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BioC 2.13: CHECK report for ggbio on moscato1

This page was generated on 2014-04-05 09:50:31 -0700 (Sat, 05 Apr 2014).

Package 308/750HostnameOS / ArchBUILDCHECKBUILD BIN
ggbio 1.10.16
Tengfei Yin
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/ggbio
Last Changed Rev: 88437 / Revision: 88450
Last Changed Date: 2014-04-04 11:55:00 -0700 (Fri, 04 Apr 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: ggbio
Version: 1.10.16
Command: rm -rf ggbio.buildbin-libdir && mkdir ggbio.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ggbio.buildbin-libdir ggbio_1.10.16.tar.gz >ggbio-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=ggbio.buildbin-libdir --install="check:ggbio-install.out" --force-multiarch --no-vignettes --timings ggbio_1.10.16.tar.gz && mv ggbio.buildbin-libdir/* ggbio.Rcheck/ && rmdir ggbio.buildbin-libdir
StartedAt: 2014-04-05 04:11:34 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:36:27 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 1493.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ggbio.Rcheck
Warnings: 1

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/ggbio.Rcheck'
* using R version 3.0.3 (2014-03-06)
* 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 '1.10.16'
* 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 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'ggplot2'
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'Biobase'
  All declared Imports should be used.
':::' calls which should be '::':
  'biovizBase:::flatGrl' 'biovizBase:::isIdeogram'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'ggplot2:::add_ggplot' 'ggplot2:::cunion' 'ggplot2:::rescale01'
  'ggplot2:::set_last_plot' 'ggplot2:::zeroGrob'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Ideogram: warning in getIdeogram(genome = genome, subchr = subchr,
  cytoband = cytoband): partial argument match of 'cytoband' to
  'cytobands'
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'
plotKaryogram: warning in getIdeogram(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'
.combineNames: no visible binding for global variable
  '.layout_circle.geoms'
.combineNames: no visible binding for global variable
  '.layout_circle.stats'
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'
align.plots: no visible binding for global variable 'lgrobs'
alignPlots: no visible binding for global variable 'lgrobs'
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'
height,GGbio: no visible binding for global variable 'mt'
height,Tracked: no visible binding for global variable 'mt'
height,gg: no visible binding for global variable 'mt'
* checking Rd files ... NOTE
prepare_Rd: Grob-class.Rd:22-24: Dropping empty section \usage
prepare_Rd: Grob-class.Rd:25-26: Dropping empty section \arguments
prepare_Rd: Grob-class.Rd:29-30: Dropping empty section \details
prepare_Rd: Grob-class.Rd:27-28: Dropping empty section \value
prepare_Rd: Grob-class.Rd:31-32: Dropping empty section \references
prepare_Rd: Grob-class.Rd:33-34: Dropping empty section \seealso
prepare_Rd: Grob-class.Rd:35-36: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'tracks':
tracks
  Code: function(..., heights, xlim, xlab = NULL, main = NULL, title =
                 NULL, theme = NULL, track.plot.color = NULL,
                 track.bg.color = NULL, main.height = unit(1.5,
                 "lines"), scale.height = unit(1, "lines"), xlab.height
                 = unit(1.5, "lines"), padding = unit(-1, "lines"),
                 labeled = NULL, label.bg.color = "white",
                 label.bg.fill = "gray80", label.text.color = "black",
                 label.text.cex = 1, label.width = unit(2.5, "lines"))
  Docs: function(..., heights, xlim, xlab = NULL, main = NULL, title =
                 NULL, theme = NULL, track.plot.color = NULL,
                 track.bg.color = NULL, main.height = unit(2, "lines"),
                 scale.height = unit(2, "lines"), xlab.height = unit(2,
                 "lines"), padding = unit(-1, "lines"), labeled = NULL,
                 label.bg.color = "white", label.bg.fill = "gray80",
                 label.text.color = "black", label.text.cex = 1,
                 label.width = unit(2.5, "lines"))
  Mismatches in argument default values:
    Name: 'main.height' Code: unit(1.5, "lines") Docs: unit(2, "lines")
    Name: 'scale.height' Code: unit(1, "lines") Docs: unit(2, "lines")
    Name: 'xlab.height' Code: unit(1.5, "lines") Docs: unit(2, "lines")

* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'ggbio.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [525s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
autoplot-method            188.50   0.92  191.93
tracks                      48.99   0.15   49.35
geom_alignment-method       33.12   0.41   34.56
layout_karyogram-method     31.12   0.11   31.32
plotRangesLinkedToData      25.63   0.51   26.18
stat_aggregate-method       20.79   0.00   20.79
geom_arrow-method           18.87   0.03   18.91
ggplot-method               14.94   0.08   15.05
stat_bin-method             12.12   0.00   12.12
layout_circle-method        11.07   0.00   11.08
stat_reduce-method          10.63   0.19   10.82
plotGrandLinear              9.61   0.08   10.73
geom_chevron-method          9.50   0.05    9.61
geom_rect-method             7.20   0.03    7.24
stat_identity-method         6.33   0.03    6.37
geom_arrowrect-method        6.30   0.03    6.37
stat_slice-method            6.30   0.03    6.33
stat_stepping-method         6.13   0.03    6.16
scale_fill_giemsa            5.99   0.00    5.99
arrangeGrobByParsingLegend   5.08   0.03    5.11
** running examples for arch 'x64' ... [594s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
autoplot-method            214.36   0.94  215.53
tracks                      53.06   0.19   53.43
layout_karyogram-method     39.05   0.01   39.22
geom_alignment-method       35.08   0.46   35.55
plotRangesLinkedToData      28.58   0.36   28.96
geom_arrow-method           26.03   0.09   26.47
stat_aggregate-method       21.89   0.03   21.95
ggplot-method               19.07   0.03   19.10
layout_circle-method        16.53   0.02   16.55
stat_bin-method             11.73   0.02   11.75
plotGrandLinear             11.11   0.04   11.15
arrangeGrobByParsingLegend   9.35   0.05    9.40
geom_chevron-method          9.33   0.04    9.43
stat_reduce-method           9.09   0.16    9.89
scale_fill_giemsa            7.97   0.05    8.02
geom_rect-method             7.55   0.03    7.58
geom_arrowrect-method        7.52   0.03    7.58
geom_segment-method          7.44   0.01    7.46
stat_slice-method            6.30   0.03    6.33
stat_identity-method         5.68   0.00    5.74
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'test-all.R' [12s]
 [12s] OK
** running tests for arch 'x64'
  Running 'test-all.R' [12s]
 [13s] OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 6 notes.
See
  'D:/biocbld/bbs-2.13-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
in method for 'getLimits' with signature '"GGbio"': no definition for class "GGbio"
in method for 'getLimits' with signature '"ggplotPlot"': no definition for class "ggplotPlot"
in method for 'getLimits' with signature '"ggbioPlot"': no definition for class "ggbioPlot"
Creating a new generic function for 'rescale' in package 'ggbio'
Creating a new generic function for 'xlim' in package 'ggbio'
in method for 'labeled' with signature '"Ideogram"': no definition for class "Ideogram"
in method for 'labeled<-' with signature '"Ideogram","logical"': no definition for class "Ideogram"
Creating a generic function for 'print' from package 'base' in package 'ggbio'
NOTE: arguments in definition for validity method for class 'PlotList' changed from (x) to (object)
Creating a generic function for 'summary' from package 'base' 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_1.10.16.zip
* DONE (ggbio)

ggbio.Rcheck/examples_i386/ggbio-Ex.timings:

nameusersystemelapsed
arrangeGrobByParsingLegend5.080.035.11
autoplot-method188.50 0.92191.93
geom_alignment-method33.12 0.4134.56
geom_arch-method2.340.012.35
geom_arrow-method18.87 0.0318.91
geom_arrowrect-method6.300.036.37
geom_bar-method1.70.01.7
geom_chevron-method9.500.059.61
geom_rect-method7.200.037.24
geom_segment-method4.840.084.92
ggbio-class0.020.000.01
ggplot-method14.94 0.0815.05
layout_circle-method11.07 0.0011.08
layout_karyogram-method31.12 0.1131.32
mold-method1.890.061.95
plotFragLength000
plotGrandLinear 9.61 0.0810.73
plotRangesLinkedToData25.63 0.5126.18
plotSingleChrom0.010.000.01
plotSpliceSum000
plotStackedOverview0.350.000.35
rescale-method0.150.000.15
scale_fill_fold_change0.690.000.69
scale_fill_giemsa5.990.005.99
scale_x_sequnit0.690.000.69
stat_aggregate-method20.79 0.0020.79
stat_bin-method12.12 0.0012.12
stat_coverage-method4.880.004.88
stat_gene-method0.070.000.06
stat_identity-method6.330.036.37
stat_reduce-method10.63 0.1910.82
stat_slice-method6.300.036.33
stat_stepping-method6.130.036.16
stat_table-method3.460.043.49
theme3.770.033.80
tracks48.99 0.1549.35

ggbio.Rcheck/examples_x64/ggbio-Ex.timings:

nameusersystemelapsed
arrangeGrobByParsingLegend9.350.059.40
autoplot-method214.36 0.94215.53
geom_alignment-method35.08 0.4635.55
geom_arch-method2.690.022.70
geom_arrow-method26.03 0.0926.47
geom_arrowrect-method7.520.037.58
geom_bar-method2.730.002.73
geom_chevron-method9.330.049.43
geom_rect-method7.550.037.58
geom_segment-method7.440.017.46
ggbio-class0.010.000.01
ggplot-method19.07 0.0319.10
layout_circle-method16.53 0.0216.55
layout_karyogram-method39.05 0.0139.22
mold-method1.920.041.95
plotFragLength000
plotGrandLinear11.11 0.0411.15
plotRangesLinkedToData28.58 0.3628.96
plotSingleChrom000
plotSpliceSum000
plotStackedOverview0.020.000.02
rescale-method0.170.000.17
scale_fill_fold_change1.110.001.11
scale_fill_giemsa7.970.058.02
scale_x_sequnit0.710.000.72
stat_aggregate-method21.89 0.0321.95
stat_bin-method11.73 0.0211.75
stat_coverage-method4.540.044.58
stat_gene-method000
stat_identity-method5.680.005.74
stat_reduce-method9.090.169.89
stat_slice-method6.300.036.33
stat_stepping-method4.360.014.47
stat_table-method2.950.023.60
theme3.610.003.62
tracks53.06 0.1953.43