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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: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ggbio_1.6.6.tar.gz
StartedAt: 2013-03-24 23:45:36 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-25 00:00:57 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 920.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ggbio.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/ggbio.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.6.6'
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
autoplot-method            224.718 76.057 311.562
geom_alignment-method       38.172  1.889  40.694
tracks                      39.151  0.400  40.353
plotRangesLinkedToData      29.817  2.699  33.010
layout_karyogram-method     31.336  0.180  31.819
geom_arrow-method           19.193  0.155  19.520
stat_aggregate-method       17.391  0.196  17.692
layout_circle-method        16.651  0.387  17.205
ggplot-method               14.339  2.054  16.665
stat_reduce-method          11.898  0.624  12.679
plotGrandLinear             10.579  1.117  11.978
stat_bin-method              7.720  1.014   8.910
geom_chevron-method          7.612  0.071   7.748
scale_fill_giemsa            6.114  0.035   6.199
arrangeGrobByParsingLegend   5.550  0.093   5.673
geom_arrowrect-method        5.521  0.050   5.609
stat_slice-method            5.108  0.435   5.612
geom_rect-method             5.454  0.051   5.536
stat_identity-method         4.645  0.704   5.749
* 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
  '/Users/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
arrangeGrobByParsingLegend5.5500.0935.673
autoplot-method224.718 76.057311.562
geom_alignment-method38.172 1.88940.694
geom_arch-method3.1810.4073.903
geom_arrow-method19.193 0.15519.520
geom_arrowrect-method5.5210.0505.609
geom_bar-method1.6910.0291.731
geom_chevron-method7.6120.0717.748
geom_rect-method5.4540.0515.536
geom_segment-method4.8280.0454.899
ggbio-class0.0080.0000.008
ggplot-method14.339 2.05416.665
layout_circle-method16.651 0.38717.205
layout_karyogram-method31.336 0.18031.819
mold-method2.7160.4263.353
plotFragLength0.0000.0000.001
plotGrandLinear10.579 1.11711.978
plotRangesLinkedToData29.817 2.69933.010
plotSingleChrom0.0000.0010.000
plotSpliceSum000
plotStackedOverview0.0000.0000.001
rescale-method0.1620.0030.166
scale_fill_fold_change0.8200.3411.175
scale_fill_giemsa6.1140.0356.199
scale_x_sequnit0.5020.0110.518
stat_aggregate-method17.391 0.19617.692
stat_bin-method7.7201.0148.910
stat_coverage-method3.7090.0683.816
stat_gene-method0.0010.0000.000
stat_identity-method4.6450.7045.749
stat_reduce-method11.898 0.62412.679
stat_slice-method5.1080.4355.612
stat_stepping-method3.9320.0324.032
stat_table-method2.9820.3733.458
theme3.3670.0343.425
tracks39.151 0.40040.353