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Package 256/609HostnameOS / ArchBUILDCHECKBUILD BIN
ggbio 1.6.6
Tengfei Yin
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/ggbio
Last Changed Rev: 72747 / Revision: 74773
Last Changed Date: 2013-01-21 14:58:26 -0800 (Mon, 21 Jan 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: ggbio
Version: 1.6.6
Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings ggbio_1.6.6.tar.gz
StartedAt: 2013-03-25 01:34:51 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:50:12 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 920.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ggbio.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ggbio.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.6.6’
* 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  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
* 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 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’
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 ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
autoplot-method            233.266  1.112 275.279
tracks                      41.174  0.448  44.578
geom_alignment-method       34.834  0.568  36.414
layout_karyogram-method     32.162  0.168  34.673
plotRangesLinkedToData      31.010  0.352  33.725
geom_arrow-method           21.161  0.160  22.830
layout_circle-method        17.874  0.076  18.662
stat_aggregate-method       17.625  0.104  19.003
ggplot-method               14.480  0.088  15.340
plotGrandLinear             10.984  0.048  11.593
stat_reduce-method          10.257  0.200  11.420
geom_chevron-method          7.945  0.092   8.753
stat_bin-method              7.752  0.024   7.909
scale_fill_giemsa            6.653  0.040   7.172
arrangeGrobByParsingLegend   6.057  0.060   6.335
geom_rect-method             5.500  0.056   5.831
stat_slice-method            5.392  0.020   5.867
geom_arrowrect-method        5.104  0.016   5.301
stat_identity-method         5.076  0.036   5.359
* 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
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/ggbio.Rcheck/00check.log’
for details.

ggbio.Rcheck/00install.out:

* 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

* DONE (ggbio)

ggbio.Rcheck/ggbio-Ex.timings:

nameusersystemelapsed
arrangeGrobByParsingLegend6.0570.0606.335
autoplot-method233.266 1.112275.279
geom_alignment-method34.834 0.56836.414
geom_arch-method2.5610.0242.862
geom_arrow-method21.161 0.16022.830
geom_arrowrect-method5.1040.0165.301
geom_bar-method1.5400.0121.641
geom_chevron-method7.9450.0928.753
geom_rect-method5.5000.0565.831
geom_segment-method4.7690.0164.950
ggbio-class0.0080.0000.010
ggplot-method14.480 0.08815.340
layout_circle-method17.874 0.07618.662
layout_karyogram-method32.162 0.16834.673
mold-method2.6720.0362.913
plotFragLength000
plotGrandLinear10.984 0.04811.593
plotRangesLinkedToData31.010 0.35233.725
plotSingleChrom000
plotSpliceSum0.0000.0000.001
plotStackedOverview0.0000.0000.007
rescale-method0.1720.0040.350
scale_fill_fold_change0.8240.0161.240
scale_fill_giemsa6.6530.0407.172
scale_x_sequnit0.5080.0000.532
stat_aggregate-method17.625 0.10419.003
stat_bin-method7.7520.0247.909
stat_coverage-method3.4650.0243.560
stat_gene-method0.0000.0000.001
stat_identity-method5.0760.0365.359
stat_reduce-method10.257 0.20011.420
stat_slice-method5.3920.0205.867
stat_stepping-method3.9640.0084.149
stat_table-method2.9560.0083.082
theme3.6650.0123.703
tracks41.174 0.44844.578