Back to the "Multiple platform build/check report" A  B  C  D  E  F [G] H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.12: CHECK report for ggbio on moscato2

This page was generated on 2013-10-09 09:39:02 -0700 (Wed, 09 Oct 2013).

Package 279/671HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: ggbio
Version: 1.8.8
Command: rm -rf ggbio.buildbin-libdir && mkdir ggbio.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggbio.buildbin-libdir ggbio_1.8.8.tar.gz >ggbio-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=ggbio.buildbin-libdir --install="check:ggbio-install.out" --force-multiarch --no-vignettes --timings ggbio_1.8.8.tar.gz && mv ggbio.buildbin-libdir/* ggbio.Rcheck/ && rmdir ggbio.buildbin-libdir
StartedAt: 2013-10-09 02:19:43 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:46:29 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 1606.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ggbio.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/ggbio.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '1.8.8'
* 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 whether package 'ggbio' can be installed ... 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
* 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'
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 ...
** running examples for arch 'i386' ... [586s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
autoplot-method            232.12   1.45  234.56
tracks                      47.25   0.23   47.79
geom_alignment-method       41.21   0.83   42.06
plotRangesLinkedToData      34.74   0.88   35.64
layout_karyogram-method     23.97   0.03   24.04
geom_arrow-method           20.67   0.08   20.75
layout_circle-method        17.88   0.05   17.92
ggplot-method               16.47   0.10   16.58
stat_aggregate-method       16.13   0.01   16.15
stat_reduce-method          12.98   0.59   13.58
plotGrandLinear             10.90   0.07   10.98
stat_bin-method             10.33   0.03   10.48
arrangeGrobByParsingLegend   8.45   0.06    8.52
scale_fill_giemsa            8.02   0.03    8.05
geom_chevron-method          7.93   0.03    8.49
geom_rect-method             7.07   0.05    7.27
stat_slice-method            6.61   0.03    6.64
geom_arrowrect-method        6.51   0.02    6.63
stat_identity-method         5.22   0.04    5.26
geom_segment-method          5.10   0.02    5.12
** running examples for arch 'x64' ... [11m] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
autoplot-method            258.67   1.22  260.99
tracks                      55.17   0.19   55.77
geom_alignment-method       43.62   0.73   44.38
plotRangesLinkedToData      39.24   0.86   40.21
geom_arrow-method           26.21   0.01   26.22
layout_karyogram-method     26.01   0.08   26.44
stat_aggregate-method       21.47   0.06   21.60
layout_circle-method        20.71   0.02   20.74
ggplot-method               17.47   0.09   17.58
stat_reduce-method          12.26   0.39   12.87
stat_bin-method             11.92   0.05   12.03
geom_chevron-method         11.31   0.03   11.34
plotGrandLinear             10.88   0.03   10.92
scale_fill_giemsa            9.62   0.02    9.64
arrangeGrobByParsingLegend   7.65   0.04    7.69
geom_rect-method             7.38   0.00    7.38
geom_segment-method          7.37   0.00    7.55
geom_arrowrect-method        6.87   0.03    6.89
stat_slice-method            6.28   0.10    6.37
stat_identity-method         5.97   0.03    6.00
stat_stepping-method         5.61   0.05    5.69
stat_coverage-method         4.79   0.01    5.06
* 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
  'E:/biocbld/bbs-2.12-bioc/meat/ggbio.Rcheck/00check.log'
for details.

ggbio.Rcheck/00install.out:


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
** 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_1.8.8.zip
* DONE (ggbio)