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cati log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck'
* using R version 3.0.3 Patched (2014-03-06 r65385)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-examples --no-tests --no-vignettes'
* checking for file 'cati/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cati' version '0.5'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Adrien Taudiere '
New submission
Possibly mis-spelled fields in DESCRIPTION:
  'Author@R'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'cati' 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:
  'ade4' 'ape' 'e1071' 'hypervolume' 'lattice' 'mice' 'moments' 'nlme'
  'rasterVis'
  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 ... WARNING
summary:
  function(object, ...)
summary.Tstats:
  function(object, val.quant, type)

See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
com.index.multi: no visible binding for global variable
  'names_sp_ind_plot'

Found the following calls to attach():
File 'cati/R/allfunctions_cati.r':
  attach(as.data.frame(factors))
  attach(as.data.frame(factors))
See section 'Good practice' in '?attach'.
* checking Rd files ... WARNING
prepare_Rd: CVNND.Rd:26-27: Dropping empty section \details
prepare_Rd: CVNND.Rd:42-43: Dropping empty section \note
prepare_Rd: CVNND.Rd:45-46: Dropping empty section \seealso
RaoRel.Rd: non-ASCII input and no declared encoding
prepare_Rd: Tstats.Rd:137-138: Dropping empty section \note
prepare_Rd: as.listofindex.Rd:25-26: Dropping empty section \details
prepare_Rd: as.listofindex.Rd:39-40: Dropping empty section \note
prepare_Rd: as.listofindex.Rd:32-33: Dropping empty section \references
prepare_Rd: as.listofindex.Rd:47-48: Dropping empty section \examples
prepare_Rd: bar_partvar.Rd:29-30: Dropping empty section \details
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prepare_Rd: cati-package.Rd:35-36: Dropping empty section \seealso
prepare_Rd: cati-package.Rd:38-39: Dropping empty section \examples
prepare_Rd: com.index.Rd:83-84: Dropping empty section \note
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prepare_Rd: com.index.multi.Rd:55-57: Dropping empty section \details
prepare_Rd: com.index.multi.Rd:80-81: Dropping empty section \note
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decomp_whithin.Rd: non-ASCII input and no declared encoding
prepare_Rd: finch.ind.Rd:29-30: Dropping empty section \value
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prepare_Rd: finch.ind.Rd:32-33: Dropping empty section \references
prepare_Rd: finch.ind.Rd:39-40: Dropping empty section \seealso
prepare_Rd: partvar.Rd:30-31: Dropping empty section \details
prepare_Rd: partvar.Rd:46-47: Dropping empty section \note
prepare_Rd: pie_partvar.Rd:30-31: Dropping empty section \details
prepare_Rd: pie_partvar.Rd:44-45: Dropping empty section \note
prepare_Rd: pie_partvar.Rd:37-38: Dropping empty section \references
prepare_Rd: plot.listofindex.Rd:79-80: Dropping empty section \details
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prepare_Rd: plot.listofindex.Rd:102-103: Dropping empty section \examples
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prepare_Rd: plot_dens.Rd:60-61: Dropping empty section \details
prepare_Rd: plot_dens.Rd:74-75: Dropping empty section \note
prepare_Rd: plot_dens.Rd:67-68: Dropping empty section \references
prepare_Rd: plot_ses.var.Rd:46-47: Dropping empty section \details
prepare_Rd: plot_ses.var.Rd:60-61: Dropping empty section \note
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prepare_Rd: ses.Rd:30-31: Dropping empty section \details
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prepare_Rd: ses.listofindex.Rd:26-27: Dropping empty section \details
prepare_Rd: ses.listofindex.Rd:42-43: Dropping empty section \note
prepare_Rd: ses.listofindex.Rd:35-36: Dropping empty section \references
trait.flex.anova.Rd: non-ASCII input and no declared encoding
problems found in 'RaoRel.Rd', 'decomp_whithin.Rd', 'trait.flex.anova.Rd'
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/RaoRel.Rd':
  \examples lines wider than 100 characters:
             traits.finch.sp<-apply( apply(traits.finch, 2, scale ), 2, function(x) tapply(x, sp.finch, mean, na.rm=TRUE))
             res.rao<-RaoRel(sample=as.matrix(comm.sp), dfunc=mat.dist, dphyl=NULL, weight=FALSE, Jost=FALSE, structure=NULL)
             res.rao.w<-RaoRel(sample=as.matrix(comm.sp), dfunc=mat.dist, dphyl=NULL, weight=TRUE, Jost=FALSE, structure=NULL)
             barplot(cbind(c(witRao.w, betRao.w), c(witRao, betRao)), names.arg =c("abundance" ,"presence"), legend.text=c("within species", ... [TRUNCATED]
             #We can do this analysis for each trait separately. First we need to remplace (or exclude) NA values. For this example, we use  ... [TRUNCATED]
             traits.finch.mice.sp<-apply(apply(traits.finch.mice, 2, scale ), 2, function(x) tapply(x, sp.finch, mean, na.rm=TRUE))
               trait.rao.w[[t]]<-RaoRel(sample=as.matrix(comm.sp), dfunc=dist(traits.finch.mice.sp[,t]), dphyl=NULL, weight=TRUE, Jost=FALSE ... [TRUNCATED]
             barplot(t(cbind( witRao.w.bytrait, betRao.w.bytrait)), names.arg = colnames(traits.finch),legend.text=c("within species", "betw ... [TRUNCATED]

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/Tstats.Rd':
  \usage lines wider than 90 characters:
     barplot(height, val.quant = c(0.025, 0.975), col.Tstats = c("red", "purple", "green", "white"), ylim=NULL, ...)
     plot(x, val.quant = c(0.025, 0.975), col.Tstats = c("red", "purple", "green"), type = "normal", add.conf = TRUE, ...)
  \examples lines wider than 100 characters:
             levelplot(t(ses(res.finch$T_IP.IC,res.finch$T_IP.IC_nm)$ses), colorkey=my.ckey, par.settings=my.theme,border="black")

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/bar_partvar.Rd':
  \examples lines wider than 100 characters:
             genus<-as.vector(unlist(strsplit(as.vector(sp.finch),"_")) [seq(1,length(sp.finch)*2, by=2)])
             res.partvar.finch<-partvar(traits = traits.finch, factors = cbind(sites = as.factor(as.vector(ind.plot.finch)), species = as.fa ... [TRUNCATED]

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/com.index.Rd':
  \usage lines wider than 90 characters:
             com.index(traits = NULL, index = NULL, namesindex = NULL, nullmodels = NULL, ind.plot = NULL, sp = NULL, nperm = 99, printprogr ... [TRUNCATED]
  \examples lines wider than 100 characters:
             #The function \code(com.index) allow to choose your own function (like mean, range, variance...) to calculate customize index.
             funct<-c("mean(x, na.rm=TRUE)", "kurtosis(x, na.rm=TRUE)", "max(x, na.rm=TRUE) - min(x, na.rm=TRUE)", "CVNND(x)"  )
             res.finch.sp_mn2<-com.index(traits=traits.finch, index=funct, sp=sp.finch, nullmodels=c(2,2,2,2), ind.plot=ind.plot.finch, nper ... [TRUNCATED]
             res.finch.sp_mn3<-com.index(traits=traits.finch, index=funct, sp=sp.finch, nullmodels=c(3,3,3,3), ind.plot=ind.plot.finch, nper ... [TRUNCATED]
             #We can represent Standardized Effect Size (ses) using the function \code(plot(as.listofindex(list1, list2, list3)))
             funct<-c("tapply(x, ind.plot.finch, function(x) mean(x, na.rm=TRUE))", "tapply(x, ind.plot.finch, function(x) kurtosis(x, na.rm ... [TRUNCATED]
             res.finch.ind_mn1<-com.index(traits=traits.finch, index=funct, sp=sp.finch, nullmodels=c(1,1,1,1), ind.plot=ind.plot.finch, npe ... [TRUNCATED]
             res.finch.ind_mn2<-com.index(traits=traits.finch, index=funct, sp=sp.finch, nullmodels=c(2,2,2,2), ind.plot=ind.plot.finch, npe ... [TRUNCATED]
             #Calcul of means by population (name_sp_site is a name of a population) like in the function com.index and determine the site f ... [TRUNCATED]
             traits.by.pop<-apply(traits.finch, 2 , function (x) tapply(x, name_sp_sites, mean , na.rm=TRUE))
             sites_bypop<-lapply(strsplit(paste(rownames(traits.by.pop), sep="_"), split="_"), function(x) x[3])
             funct.whithoutIV<-c("tapply(x, unlist(sites_bypop), function(x) mean(x, na.rm=TRUE))", "tapply(x, unlist(sites_bypop), function ... [TRUNCATED]
             funct.whithIV<-c("tapply(x, ind.plot.finch, function(x) mean(x, na.rm=TRUE))", "tapply(x, ind.plot.finch, function(x) kurtosis( ... [TRUNCATED]
             res.finch.whithIV<-com.index(traits=traits.finch, index=funct.whithIV, sp=sp.finch, nullmodels=c(2,2,2,2), ind.plot=ind.plot.fi ... [TRUNCATED]
             res.finch.whithoutIV<-com.index(traits=traits.finch, index=funct.whithoutIV, sp=sp.finch, nullmodels=c(3,3,3,3), ind.plot=ind.p ... [TRUNCATED]
             #We can also represent T-statistics and custom index thanks to the \code(plot.listofindex) function.
             index.list1<-as.listofindex(list.ind, namesindex=c("mean", "kurtosis", "range", "CVNND", "mean.pop", "kurtosis.pop", "range.pop ... [TRUNCATED]

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/com.index.multi.Rd':
  \usage lines wider than 90 characters:
             com.index.multi(traits = NULL, index = NULL, by.factor = NULL, namesindex = NULL, nullmodels = NULL, ind.plot = NULL, sp = NULL ... [TRUNCATED]
  \examples lines wider than 100 characters:
             #For most multivariate functions we need to remplace (or exclude) NA values. For this example, we use the package mice to compl ... [TRUNCATED]
             res.sum.1<-com.index.multi(traits.finch, index=c("sum(scale(x), na.rm=TRUE)", "sum(x, na.rm=TRUE)"), by.factor=names_sp_ind_plo ... [TRUNCATED]
             #A more interesting example using the function hypervolume from the package hypervolume.  We show here several results which di ... [TRUNCATED]
             res.hv.1<-com.index.multi(traits.finch.mice, index=c("as.numeric(try(hypervolume(na.omit(x), reps=100, bandwidth=0.2, verbose=F ... [TRUNCATED]
             res.hv.2<-com.index.multi(traits.finch.mice, index=c("as.numeric(try(hypervolume(na.omit(x), reps=100, bandwidth=0.2, verbose=F ... [TRUNCATED]
             res.hv.3<-com.index.multi(traits.finch.mice, index=c("as.numeric(try(hypervolume(na.omit(x), reps=100, bandwidth=0.2, verbose=F ... [TRUNCATED]
             res.hv.4<-com.index.multi(traits.finch.mice, index=c("as.numeric(try(hypervolume(na.omit(x), reps=100, bandwidth=0.2, verbose=F ... [TRUNCATED]

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/decomp_whithin.Rd':
  \usage lines wider than 90 characters:
             decomp_whithin(traits = NULL, formula = ~1, ind.plot = NULL, sp = NULL, printprogress = TRUE, ...)
  \examples lines wider than 100 characters:
             res.decomp<-decomp_whithin(traits=traits.finch, sp=sp.finch, ind.plot=ind.plot.finch, print=FALSE)

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/partvar.Rd':
  \examples lines wider than 100 characters:
             genus<-as.vector(unlist(strsplit(as.vector(sp.finch),"_")) [seq(1,length(sp.finch)*2, by=2)])
             res.partvar.finch<-partvar(traits=traits.finch, factors=cbind(sites=as.factor(as.vector(ind.plot.finch)), species=as.factor(as. ... [TRUNCATED]

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/pie_partvar.Rd':
  \examples lines wider than 100 characters:
             res.partvar.finch<-partvar( traits=traits.finch, factors=cbind(as.factor(as.vector(ind.plot.finch)), as.factor(as.vector(sp.fin ... [TRUNCATED]

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/plot.listofindex.Rd':
  \usage lines wider than 90 characters:
             plot.listofindex(x, type = "normal", col.index = c("red", "purple", "green"), add.conf = TRUE, color.cond = TRUE, val.quant = c ... [TRUNCATED]

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/plot_cor.Tstats.Rd':
  \usage lines wider than 90 characters:
             plot_cor.Tstats(tstats = NULL, val.quant = c(0.025, 0.975), add.text= FALSE, bysites= FALSE, col.obj = NULL, plot.ask = TRUE, m ... [TRUNCATED]

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/plot_dens.Rd':
  \usage lines wider than 90 characters:
             plot_dens(traits=NULL, var.1=NULL, var.2=NULL, col.dens=NULL, plot.ask=TRUE, ylim.cex=1, cex.leg=0.8, polyg=TRUE, multipanel=TR ... [TRUNCATED]
  \examples lines wider than 100 characters:
             #Plot the distribution of traits values for populations, species, sites and regional scales. First, let try the distribution fo ... [TRUNCATED]
             plot_dens(traits.finch, sp.finch, ind.plot.finch, ylim.cex=3, plot.ask=FALSE, multipanel=FALSE, leg=FALSE)
             #Then we can inverse the second and the third arguments to plot the distribution for all finches species. 
             plot_dens(traits.finch, ind.plot.finch, sp.finch, ylim.cex=8, plot.ask=FALSE, multipanel=FALSE, leg=FALSE)
             plot_dens(traits.finch, rep("region", times=dim(traits.finch)[1]), sp.finch, ylim.cex=6, plot.ask=FALSE, leg=FALSE)
             plot_dens(traits.finch, rep("toutes_sp", times=dim(traits.finch)[1]), ind.plot.finch, ylim.cex=3, plot.ask=FALSE)

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/plot_ses.var.Rd':
  \usage lines wider than 90 characters:
             plot_ses.var(index.list, variable = NULL, ylab = "variable", color.traits = NULL, val.quant = c(0.025, 0.975), resume = FALSE,  ... [TRUNCATED]
  \examples lines wider than 100 characters:
             plot_ses.var(as.listofindex(list(res.finch)), species.richness, resume=TRUE, multipanel=FALSE)

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/plot_sp_pop.Rd':
  \usage lines wider than 90 characters:
             plot_sp_pop(traits = NULL, ind.plot = NULL, sp = NULL, col.ind = rgb(0.5, 0.5, 0.5, 0.5), col.pop = NULL, col.sp = NULL, col.si ... [TRUNCATED]
  \examples lines wider than 100 characters:
             #If we change the value of the threshold (alpha=10% instead of 5% and the minimum individual to represent singificativity fixed ... [TRUNCATED]
             plot_sp_pop(traits.finch, ind.plot.finch, sp.finch, p.val=0.1,  min.ind.signif=3, silent=TRUE)
             #For a more simple figure, add the option resume=TRUE. Again if we change the value of the threshold (alpha=10% instead of 5% a ... [TRUNCATED]
             plot_sp_pop(traits.finch, ind.plot.finch, sp.finch, silent=TRUE, resume=TRUE, col.pop="grey")
             plot_sp_pop(traits.finch, ind.plot.finch, sp.finch, silent=TRUE, resume=TRUE, col.pop="grey", col.sp="black")
             plot_sp_pop(traits.finch, ind.plot.finch, sp.finch, silent=TRUE, resume=TRUE, col.pop="grey", col.sp="black", p.val=0.1,  min.i ... [TRUNCATED]

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/ses.listofindex.Rd':
  \examples lines wider than 100 characters:
             #Calcul of means by population (name_sp_site is a name of a population) like in the function com.index and determine the site f ... [TRUNCATED]
             traits.by.pop<-apply(traits.finch, 2 , function (x) tapply(x, name_sp_sites, mean , na.rm=TRUE))
             sites_bypop<-lapply(strsplit(paste(rownames(traits.by.pop), sep="_"), split="_"), function(x) x[3])
             levelplot(t(rbind(ses.list[[1]]$ses, ses.list[[2]]$ses, ses.list[[3]]$ses,  ses.list[[4]]$ses)), colorkey=my.ckey, par.settings ... [TRUNCATED]
             levelplot(t(rbind(ses.list[[1]]$ses>ses.list[[1]]$ses.sup, ses.list[[2]]$ses>ses.list[[2]]$ses.sup, ses.list[[3]]$ses>ses.list[ ... [TRUNCATED]

Rd file 'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00_pkg_src/cati/man/trait.flex.anova.Rd':
  \usage lines wider than 90 characters:
     plot(x, plot.total= FALSE, use.percentage = TRUE, plot.covar= FALSE, cumul= FALSE, legend.pos = if (plot.total) "topleft" else "toprigh ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  '.Random.seed'
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'plot.listofindex':
  'plot.listofindex'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 3 warnings.
NOTE: There were 5 notes.
See
  'R:/run/building/build_2014-04-11-10-09/RF_PKG_CHECK/PKGS/cati.Rcheck/00check.log'
for details.

Run time: 106.62 seconds.