Package: ggbio

Version: 1.6.6

Command: rm -rf ggbio.buildbin-libdir && mkdir ggbio.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggbio.buildbin-libdir ggbio_1.6.6.tar.gz >ggbio-install.out 2>&1 && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD check --library=ggbio.buildbin-libdir --install="check:ggbio-install.out" --force-multiarch --no-vignettes --timings ggbio_1.6.6.tar.gz && mv ggbio.buildbin-libdir/* ggbio.Rcheck/ && rmdir ggbio.buildbin-libdir

StartedAt: 2013-03-25 01:15:21 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:37:10 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 1308.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ggbio.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/ggbio.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggbio/DESCRIPTION' ... OK
* this is package 'ggbio' version '1.6.6'
* 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 whether package 'ggbio' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
* checking package directory ... OK
* checking for portable file names ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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'
plotIdeogram: no visible binding for global variable 'x1'
plotIdeogram: no visible binding for global variable 'x2'
plotSingleChrom: no visible binding for global variable 'x1'
plotSingleChrom: no visible binding for global variable 'x2'
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
autoplot-method            181.35   0.69  182.60
tracks                      40.36   0.14   40.55
geom_alignment-method       33.00   0.64   33.67
layout_karyogram-method     29.32   0.03   29.35
plotRangesLinkedToData      23.87   0.35   24.21
geom_arrow-method           17.51   0.01   17.54
stat_aggregate-method       15.91   0.00   15.92
layout_circle-method        15.02   0.01   15.05
ggplot-method               11.84   0.03   11.99
stat_reduce-method          11.35   0.19   11.55
stat_bin-method              8.88   0.02    8.94
plotGrandLinear              8.77   0.01    8.79
stat_slice-method            8.24   0.04    8.29
geom_chevron-method          6.55   0.02    6.57
stat_stepping-method         5.46   0.00    5.46
arrangeGrobByParsingLegend   5.29   0.08    5.37
scale_fill_giemsa            5.35   0.00    5.35
geom_rect-method             5.12   0.00    5.16
geom_arrowrect-method        5.09   0.02    5.10
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
autoplot-method            203.24   0.70  204.45
tracks                      46.97   0.12   47.44
geom_alignment-method       33.34   0.33   33.66
plotRangesLinkedToData      30.74   0.66   31.39
layout_karyogram-method     30.76   0.01   30.92
geom_arrow-method           19.66   0.00   19.66
stat_aggregate-method       17.84   0.00   17.85
layout_circle-method        17.37   0.03   17.41
ggplot-method               14.18   0.06   14.77
stat_reduce-method          11.73   0.22   11.95
stat_bin-method             11.56   0.07   12.31
plotGrandLinear             10.25   0.03   10.48
stat_identity-method         7.76   0.02    7.76
geom_chevron-method          6.93   0.02    6.94
scale_fill_giemsa            6.47   0.03    6.51
stat_coverage-method         5.73   0.01    5.74
stat_slice-method            5.53   0.01    5.54
stat_stepping-method         5.36   0.03    5.40
geom_segment-method          5.37   0.02    5.49
arrangeGrobByParsingLegend   5.31   0.04    5.42
theme                        5.32   0.00    5.67
geom_rect-method             4.93   0.03    5.57
* 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 3 notes.
See
  'D:/biocbld/bbs-2.11-bioc/meat/ggbio.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ggbio' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'rescale' in package 'ggbio'
Creating a generic function for 'summary' from package 'base' in package 'ggbio'
Creating a generic function for 'print' from package 'base' in package 'ggbio'
Creating a new generic function for 'xlim' in package 'ggbio'
Creating a generic function for 'update' from package 'stats' in package 'ggbio'
Creating a new generic function for 'geom_rect' in package 'ggbio'
Creating a new generic function for 'geom_segment' in package 'ggbio'
Creating a new generic function for 'geom_bar' in package 'ggbio'
Creating a new generic function for 'stat_identity' in package 'ggbio'
Creating a new generic function for 'stat_bin' in package 'ggbio'
** help
*** installing help indices
** building package indices
** installing vignettes
   'ggbio.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'ggbio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggbio' as ggbio_1.6.6.zip

* DONE (ggbio)