ggbio 1.16.1
Tengfei Yin
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ggbio | | Last Changed Rev: 106492 / Revision: 109384 | | Last Changed Date: 2015-07-16 10:07:13 -0700 (Thu, 16 Jul 2015) |
| zin2 | Linux (Ubuntu 14.04.2 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 ggbio_1.16.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ggbio.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.16.1’
* 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 ... [37s/38s] WARNING
Found the following significant warnings:
Warning: 'eval' is deprecated.
See ‘/Users/biocbuild/bbs-3.1-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 ... NOTE
Malformed Title field: should not end in a period.
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
stat_mismatch,BamFile : .local: warning in pileupAsGRanges(data, region
= which): partial argument match of 'region' to 'regions'
.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’
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’
Ideogram: no visible binding for global variable ‘cytobands’
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’
autoplot,ExpressionSet : .local: no visible binding for global variable
‘variable’
autoplot,SummarizedExperiment : .local: no visible binding for global
variable ‘sset’
autoplot,SummarizedExperiment : .local: no visible binding for global
variable ‘variable’
autoplot,TabixFile : .local: no visible global function definition for
‘file_ext’
autoplot,TabixFile : .local: no visible global function definition for
‘file_path_sans_ext’
autoplot,TabixFile : .local: no visible global function definition for
‘readVcf’
autoplot,VCF : .local: no visible binding for global variable
‘stepping’
autoplot,VCF : .local: no visible binding for global variable ‘value’
autoplot,Views : .local: no visible binding for global variable ‘x’
autoplot,Views : .local: no visible binding for global variable ‘value’
autoplot,VRanges : .local: no visible binding for global variable
‘midpoint’
geom_alignment,BamFile : .local: no visible binding for global variable
‘fl’
geom_alignment,BamFile : .local: no visible binding for global variable
‘stepping’
geom_alignment,OrganismDb : .local: no visible global function
definition for ‘select’
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’
layout_karyogram,GRanges : .local: no visible binding for global
variable ‘gieStain’
layout_karyogram,GRanges : .local: no visible binding for global
variable ‘x’
layout_karyogram,GRanges : .local: no visible binding for global
variable ‘y’
layout_karyogram,GRanges : .local: no visible binding for global
variable ‘xend’
layout_karyogram,GRanges : .local: no visible binding for global
variable ‘yend’
layout_karyogram,GRanges : .local: no visible binding for global
variable ‘y2’
layout_karyogram,GRanges : .local: no visible binding for global
variable ‘yend2’
layout_karyogram,GRanges : .local : <anonymous>: no visible binding for
global variable ‘name’
layout_karyogram,GRanges : .local : <anonymous>: no visible binding for
global variable ‘gieStain’
plotFragLength,character-GRanges : .local: no visible global function
definition for ‘qutoplot’
plotFragLength,character-GRanges : .local: no visible binding for
global variable ‘.fragLength’
stat_mismatch,GRanges : .local: no visible binding for global variable
‘sts’
stat_mismatch,GRanges : .local: no visible binding for global variable
‘eds’
stat_mismatch,GRanges : .local: no visible binding for global variable
‘read’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [421s/426s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 99.757 1.783 101.811
layout_karyogram-method 46.071 0.146 46.335
tracks 44.416 0.129 44.755
geom_alignment-method 34.013 0.159 34.213
stat_aggregate-method 19.297 0.051 19.696
plotRangesLinkedToData 18.545 0.439 19.388
geom_arrow-method 18.500 0.063 18.664
ggplot-method 14.856 0.132 15.027
layout_circle-method 11.241 0.029 11.274
stat_bin-method 8.668 0.057 8.742
plotGrandLinear 8.623 0.070 9.016
geom_chevron-method 8.131 0.027 8.172
stat_reduce-method 7.637 0.042 7.691
scale_fill_giemsa 7.156 0.044 7.204
geom_rect-method 5.872 0.023 7.036
geom_arrowrect-method 5.857 0.022 5.889
stat_slice-method 5.805 0.031 5.844
geom_segment-method 5.168 0.019 5.705
stat_identity-method 4.993 0.071 5.186
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’ [17s/17s]
[18s/18s] 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
* DONE
Status: 1 WARNING, 3 NOTEs
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/ggbio.Rcheck/00check.log’
for details.
* installing *source* package ‘ggbio’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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 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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (ggbio)