BioC 3.2: CHECK report for ggbio on oaxaca

Package: ggbio

Version: 1.18.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggbio_1.18.5.tar.gz

StartedAt: 2016-04-23 00:39:20 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:49:46 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 625.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ggbio.Rcheck

Warnings: 2

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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_1.18.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ggbio.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggbio/DESCRIPTION’ ... OK
* this is package ‘ggbio’ version ‘1.18.5’
* 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 ... [28s/30s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
See ‘/Users/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:
  ‘S4Vectors:::top_prenv’ ‘ggplot2:::add_ggplot’ ‘ggplot2:::cunion’
  ‘ggplot2:::rescale01’ ‘ggplot2:::set_last_plot’
  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
autoplot,matrix : .local: warning in scale_x_continuous(breaks = x,
  label = x.lab, expand = c(0, 0)): partial argument match of 'label'
  to 'labels'
autoplot,matrix : .local: warning in scale_x_continuous(breaks = NULL,
  label = NULL, expand = c(0, 0)): partial argument match of 'label' to
  'labels'
print,Ideogram : .local: warning in scale_y_continuous(breaks = 5,
  label = subchr): partial argument match of 'label' to 'labels'
.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’
getNR: no visible global function definition for ‘se’
getNR: no visible global function definition for ‘indexProbesProcessed’
getNR: no visible global function definition for ‘coefs’
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 ‘variable’
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 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 ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'PlotList,numeric,missing,ANY'
  generic '[' and siglist 'Tracks,numeric,missing,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See 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 ... [303s/334s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
autoplot-method         67.971  1.795  77.072
geom_alignment-method   38.941  0.975  41.213
tracks                  34.569  0.108  36.169
layout_karyogram-method 21.703  0.074  30.441
stat_aggregate-method   13.897  0.031  14.761
geom_arrow-method       12.247  0.037  12.912
plotRangesLinkedToData  11.472  0.246  11.806
ggplot-method            8.896  0.105   9.050
stat_reduce-method       8.713  0.257   9.128
layout_circle-method     7.499  0.032  10.300
stat_bin-method          6.980  0.042   7.059
plotGrandLinear          6.397  0.049   7.551
geom_arrowrect-method    4.839  0.038   5.043
geom_chevron-method      4.786  0.014   7.551
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [14s/14s]
 [14s/14s] 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: 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/ggbio.Rcheck/00check.log’
for details.

* installing *source* package ‘ggbio’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
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’
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
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
* DONE (ggbio)

name	user	system	elapsed
arrangeGrobByParsingLegend	3.643	0.038	3.741
autoplot-method	67.971	1.795	77.072
geom_alignment-method	38.941	0.975	41.213
geom_arch-method	1.817	0.012	1.830
geom_arrow-method	12.247	0.037	12.912
geom_arrowrect-method	4.839	0.038	5.043
geom_bar-method	1.527	0.007	1.535
geom_chevron-method	4.786	0.014	7.551
geom_rect-method	3.535	0.012	3.738
geom_segment-method	3.504	0.011	3.518
ggbio-class	0.007	0.000	0.007
ggplot-method	8.896	0.105	9.050
layout_circle-method	7.499	0.032	10.300
layout_karyogram-method	21.703	0.074	30.441
plotFragLength	0.001	0.000	0.001
plotGrandLinear	6.397	0.049	7.551
plotRangesLinkedToData	11.472	0.246	11.806
plotSingleChrom	0.000	0.000	0.001
plotSpliceSum	0.001	0.000	0.001
plotStackedOverview	0.002	0.000	0.002
rescale-method	0.186	0.001	0.209
scale_fill_fold_change	0.611	0.005	0.720
scale_fill_giemsa	3.578	0.013	3.901
scale_x_sequnit	0.452	0.002	0.470
stat_aggregate-method	13.897	0.031	14.761
stat_bin-method	6.980	0.042	7.059
stat_coverage-method	3.740	0.015	3.822
stat_gene-method	0.002	0.000	0.001
stat_identity-method	3.686	0.034	4.440
stat_reduce-method	8.713	0.257	9.128
stat_slice-method	3.782	0.027	4.281
stat_stepping-method	2.653	0.015	3.889
stat_table-method	1.563	0.007	1.629
theme	2.461	0.008	2.535
tracks	34.569	0.108	36.169