ggbio 1.8.2
Tengfei Yin
| Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/ggbio | | Last Changed Rev: 75327 / Revision: 76155 | | Last Changed Date: 2013-04-04 19:46:27 -0700 (Thu, 04 Apr 2013) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | WARNINGS | OK |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ggbio.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ggbio/DESCRIPTION' ... OK
* this is package 'ggbio' version '1.8.2'
* 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 ... [34s/35s] 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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 ... [13m/13m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 292.724 28.747 328.096
geom_alignment-method 59.509 1.896 62.374
tracks 50.169 0.759 51.890
plotRangesLinkedToData 43.930 2.208 47.212
layout_karyogram-method 40.894 0.397 41.828
geom_arrow-method 23.352 0.341 24.263
stat_aggregate-method 21.518 0.213 22.150
layout_circle-method 20.409 0.359 21.099
ggplot-method 19.230 1.125 20.818
stat_reduce-method 17.646 0.625 18.553
plotGrandLinear 12.685 0.523 13.436
stat_bin-method 10.944 0.441 11.704
geom_chevron-method 9.358 0.125 9.725
arrangeGrobByParsingLegend 8.335 0.134 8.817
scale_fill_giemsa 7.733 0.078 8.104
geom_rect-method 6.772 0.146 7.032
geom_arrowrect-method 6.803 0.089 7.043
stat_slice-method 6.405 0.199 6.727
stat_identity-method 5.909 0.310 6.342
geom_segment-method 5.852 0.092 6.155
stat_stepping-method 4.846 0.072 5.031
* 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 was 1 warning.
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/ggbio.Rcheck/00check.log'
for details.