- using R version 2.15.0 (2012-03-30)
- using platform: i686-pc-linux-gnu (32-bit)
- using session charset: UTF-8
- using options ‘--no-examples --no-tests --no-vignettes’
- checking for file ‘adegenet/DESCRIPTION’ ... OK
- this is package ‘adegenet’ version ‘1.3-4’
- 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 executable files ... OK
- checking whether package ‘adegenet’ can be installed ... OK
- checking installed package size ... NOTE
installed size is 6.6Mb
sub-directories of 1Mb or more:
data 1.3Mb
doc 2.8Mb
files 1.6Mb
- checking package directory ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level 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 for unstated dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File 'R/haploGen.R':
found unlockBinding("as.list.DNAbin", env)
found assignInNamespace("as.list.DNAbin", as.list.DNAbin.new, ns =
"ape", envir = env)
assignplot: warning in require(ade4, quiet = TRUE): partial argument
match of 'quiet' to 'quietly'
assignplot: warning in axis(side = 1, at = 1:n.grp, tick = FALSE, label
= colnames(x$posterior)): partial argument match of 'label' to
'labels'
assignplot: warning in axis(side = 2, at = seq(0.5, by = 1, le =
n.ind), label = rev(rownames(x$posterior)), las = 1, cex.axis =
cex.lab): partial argument match of 'label' to 'labels'
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'
compoplot: warning in require(ade4, quiet = TRUE): partial argument
match of 'quiet' to 'quietly'
dapc.data.frame: warning in require(ade4, quiet = TRUE): partial
argument match of 'quiet' to 'quietly'
dapc.data.frame: warning in require(MASS, quiet = TRUE): partial
argument match of 'quiet' to 'quietly'
dapc.genind: warning in require(ade4, quiet = TRUE): partial argument
match of 'quiet' to 'quietly'
dapc.genind: warning in require(MASS, quiet = TRUE): partial argument
match of 'quiet' to 'quietly'
dapc.genlight: warning in require(ade4, quiet = TRUE): partial argument
match of 'quiet' to 'quietly'
dapc.genlight: warning in require(MASS, quiet = TRUE): partial argument
match of 'quiet' to 'quietly'
find.clusters.data.frame: warning in require(ade4, quiet = TRUE):
partial argument match of 'quiet' to 'quietly'
find.clusters.data.frame: warning in require(MASS, quiet = TRUE):
partial argument match of 'quiet' to 'quietly'
find.clusters.genind: warning in require(ade4, quiet = TRUE): partial
argument match of 'quiet' to 'quietly'
find.clusters.genind: warning in require(MASS, quiet = TRUE): partial
argument match of 'quiet' to 'quietly'
find.clusters.genlight: warning in require(ade4, quiet = TRUE): partial
argument match of 'quiet' to 'quietly'
find.clusters.genlight: warning in require(MASS, quiet = TRUE): partial
argument match of 'quiet' to 'quietly'
glPlot: warning in axis(side = 2, at = nInd(x) - ylabpos + 1, lab =
ylabpos): partial argument match of 'lab' to 'labels'
loadingplot.default: warning in jitter(x.ann, fac = lab.jitter):
partial argument match of 'fac' to 'factor'
loadingplot.default: warning in jitter(y.ann, fac = lab.jitter):
partial argument match of 'fac' to 'factor'
monmonier: warning in sort(unique(D)[unique(D) > 0], dec = TRUE):
partial argument match of 'dec' to 'decreasing'
optimize.monmonier: warning in sort(unique(D)[unique(D) > 0], dec =
TRUE): partial argument match of 'dec' to 'decreasing'
optimize.monmonier: warning in monmonier(xy, dist, cn.nb, skip = i,
scanthres = FALSE, threshold = Dlim, bd.length = bd.length, allowLoop
= allowLoop): partial argument match of 'skip' to 'skip.local.diff'
plot.monmonier: warning in s.value(xy, variable, grid = FALSE,
include.ori = FALSE, addaxes = FALSE, neig = neig, cneig = cneig,
clegend = clegend, csize = csize, cpoint = cpoint, pch = 20, pixmap =
pixmap, method = method, sub = sub, csub = csub, possub = possub,
add.plot = add.plot): partial argument match of 'include.ori' to
'include.origin'
plot.spca: warning in s.label(xy, clab = clab, include.ori = FALSE,
addaxes = FALSE, neig = neig, cneig = 1, sub = "Connection network",
csub = 2): partial argument match of 'clab' to 'clabel'
plot.spca: warning in s.label(xy, clab = clab, include.ori = FALSE,
addaxes = FALSE, neig = neig, cneig = 1, sub = "Connection network",
csub = 2): partial argument match of 'include.ori' to
'include.origin'
plot.spca: warning in s.image(xy, z, include.ori = FALSE, grid = TRUE,
kgrid = 10, cgrid = 1, sub = sub, csub = csub, possub =
"bottomleft"): partial argument match of 'include.ori' to
'include.origin'
plot.spca: warning in s.value(xy, z, include.ori = FALSE, addaxes =
FALSE, clegend = 0, csize = 0.6, neig = neig, sub = sub, csub = csub,
possub = "bottomleft"): partial argument match of 'include.ori' to
'include.origin'
plot.spca: warning in s.value(xy, z, include.ori = FALSE, addaxes =
FALSE, clegend = 0, csize = 0.6, method = "greylevel", neig = neig,
sub = sub, csub = csub, possub = "bottomleft"): partial argument
match of 'include.ori' to 'include.origin'
read.genepop: warning in sort(splited, dec = TRUE): partial argument
match of 'dec' to 'decreasing'
repool: warning in unlist(listPop, use.name = FALSE): partial argument
match of 'use.name' to 'use.names'
scatter.dapc: warning in require(ade4, quiet = TRUE): partial argument
match of 'quiet' to 'quietly'
scatter.dapc: warning in add.scatter(inset(), posi = posi.da, ratio =
ratio.da, bg = bg.inset, inset = inset.da): partial argument match of
'bg' to 'bg.col'
scatter.dapc: warning in add.scatter(inset(), posi = posi.pca, ratio =
ratio.pca, bg = bg.inset, inset = inset.pca): partial argument match
of 'bg' to 'bg.col'
scatter.glPca: warning in require(ade4, quiet = TRUE): partial argument
match of 'quiet' to 'quietly'
spca: warning in require(ade4, quiet = TRUE): partial argument match of
'quiet' to 'quietly'
spca: warning in require(spdep, quiet = TRUE): partial argument match
of 'quiet' to 'quietly'
summary.dapc: warning in require(ade4, quiet = TRUE): partial argument
match of 'quiet' to 'quietly'
- checking Rd files ... OK
- checking Rd metadata ... OK
- 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 line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking compiled code ... NOTE
File ‘/home/hornik/tmp/R.check/r-release/Work/build/Packages/adegenet/libs/adegenet.so’:
Found ‘printf’, possibly from ‘printf’ (C)
Object: ‘snpbin.o’
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking examples ... SKIPPED
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking running R code from vignettes ... SKIPPED
- checking re-building of vignettes ... SKIPPED
- checking PDF version of manual ... OK
NOTE: There were 3 notes.
See
‘/home/hornik/tmp/R.check/r-release/Work/PKGS/adegenet.Rcheck/00check.log’
for details.