ggbio 1.8.8
Tengfei Yin
| Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/ggbio | | Last Changed Rev: 81156 / Revision: 81334 | | Last Changed Date: 2013-10-04 11:18:52 -0700 (Fri, 04 Oct 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 |
* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ggbio.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggbio/DESCRIPTION’ ... OK
* this is package ‘ggbio’ version ‘1.8.8’
* 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 ... [44s/46s] 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 364.003 1.768 369.695
tracks 61.876 0.208 62.440
plotRangesLinkedToData 48.259 0.340 48.677
geom_alignment-method 43.211 0.392 43.605
layout_karyogram-method 29.142 0.064 29.384
geom_arrow-method 25.650 0.036 25.760
stat_aggregate-method 24.241 0.032 24.401
layout_circle-method 21.589 0.024 21.670
ggplot-method 18.093 0.040 18.244
stat_bin-method 13.969 0.028 14.452
stat_reduce-method 11.965 0.216 12.312
plotGrandLinear 11.073 0.032 11.105
arrangeGrobByParsingLegend 10.500 0.080 10.602
geom_chevron-method 10.509 0.024 10.952
scale_fill_giemsa 9.321 0.012 9.385
geom_rect-method 7.792 0.036 8.004
geom_arrowrect-method 7.408 0.004 7.900
stat_identity-method 6.824 0.048 6.913
stat_slice-method 6.560 0.012 6.577
geom_segment-method 6.097 0.072 6.467
stat_coverage-method 6.069 0.020 6.124
* 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
‘/home/biocbuild/bbs-2.12-bioc/meat/ggbio.Rcheck/00check.log’
for details.