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VirtualCom log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2014-11-03-15-04/RF_PKG_CHECK/PKGS/VirtualCom.Rcheck'
* using R version 3.1.2 Patched (2014-10-31 r66921)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'VirtualCom/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VirtualCom' version '1.0'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Laure Gallien , Tamara Munkemuller
'
New submission
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped

Depends: includes the non-default packages:
  'geiger' 'picante' 'Hmisc' 'apTreeshape' 'FD' 'OUwie' 'ggplot2'
  'snowfall' 'reshape2'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'VirtualCom' 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'FD' 'Hmisc' 'OUwie' 'apTreeshape' 'geiger' 'ggplot2' 'picante'
  'reshape2' 'snowfall'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
colless.test.no.print: no visible global function definition for
  'rtreeshape'
colless.test.no.print: no visible binding for global variable 'colless'
colless.test.no.print: no visible global function definition for
  'colless'
create.pool: no visible global function definition for 'phylosignal'
create.pool: no visible global function definition for 'as.treeshape'
create.pool: no visible global function definition for 'colless'
div.param.invasion : : no visible global function definition
  for 'taxaShuffle'
div.param.native: no visible global function definition for
  'randomizeMatrix'
div.param.native.obs: no visible global function definition for 'dbFD'
div.param.native.obs: no visible global function definition for
  'diversity'
div.param.native.obs: no visible global function definition for 'mpd'
div.param.native.obs: no visible global function definition for 'mntd'
div.param.native.obs : : no visible global function
  definition for 'wtd.var'
div.param.native.obs: no visible global function definition for
  'treedive'
div.param.native.obs : : no visible global function
  definition for 'drop.tip'
div.param.native.obs : : no visible global function
  definition for 'maxlik.betasplit'
div.param.native.obs : : no visible global function
  definition for 'as.treeshape'
get.attractors: no visible global function definition for
  'cophenetic.phylo'
simulation.experiment: no visible global function definition for
  'drop.tip'
trait.evolution: no visible global function definition for 'sim.bdtree'
trait.evolution: no visible global function definition for 'rTraitCont'
trait.evolution: no visible global function definition for 'OUwie.sim'
trait.evolution: no visible global function definition for
  'cophenetic.phylo'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'create.pool.Rd':
  \examples lines wider than 100 characters:
     pool <- create.pool(n.species.pool=500, n.invader.pool=1, evol.model="deltaTree", min.phyl.signal=NA, evol.model.param=0.1, nrep=1)

Rd file 'get.results.Rd':
  \examples lines wider than 100 characters:
       result.table$process <- ifelse(result.table$beta.env==0 & result.table$beta.comp==0, "Random", ifelse(result.table$beta.env!=0 & resu ... [TRUNCATED]
       ggplot(data=result.table, aes(x=process, y=FD_ab_mpd)) + geom_boxplot(width=0.8) +  xlab("Assembly rules") +  ylab("Functional divers ... [TRUNCATED]

Rd file 'simulation.experiment.Rd':
  \examples lines wider than 100 characters:
       result.table$process <- ifelse(result.table$beta.env==0 & result.table$beta.comp==0, "Random", ifelse(result.table$beta.env!=0 & resu ... [TRUNCATED]
       ggplot(data=result.table, aes(x=process, y=FD_ab_mpd)) + geom_boxplot(width=0.8) +  xlab("Assembly rules") +  ylab("Functional divers ... [TRUNCATED]

Rd file 'tamaure.Rd':
  \examples lines wider than 100 characters:
     pool <- create.pool(n.species.pool=500, n.invader.pool=1, evol.model="deltaTree", min.phyl.signal=NA, evol.model.param=0.1, nrep=1)
     env.filter.community <- tamaure(niche.breadth=2, niche.optima=niche.optima, env=50, beta.env=1, beta.comp=0, beta.abun=1, years=10, K=1 ... [TRUNCATED]
     competition.community <- tamaure(niche.breadth=2, niche.optima=niche.optima, env=50, beta.env=0, beta.comp=10, beta.abun=1, years=10, K ... [TRUNCATED]

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 ... WARNING
Codoc mismatches from documentation object 'create.pool':
create.pool
  Code: function(n.species.pool, n.invader.pool, evol.model, rescale =
                 TRUE, min.phyl.signal, evol.model.param = NA,
                 OUwie.sigma.sq = NA, OUwie.theta = NA, OUwie.alpha =
                 NA, nrep = 499)
  Docs: function(n.species.pool, n.invader.pool, evol.model,
                 min.phyl.signal, evol.model.param, nrep = 499)
  Argument names in code not in docs:
    rescale OUwie.sigma.sq OUwie.theta OUwie.alpha
  Mismatches in argument names:
    Position: 4 Code: rescale Docs: min.phyl.signal
    Position: 5 Code: min.phyl.signal Docs: evol.model.param
    Position: 6 Code: evol.model.param Docs: nrep
  Mismatches in argument default values:
    Name: 'evol.model.param' Code: NA Docs: 

Codoc mismatches from documentation object 'tamaure':
tamaure
  Code: function(niche.breadth = 5, niche.optima, env, beta.env = 0,
                 beta.comp = 0, beta.abun = 0, years = 20, K = 20,
                 community.in = NA, species.pool.abundance = NA, plot =
                 FALSE, competition = "symmetric", intra.sp.com = 1)
  Docs: function(niche.breadth = 5, niche.optima, env, beta.env = 0,
                 beta.comp = 0, beta.abun = 0, years = 20, K = 20,
                 community.in = NA, species.pool.abundance = NA, plot =
                 FALSE)
  Argument names in code not in docs:
    competition intra.sp.com

* 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 ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
simulation.experiment 214.80   3.09  217.89
get.results           173.64   2.85  176.58
tamaure                10.25   0.13   10.38
create.pool             5.30   0.07    5.40
* checking PDF version of manual ... OK
* DONE

WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
  'R:/run/building/build_2014-11-03-15-04/RF_PKG_CHECK/PKGS/VirtualCom.Rcheck/00check.log'
for details.

Run time: 558.12 seconds.

Additional Logs:   00install.out
Thanks to:
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