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PCNM log file (check_x86_64_linux)

Mon Jul 13 14:45:11 2015: Checking package PCNM (SVN revision 128) ...
* using log directory ‘/mnt/building/build_2015-07-13-14-43/RF_PKG_CHECK/PKGS/PCNM.Rcheck’
* using R version 3.2.1 Patched (2015-07-12 r68650)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PCNM’ can be installed ... [5s/5s] 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.
* 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 ... [146s/146s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
STImodels    65.288  0.000  65.287
PCNM         29.550  0.012  29.560
quickPCNM    28.514  0.012  28.557
PCNM-package 19.889  0.012  19.901
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/mnt/building/build_2015-07-13-14-43/RF_PKG_CHECK/PKGS/PCNM.Rcheck/00check.log’
for details.


Run time: 211.37 seconds.