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 |
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ggbio.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ggbio’ can be installed ... [40s/41s] 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
* 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
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'
Ideogram: warning in getIdeogram(genome = genome, subchr = subchr,
cytoband = cytoband): partial argument match of 'cytoband' to
'cytobands'
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’
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’
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’
height,gg: no visible binding for global variable ‘mt’
height,GGbio: no visible binding for global variable ‘mt’
height,Tracked: 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 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 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 ... [11m/11m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 243.904 17.387 265.162
tracks 53.086 0.674 54.507
geom_alignment-method 36.682 1.051 38.461
layout_karyogram-method 37.293 0.408 38.330
plotRangesLinkedToData 26.675 1.760 28.719
geom_arrow-method 23.575 0.199 24.011
stat_aggregate-method 20.927 0.168 21.625
ggplot-method 17.973 0.637 18.940
layout_circle-method 14.796 0.181 15.260
plotGrandLinear 11.888 0.160 12.289
stat_reduce-method 11.017 0.382 11.562
stat_bin-method 9.759 0.207 10.168
geom_chevron-method 9.335 0.134 9.632
geom_arrowrect-method 7.650 0.137 7.900
arrangeGrobByParsingLegend 7.403 0.127 7.588
scale_fill_giemsa 7.155 0.073 7.363
geom_rect-method 7.049 0.095 7.231
stat_slice-method 6.842 0.150 7.103
geom_segment-method 6.835 0.093 6.988
stat_identity-method 6.605 0.205 6.944
stat_stepping-method 5.875 0.127 6.114
stat_coverage-method 5.610 0.099 5.788
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘test-all.R’ [18s/19s]
[19s/19s] 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
‘/Users/biocbuild/bbs-2.13-bioc/meat/ggbio.Rcheck/00check.log’
for details.