ggbio 1.19.0
Tengfei Yin
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggbio | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ggbio_1.19.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ggbio.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggbio/DESCRIPTION’ ... OK
* this is package ‘ggbio’ version ‘1.19.0’
* 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 ... [19s/19s] WARNING
Found the following significant warnings:
Warning: 'eval' is deprecated.
See ‘/home/biocbuild/bbs-3.3-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: 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’
Ideogram: no visible binding for global variable ‘ideoCyto’
Ideogram: no visible binding for global variable ‘cytobands’
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’
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’
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’
autoplot,ExpressionSet: no visible binding for global variable
‘variable’
autoplot,RangedSummarizedExperiment: no visible binding for global
variable ‘sset’
autoplot,RangedSummarizedExperiment: no visible binding for global
variable ‘variable’
autoplot,TabixFile: no visible global function definition for
‘file_ext’
autoplot,TabixFile: no visible global function definition for
‘file_path_sans_ext’
autoplot,TabixFile: no visible global function definition for ‘readVcf’
autoplot,VCF: no visible binding for global variable ‘stepping’
autoplot,VCF: no visible binding for global variable ‘value’
autoplot,VRanges: no visible binding for global variable ‘midpoint’
autoplot,Views: no visible binding for global variable ‘x’
autoplot,Views: no visible binding for global variable ‘value’
geom_alignment,BamFile: no visible binding for global variable ‘fl’
geom_alignment,BamFile: no visible binding for global variable
‘stepping’
geom_alignment,OrganismDb: no visible global function definition for
‘select’
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’
layout_karyogram,GRanges: no visible binding for global variable
‘gieStain’
layout_karyogram,GRanges: no visible binding for global variable ‘x’
layout_karyogram,GRanges: no visible binding for global variable ‘y’
layout_karyogram,GRanges: no visible binding for global variable ‘xend’
layout_karyogram,GRanges: no visible binding for global variable ‘yend’
layout_karyogram,GRanges: no visible binding for global variable ‘y2’
layout_karyogram,GRanges: no visible binding for global variable
‘yend2’
layout_karyogram,GRanges : <anonymous>: no visible binding for global
variable ‘name’
layout_karyogram,GRanges : <anonymous>: no visible binding for global
variable ‘gieStain’
plotFragLength,character-GRanges: no visible global function definition
for ‘qutoplot’
plotFragLength,character-GRanges: no visible binding for global
variable ‘.fragLength’
stat_mismatch,GRanges: no visible binding for global variable ‘sts’
stat_mismatch,GRanges: no visible binding for global variable ‘eds’
stat_mismatch,GRanges: no visible binding for global variable ‘read’
Undefined global functions or variables:
.fragLength .layout_circle.geoms .layout_circle.stats .x breaks coefs
cytobands digest.ggplot eds fe file_ext file_path_sans_ext fl
gieStain ideoCyto indexProbesProcessed lgrobs midpoint mt name
qutoplot read readVcf se select sset stepping sts value variable x
xend y y.text y2 yend yend2
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [222s/223s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 55.313 0.255 55.610
geom_alignment-method 31.332 0.080 31.435
tracks 22.356 0.004 22.723
layout_karyogram-method 20.072 0.046 20.133
plotRangesLinkedToData 11.510 0.108 11.635
stat_aggregate-method 8.121 0.000 8.121
geom_arrow-method 7.730 0.004 7.741
stat_reduce-method 6.760 0.016 6.778
ggplot-method 5.935 0.004 5.947
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-all.R’ [9s/9s]
[9s/9s] 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
‘/home/biocbuild/bbs-3.3-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 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
* DONE (ggbio)