be set
Warning in par(op) : graphical parameter "cra" cannot be set
Warning in par(op) : graphical parameter "csi" cannot be set
Warning in par(op) : graphical parameter "cxy" cannot be set
Warning in par(op) : graphical parameter "din" cannot be set
Warning in par(op) : graphical parameter "page" cannot be set
> obs <- sf$data$y # 'observations'
> 
> # re-estimate parameters
> path <- paste0(here::here(), "/SofiaOpt_test1") # directory for optimization outputs
Error in loadNamespace(name) : there is no package called ‘here’
Calls: paste0 ... tryCatch -> tryCatchList -> tryCatchOne -> 
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 5 WARNINGs, 4 NOTEs
See
  ‘/srv/rf/building/build_2018-04-05-12-44/RF_PKG_CHECK/PKGS/SOfireA.Rcheck/00check.log’
for details.

Run time: 116.93 seconds.