* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ggbio.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ggbio/DESCRIPTION' ... OK
* this is package 'ggbio' version '1.7.14'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'ggbio' can be installed ... [33s/34s] 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... WARNING
'bgColor<-' 'hasAxis<-' 'height<-' 'labeled<-' 'mutable<-'
'\S4method{bgColor<-}{gg,character}'
'\S4method{bgColor<-}{gtable,character}'
'\S4method{bgColor<-}{ideogram,character}'
'\S4method{hasAxis<-}{gg,logical}'
'\S4method{hasAxis<-}{gtable,logical}'
'\S4method{hasAxis<-}{ideogram,logical}'
'\S4method{height<-}{gg,numericORunit}'
'\S4method{height<-}{gtable,numericORunit}'
'\S4method{height<-}{ideogram,numericORunit}'
'\S4method{labeled<-}{gg,logical}'
'\S4method{labeled<-}{gtable,logical}'
'\S4method{labeled<-}{ideogram,logical}'
'\S4method{mutable<-}{gg,logical}'
'\S4method{mutable<-}{gtable,logical}'
'\S4method{mutable<-}{ideogram,logical}'
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
align.plots : addLabel : <anonymous>: warning in gtable(width =
unit.c(label.width, unit(1, "null")), height = unit(1, "null")):
partial argument match of 'width' to 'widths'
align.plots : addLabel : <anonymous>: warning in gtable(width =
unit.c(label.width, unit(1, "null")), height = unit(1, "null")):
partial argument match of 'height' to 'heights'
align.plots : addLabel : <anonymous>: warning in gtable(width = unit(1,
"null"), height = unit.c(label.width, unit(1, "null"))): partial
argument match of 'width' to 'widths'
align.plots : addLabel : <anonymous>: warning in gtable(width = unit(1,
"null"), height = unit.c(label.width, unit(1, "null"))): partial
argument match of 'height' to 'heights'
alignPlots : addLabel : <anonymous>: warning in gtable(width =
unit.c(label.width, unit(1, "null")), height = unit(1, "null")):
partial argument match of 'width' to 'widths'
alignPlots : addLabel : <anonymous>: warning in gtable(width =
unit.c(label.width, unit(1, "null")), height = unit(1, "null")):
partial argument match of 'height' to 'heights'
alignPlots : addLabel : <anonymous>: warning in gtable(width = unit(1,
"null"), height = unit.c(label.width, unit(1, "null"))): partial
argument match of 'width' to 'widths'
alignPlots : addLabel : <anonymous>: warning in gtable(width = unit(1,
"null"), height = unit.c(label.width, unit(1, "null"))): partial
argument match of 'height' to 'heights'
getAxisHeight: warning in convertUnit(h1, "cm", value = TRUE): partial
argument match of 'value' to 'valueOnly'
getAxisHeight: warning in convertUnit(h2, "cm", value = TRUE): partial
argument match of 'value' to 'valueOnly'
gfun : <anonymous>: warning in selectMethod(.method, sig = "GRanges"):
partial argument match of 'sig' to 'signature'
ifun : <anonymous>: warning in selectMethod(.method, sig = "GRanges"):
partial argument match of 'sig' to 'signature'
plotIdeogram: warning in getIdeogram(genome = genome, subchr = subchr,
cytoband = cytoband): partial argument match of 'cytoband' to
'cytobands'
plotKaryogram: warning in getIdeogram(cytoband = cytoband): partial
argument match of 'cytoband' to 'cytobands'
plotSingleChrom: warning in getIdeogram(genome = genome, subchr =
subchr, cytoband = cytoband): partial argument match of 'cytoband' to
'cytobands'
plotStackedOverview: warning in getIdeogram(cytoband = cytoband):
partial argument match of 'cytoband' to 'cytobands'
layout_linear,GRanges: warning in facet_grid(scale = "free_x", space =
"free_x"): partial argument match of 'scale' to 'scales'
ScalePlot: no visible binding for global variable 'y'
ScalePlot2: no visible binding for global variable 'breaks'
ScalePlot2: no visible binding for global variable 'yend'
ScalePlot2: no visible binding for global variable 'y.text'
ggsave : default_name: no visible global function definition for
'digest.ggplot'
plotInter: no visible binding for global variable 'fe'
plotInter: no visible binding for global variable 'value'
plotInter2: no visible binding for global variable 'fe'
plotInter2: no visible binding for global variable 'value'
scale_x_sequnit: no visible binding for global variable '.x'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'ggsave' 'theme_genome'
Undocumented S4 methods:
generic 'coord_genome' and siglist 'GRanges'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'autoplot':
\S4method{autoplot}{GRanges}
Code: function(object, ..., chr, xlab, ylab, main, truncate.gaps =
FALSE, truncate.fun = NULL, ratio = 0.0025, space.skip
= 0.1, legend = TRUE, geom = NULL, stat = NULL,
chr.weight = NULL, coord = c("default", "genome",
"truncate_gaps"), layout = c("linear", "karyogram",
"circle"))
Docs: function(object, ..., chr, xlab, ylab, main, truncate.gaps =
FALSE, truncate.fun = NULL, ratio = 0.0025, space.skip
= 0.1, legend = TRUE, geom = NULL, stat = NULL, coord
= c("default", "genome", "truncate_gaps"), layout =
c("linear", "karyogram", "circle"))
Argument names in code not in docs:
chr.weight
Mismatches in argument names:
Position: 14 Code: chr.weight Docs: coord
Position: 15 Code: coord Docs: layout
\S4method{autoplot}{Seqinfo}
Code: function(object, ideogram = FALSE, ...)
Docs: function(object, chr, ...)
Argument names in code not in docs:
ideogram
Argument names in docs not in code:
chr
Mismatches in argument names:
Position: 2 Code: ideogram Docs: chr
Codoc mismatches from documentation object 'coord':
coord_genome
Code: function(data, ...)
Docs: function()
Argument names in code not in docs:
data ...
Codoc mismatches from documentation object 'layout_circle':
\S4method{layout_circle}{GRanges}
Code: function(data, ..., geom = c("point", "line", "link", "ribbon",
"rect", "bar", "segment", "hist", "scale", "heatmap",
"ideogram", "text"), linked.to, radius = 10,
trackWidth = 5, space.skip = 0.015, direction =
c("clockwise", "anticlockwise"), link.fun =
function(x, y, n = 30) bezier(x, y, evaluation = n),
rect.inter.n = 60, rank, ylim = NULL, scale.n = 60,
scale.unit = NULL, scale.type = c("M", "B", "sci"),
grid.n = 5, grid.background = "gray70", grid.line =
"white", grid = FALSE, chr.weight = NULL)
Docs: function(data, ..., geom = c("point", "line", "link", "ribbon",
"rect", "bar", "segment", "hist", "scale", "heatmap",
"ideogram", "text"), linked.to, radius = 10,
trackWidth = 5, space.skip = 0.015, direction =
c("clockwise", "anticlockwise"), link.fun =
function(x, y, n = 30) bezier(x, y, evaluation = n),
rect.inter.n = 60, rank, ylim = NULL, scale.n = 60,
scale.unit = NULL, scale.type = c("M", "B", "sci"),
grid.n = 5, grid.background = "gray70", grid.line =
"white", grid = FALSE)
Argument names in code not in docs:
chr.weight
Codoc mismatches from documentation object 'layout_karyogram':
\S4method{layout_karyogram}{GRanges}
Code: function(data, ..., xlab, ylab, main, facets = seqnames ˜ .,
cytoband = FALSE, geom = "rect", stat = NULL, ylim =
NULL, rect.height = 10)
Docs: function(data, ..., xlab, ylab, main, facets = seqnames ˜ .,
cytoband = FALSE, geom = NULL, stat = NULL, ylim =
NULL, rect.height = 10)
Mismatches in argument default values:
Name: 'geom' Code: "rect" Docs: NULL
Codoc mismatches from documentation object 'plotGrandLinear':
plotGrandLinear
Code: function(obj, ..., facets, space.skip = 0.01, geom = NULL,
cutoff = NULL, cutoff.color = "red", cutoff.size = 1,
legend = FALSE, xlim, ylim, xlab, ylab, main,
highlight.gr = NULL, highlight.name = NULL,
highlight.col = "red", highlight.label = TRUE,
highlight.label.size = 5, highlight.label.offset =
0.05, highlight.label.col = "black")
Docs: function(obj, ..., facets, space.skip = 0.01, geom = NULL,
cutoff = NULL, cutoff.color = "red", cutoff.size = 1,
legend = FALSE, xlim, ylim, xlab, ylab, main)
Argument names in code not in docs:
highlight.gr highlight.name highlight.col highlight.label
highlight.label.size highlight.label.offset highlight.label.col
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'autoplot':
'single.ideo'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
'Makefile'
Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [11m/11m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 240.570 64.460 308.018
geom_alignment-method 52.082 2.571 54.770
tracks 45.945 0.631 46.627
layout_karyogram-method 34.804 0.219 35.114
plotRangesLinkedToData 32.243 2.339 34.740
geom_arrow-method 23.221 0.192 23.441
ggplot-method 16.324 1.733 18.182
stat_aggregate-method 17.099 0.208 17.321
layout_circle-method 16.157 0.341 16.528
plotGrandLinear 12.213 1.254 13.521
stat_reduce-method 11.493 0.675 12.184
stat_bin-method 7.863 0.829 8.718
geom_chevron-method 8.333 0.130 8.865
geom_rect-method 6.441 0.098 6.560
geom_arrowrect-method 6.329 0.082 7.632
scale_fill_giemsa 6.134 0.049 6.187
arrangeGrobByParsingLegend 5.972 0.102 6.077
stat_slice-method 5.324 0.352 5.683
stat_identity-method 4.758 0.620 5.390
* 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
WARNING: There were 4 warnings.
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/ggbio.Rcheck/00check.log'
for details.