R Development Page

bat log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2015-11-12-10-14/RF_PKG_CHECK/PKGS/bat.Rcheck'
* using R version 3.2.2 Patched (2015-11-05 r69602)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'bat/DESCRIPTION' ... OK
* this is package 'bat' version '1.0'
* checking CRAN incoming feasibility ... ERROR
Maintainer: 'Pedro Cardoso '
New submission

Conflicting package names (submitted: bat, existing: BAT [http://CRAN.R-project.org])

Conflicting package names (submitted: bat, existing: BAT [CRAN archive])

The Description field should start with a capital letter.

The Date field is not in ISO 8601 yyyy-mm-dd format.
Maintainer: 'Pedro Cardoso '
New submission

Conflicting package names (submitted: bat, existing: BAT [http://CRAN.R-project.org])

Conflicting package names (submitted: bat, existing: BAT [CRAN archive])

The Description field should start with a capital letter.

The Date field is not in ISO 8601 yyyy-mm-dd format.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'bat' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* 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 ... NOTE
Package in Depends field not imported from: 'vegan'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alpha: no visible global function definition for 'rrarefy'
beta: no visible global function definition for 'rrarefy'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'Arrabida' 'Functree' 'Geres' 'Guadiana' 'Phylotree'
Undocumented data sets:
  'Arrabida' 'Functree' 'Geres' 'Guadiana' 'Phylotree'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* 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 'bat-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: beta
> ### Title: Beta diversity (TD, PD or FD).
> ### Aliases: beta
> 
> ### ** Examples
> 
> comm <- matrix(c(2,2,0,0,0,1,1,0,0,0,0,2,2,0,0,0,0,0,2,2), nrow = 4, ncol = 5, byrow = TRUE)
> tree <- hclust(dist(c(1:5), method="euclidean"), method="average")
> beta(comm)
$Btotal
          1         2         3
2 0.0000000                    
3 0.6666667 0.6666667          
4 1.0000000 1.0000000 1.0000000

$Brepl
          1         2         3
2 0.0000000                    
3 0.6666667 0.6666667          
4 1.0000000 1.0000000 1.0000000

$Brich
  1 2 3
2 0    
3 0 0  
4 0 0 0

> beta(comm, func = "Soerensen")
$Btotal
    1   2   3
2 0.0        
3 0.5 0.5    
4 1.0 1.0 1.0

$Brepl
    1   2   3
2 0.0        
3 0.5 0.5    
4 1.0 1.0 1.0

$Brich
  1 2 3
2 0    
3 0 0  
4 0 0 0

> beta(comm, tree)
$Btotal
          1         2         3
2 0.0000000                    
3 0.5833333 0.5833333          
4 1.0000000 1.0000000 0.8000000

$Brepl
          1         2         3
2 0.0000000                    
3 0.3333333 0.3333333          
4 0.9333333 0.9333333 0.6666667

$Brich
           1          2          3
2 0.00000000                      
3 0.25000000 0.25000000           
4 0.06666667 0.06666667 0.13333333

> beta(comm, raref = 1)
$Btotal
          1         2         3
2 0.1675000                    
3 0.7123333 0.6868333          
4 1.0000000 1.0000000 1.0000000

$Btotal.min
    1   2   3
2 0.0        
3 0.0 0.5    
4 1.0 1.0 1.0

$Btotal.lowCL
    1   2   3
2 0.0        
3 0.0 0.5    
4 1.0 1.0 1.0

$Btotal.upCL
    1   2   3
2 0.5        
3 1.0 1.0    
4 1.0 1.0 1.0

$Btotal.max
    1   2   3
2 0.5        
3 1.0 1.0    
4 1.0 1.0 1.0

$Brepl
          1         2         3
2 0.0000000                    
3 0.5273333 0.5393333          
4 0.8533333 0.8920000 0.8433333

$Brepl.min
          1         2         3
2 0.0000000                    
3 0.0000000 0.0000000          
4 0.6666667 0.6666667 0.6666667

$Brepl.lowCL
          1         2         3
2 0.0000000                    
3 0.0000000 0.0000000          
4 0.6666667 0.6666667 0.6666667

$Brepl.upCL
          1         2         3
2 0.0000000                    
3 1.0000000 0.6666667          
4 1.0000000 1.0000000 1.0000000

$Brepl.max
          1         2         3
2 0.0000000                    
3 1.0000000 0.6666667          
4 1.0000000 1.0000000 1.0000000

$Brich
          1         2         3
2 0.1675000                    
3 0.1850000 0.1475000          
4 0.1466667 0.1080000 0.1566667

$Brich.min
  1 2 3
2 0    
3 0 0  
4 0 0 0

$Brich.lowCL
  1 2 3
2 0    
3 0 0  
4 0 0 0

$Brich.upCL
          1         2         3
2 0.5000000                    
3 0.5000000 0.5000000          
4 0.3333333 0.3333333 0.3333333

$Brich.max
          1         2         3
2 0.5000000                    
3 0.5000000 0.5000000          
4 0.3333333 0.3333333 0.3333333

> beta(comm, tree, T, "s", raref = 2)
Error in betaObs(commBoth, tree, abund, func) : T used instead of TRUE
Calls: beta -> betaObs
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 4 NOTEs
See
  'R:/run/building/build_2015-11-12-10-14/RF_PKG_CHECK/PKGS/bat.Rcheck/00check.log'
for details.

Run time: 85.92 seconds.