SCM

R Development Page

PCNM log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2015-07-13-14-43/RF_PKG_CHECK/PKGS/PCNM.Rcheck'
* using R version 3.2.1 Patched (2015-07-08 r68644)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'PCNM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PCNM' version '2.1-4'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Pierre Legendre '
New submission

Unknown, possibly mis-spelled, fields in DESCRIPTION:
  'Namespace'

Strong dependencies not in mainstream repositories:
  AEM, packfor

The Title field should be in title case, current version then in title case:
'MEM spatial eigenfunction and principal coordinate analyses'
'MEM Spatial Eigenfunction and Principal Coordinate Analyses'

The Date field is over a month old.
* 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 'PCNM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
'library' or 'require' calls to packages already attached by Depends:
  'AEM' 'ade4' 'packfor' 'vegan'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'AEM' 'MASS' 'ade4' 'packfor' 'vegan'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: 'ade4::s.value'
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  anova.ccabyaxis biplot.pcoa
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PCNM: no visible global function definition for 'dnearneigh'
PCNM: no visible global function definition for 'listw2sn'
PCNM: no visible global function definition for 'nb2listw'
PCNM: no visible global function definition for 'moran.I.multi'

Found the following assignments to the global environment:
File 'PCNM/R/quickPCNM.R':
  assign("PCNMbase", PCNMbase, envir = .GlobalEnv)
  assign("Y.det", Y.det, envir = .GlobalEnv)
  assign("Y.det", Y.det, envir = .GlobalEnv)
  assign("Y.det", Y.det, envir = .GlobalEnv)
  assign("Y.det", Y.det, envir = .GlobalEnv)
  assign("PCNMred", PCNMred, envir = .GlobalEnv)
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'PCNM.Rd':
  \usage lines wider than 90 characters:
     PCNM(matdist, thresh=NULL, dbMEM=FALSE, moran=NULL, all=FALSE, include.zero=FALSE, silent=FALSE)

Rd file 'STImodels.Rd':
  \usage lines wider than 90 characters:
     STImodels(Y, S, T,  model="5", nperm=999, nS=-1,nT=-1, Sfixed=TRUE, Tfixed=TRUE, COD.S=NULL, COD.T=NULL, print.res=TRUE)

Rd file 'quickPCNM.Rd':
  \usage lines wider than 90 characters:
     quickPCNM(Y, space, thresh=NULL, method="fwd", myPCNM=NULL, alpha=0.05, rangexy=FALSE, detrend=TRUE, perm.max=NULL, original=FALSE)

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 ... 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 'PCNM-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PCNM-package
> ### Title: PCNM spatial eigenfunctions
> ### Aliases: PCNM-package
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> # Oribatid mite data from Borcard and Legendre (1994)
> library(vegan)
> data(mite)      # 70 peat cores, 35 species
> data(mite.xy)   # Core geographic coordinates
> 
> # Compute PCNM eigenfunctions
> res.pcnm <- PCNM(dist(mite.xy), thresh=1.012)
User-provided truncation threshold = 1.012 
Time to compute PCNMs = 6.650000  sec 
> 
> # PCNM eigenfunction analysis: quickPCNM
> mite.hel <- decostand(mite, "hellinger")
> res.quick <- quickPCNM(mite.hel, mite.xy, thresh=1.012)
User-provided truncation threshold = 1.012 
Time to compute PCNMs = 6.650000  sec 
Testing variable 1
Testing variable 2
Testing variable 3
Testing variable 4
Testing variable 5
Testing variable 6
Testing variable 7
Testing variable 8
Testing variable 9
Testing variable 10
Procedure stopped (adjR2thresh criteria) adjR2cum = 0.271295 with 10 variables (superior to 0.264554)
Error: 's.value' is not an exported object from 'namespace:ade4'
Timing stopped at: 13.52 0.03 13.56 
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 6 NOTEs
See
  'R:/run/building/build_2015-07-13-14-43/RF_PKG_CHECK/PKGS/PCNM.Rcheck/00check.log'
for details.

Run time: 92.35 seconds.

Additional Logs:   00install.out
Thanks to:
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