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sedarJombart log file (check_x86_64_linux)

Mon Aug 17 15:25:17 2015: Checking package sedarJombart (SVN revision 131) ...
* using log directory ‘/mnt/building/build_2015-08-17-15-24/RF_PKG_CHECK/PKGS/sedarJombart.Rcheck’
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘sedarJombart/DESCRIPTION’ ... OK
* this is package ‘sedarJombart’ version ‘1.0-0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Thibaut Jombart ’
New submission

Unknown, possibly mis-spelled, fields in DESCRIPTION:
  ‘Namespace’

Package has a FOSS license but eventually depends on the following
package which restricts use:
  tripack

The Title field should be in title case, current version then in title case:
‘Thibaut Jombart's contribution to SEDAR package’
‘Thibaut Jombart's Contribution to SEDAR Package’

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 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 ‘sedarJombart’ 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:
  ‘ade4’ ‘spdep’ ‘tripack’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ade4’ ‘spdep’ ‘tripack’
  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:
  print.mspa scatter.mspa
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
chooseCN: warning in require(spdep, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
chooseCN: warning in require(tripack, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
chooseCN: warning in require(ade4, quiet = TRUE): partial argument
  match of 'quiet' to 'quietly'
chooseCN: no visible global function definition for ‘tri2nb’
chooseCN: no visible global function definition for ‘gabrielneigh’
chooseCN: no visible global function definition for ‘graph2nb’
chooseCN: no visible global function definition for ‘relativeneigh’
chooseCN: no visible global function definition for ‘mstree’
chooseCN: no visible global function definition for ‘neig2nb’
chooseCN: no visible global function definition for ‘dnearneigh’
chooseCN: no visible global function definition for ‘knearneigh’
chooseCN: no visible global function definition for ‘knn2nb’
chooseCN: no visible global function definition for ‘nb2listw’
chooseCN: no visible global function definition for ‘mat2listw’
global.rtest: no visible global function definition for ‘scalewt’
global.rtest: no visible global function definition for
  ‘orthobasis.listw’
global.rtest: no visible global function definition for ‘as.randtest’
local.rtest: no visible global function definition for ‘scalewt’
local.rtest: no visible global function definition for
  ‘orthobasis.listw’
local.rtest: no visible global function definition for ‘as.randtest’
mspa: no visible global function definition for ‘scalewt’
mspa: no visible global function definition for ‘orthobasis.listw’
mspa: no visible global function definition for ‘as.dudi’
scatter.mspa: no visible global function definition for ‘s.label’
scatter.mspa: no visible global function definition for ‘s.arrow’
scatter.mspa: no visible global function definition for
  ‘add.scatter.eig’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Unknown package ‘pkg’ in Rd xrefs
* 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 ‘sedarJombart-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mspa
> ### Title: Multi-Scale Pattern Analysis
> ### Aliases: mspa scatter.mspa print.mspa
> ### Keywords: multivariate spatial
> 
> ### ** Examples
> 
> ############################
> ### using simulated data ###
> ############################
> 
> ## load data
> data(mspaIllus)
> X <- mspaIllus
> dim(X)
[1] 100  35
> lw <- attr(mspaIllus,"lw")
> 
> ## perform a PCA
> pcaX <- dudi.pca(X,scannf=FALSE,nf=4)
> 
> ## perform the MSPA
> mspa1 <- mspa(pcaX,lw,scannf=FALSE,nf=3)
Error in as.matrix(orthobasis.listw(lw)) : 
  could not find function "orthobasis.listw"
Calls: mspa -> as.matrix
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 5 NOTEs
See
  ‘/mnt/building/build_2015-08-17-15-24/RF_PKG_CHECK/PKGS/sedarJombart.Rcheck/00check.log’
for details.

Run time: 72.31 seconds.

Additional Logs:   00install.out
Thanks to:
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