ggbio 1.12.10
Tengfei Yin
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/ggbio | | Last Changed Rev: 93626 / Revision: 95116 | | Last Changed Date: 2014-08-26 15:16:30 -0700 (Tue, 26 Aug 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ WARNINGS ] | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ggbio_1.12.10.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/ggbio.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.12.10’
* 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 ... [55s/56s] WARNING
Found the following significant warnings:
Warning: 'eval' is deprecated.
See ‘/Users/biocbuild/bbs-2.14-bioc/meat/ggbio.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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
* 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
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
.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’
bioplot: no visible global function definition for ‘autofacets’
bioplot: no visible global function definition for ‘normArg_geom’
bioplot: no visible global function definition for ‘normArg_mapping’
bioplot: no visible global function definition for ‘normArg_facets’
bioplot: no visible global function definition for ‘QueryLayer’
getNR: no visible global function definition for ‘se’
getNR: no visible global function definition for ‘indexProbesProcessed’
getNR: no visible global function definition for ‘coefs’
ggsave : default_name: no visible global function definition for
‘digest.ggplot’
Ideogram: no visible binding for global variable ‘ideoCyto’
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’
plotKaryogram: no visible binding for global variable ‘cytobands’
plotStackedOverview: no visible binding for global variable ‘cytobands’
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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '+' and siglist 'Bioplot,ANY'
generic 'names' and siglist 'Geom'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12m/12m] OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 169.015 2.589 173.089
geom_alignment-method 68.569 1.351 70.739
layout_karyogram-method 66.006 0.176 68.447
tracks 65.691 0.181 68.816
plotRangesLinkedToData 42.124 0.969 44.313
geom_arrow-method 31.650 0.089 32.111
stat_aggregate-method 30.528 0.062 30.691
ggplot-method 22.736 0.188 23.228
layout_circle-method 20.812 0.053 21.148
stat_reduce-method 17.854 0.384 18.313
plotGrandLinear 16.013 0.080 17.295
geom_chevron-method 13.706 0.051 13.931
stat_bin-method 12.729 0.071 13.042
geom_rect-method 10.504 0.056 10.794
geom_arrowrect-method 10.074 0.036 10.193
scale_fill_giemsa 9.782 0.029 9.854
geom_segment-method 8.662 0.032 8.724
stat_slice-method 7.810 0.034 8.056
arrangeGrobByParsingLegend 7.669 0.050 7.748
stat_stepping-method 7.032 0.027 7.258
stat_coverage-method 6.895 0.028 6.972
stat_identity-method 6.288 0.082 6.414
* checking for unstated dependencies in tests ... WARNING
'library' or 'require' call not declared from: ‘testthat’
* checking tests ...
Running ‘test-all.R’ [24s/25s]
[25s/25s] 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 were 3 warnings.
NOTE: There were 2 notes.
See
‘/Users/biocbuild/bbs-2.14-bioc/meat/ggbio.Rcheck/00check.log’
for details.
* installing *source* package ‘ggbio’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘rescale’ in package ‘ggbio’
Creating a new generic function for ‘xlim’ in package ‘ggbio’
Creating a generic function for ‘print’ from package ‘base’ in package ‘ggbio’
Warning: 'eval' is deprecated.
Use 'plotIdeogram' instead.
See help("Deprecated")
Creating a generic function for ‘summary’ from package ‘base’ in package ‘ggbio’
in method for ‘geom_alignment’ with signature ‘"OrganismDb"’: no definition for class “OrganismDb”
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’
in method for ‘autoplot’ with signature ‘"OrganismDb"’: no definition for class “OrganismDb”
Creating a generic function for ‘aggregate’ from package ‘stats’ in package ‘ggbio’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ggbio)