BioC 3.2: CHECK report for ggbio on zin1

Package: ggbio

Version: 1.17.2

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ggbio_1.17.2.tar.gz

StartedAt: 2015-08-24 00:19:08 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:26:25 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 436.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ggbio.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ggbio_1.17.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ggbio.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.17.2’
* 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 ... [20s/20s] WARNING
Found the following significant warnings:
  Warning: 'eval' is deprecated.
See ‘/home/biocbuild/bbs-3.2-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’
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 : .local: no visible binding for global variable
  ‘variable’
autoplot,RangedSummarizedExperiment : .local: no visible binding for
  global variable ‘sset’
autoplot,RangedSummarizedExperiment : .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,VRanges : .local: no visible binding for global variable
  ‘midpoint’
autoplot,Views : .local: no visible binding for global variable ‘x’
autoplot,Views : .local: no visible binding for global variable ‘value’
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,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 : .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 ... [224s/225s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
autoplot-method         54.635  0.196  54.965
layout_karyogram-method 24.672  0.044  24.760
tracks                  24.225  0.024  24.738
geom_alignment-method   17.880  0.032  17.922
geom_arrow-method       10.790  0.012  10.830
plotRangesLinkedToData   9.840  0.052   9.885
stat_aggregate-method    9.103  0.008   9.105
ggplot-method            7.657  0.016   7.670
layout_circle-method     6.157  0.004   6.164
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [9s/9s]
 [10s/10s] 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-3.2-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)

name	user	system	elapsed
arrangeGrobByParsingLegend	2.916	0.020	2.936
autoplot-method	54.635	0.196	54.965
geom_alignment-method	17.880	0.032	17.922
geom_arch-method	1.554	0.008	1.564
geom_arrow-method	10.790	0.012	10.830
geom_arrowrect-method	3.014	0.004	3.017
geom_bar-method	0.965	0.004	0.968
geom_chevron-method	3.917	0.000	3.917
geom_rect-method	3.096	0.064	3.191
geom_segment-method	2.598	0.004	2.600
ggbio-class	0.006	0.000	0.005
ggplot-method	7.657	0.016	7.670
layout_circle-method	6.157	0.004	6.164
layout_karyogram-method	24.672	0.044	24.760
plotFragLength	0.000	0.000	0.001
plotGrandLinear	4.409	0.063	4.476
plotRangesLinkedToData	9.840	0.052	9.885
plotSingleChrom	0.001	0.000	0.000
plotSpliceSum	0.001	0.000	0.001
plotStackedOverview	0.000	0.004	0.001
rescale-method	0.093	0.004	0.098
scale_fill_fold_change	0.426	0.000	0.426
scale_fill_giemsa	3.698	0.000	3.705
scale_x_sequnit	0.237	0.000	0.237
stat_aggregate-method	9.103	0.008	9.105
stat_bin-method	4.827	0.004	4.849
stat_coverage-method	2.275	0.000	2.280
stat_gene-method	0.001	0.000	0.001
stat_identity-method	2.482	0.000	2.480
stat_reduce-method	4.021	0.008	4.041
stat_slice-method	3.095	0.000	3.094
stat_stepping-method	2.087	0.004	2.101
stat_table-method	1.423	0.004	1.426
theme	1.734	0.000	1.777
tracks	24.225	0.024	24.738