BioC 3.4: CHECK report for ggbio on malbec1

Package: ggbio

Version: 1.22.4

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ggbio_1.22.4.tar.gz

StartedAt: 2017-04-14 22:53:18 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:02:02 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 523.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: ggbio.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ggbio_1.22.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ggbio.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.22.4’
* 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 ... WARNING
Found the following significant warnings:
  Warning: subclass "SymbolFilter" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
  Warning: subclass "OnlyCodingTx" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
See ‘/home/biocbuild/bbs-3.4-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:::rename_aes' '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: warning in scale_x_continuous(breaks = x, label =
  x.lab, expand = c(0, 0)): partial argument match of 'label' to
  'labels'
autoplot,matrix: warning in scale_x_continuous(breaks = NULL, label =
  NULL, expand = c(0, 0)): partial argument match of 'label' to
  'labels'
print,Ideogram: 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 global function definition for 'data'
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: no visible binding for global variable
  'variable'
autoplot,RangedSummarizedExperiment: no visible binding for global
  variable 'variable'
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'
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 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.stats .x breaks coefs cytobands data eds
  fe fl gieStain ideoCyto indexProbesProcessed midpoint mt name read se
  stepping sts value variable x xend y y.text y2 yend yend2
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 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 ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
autoplot-method         78.984  0.284  79.414
geom_alignment-method   33.876  0.168  34.068
tracks                  32.328  0.016  32.377
layout_karyogram-method 22.120  0.100  22.248
plotRangesLinkedToData  10.812  0.132  10.951
geom_arrow-method        9.632  0.000   9.639
stat_reduce-method       8.596  0.060   8.678
stat_aggregate-method    8.292  0.004   8.306
ggplot-method            7.244  0.004   7.253
layout_circle-method     6.388  0.000   6.394
stat_bin-method          5.984  0.000   5.988
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/ggbio.Rcheck/00check.log’
for details.

* installing *source* package ‘ggbio’ ...
** R
** inst
** preparing package for lazy loading
Warning: subclass "SymbolFilter" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "OnlyCodingTx" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "SymbolFilter" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "OnlyCodingTx" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Creating a new generic function for 'rescale' in package 'ggbio'
Creating a new generic function for 'xlim' 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
* DONE (ggbio)

name	user	system	elapsed
arrangeGrobByParsingLegend	3.348	0.016	3.368
autoplot-method	78.984	0.284	79.414
geom_alignment-method	33.876	0.168	34.068
geom_arch-method	1.792	0.000	1.795
geom_arrow-method	9.632	0.000	9.639
geom_arrowrect-method	3.140	0.000	3.142
geom_bar-method	1.192	0.004	1.197
geom_chevron-method	3.940	0.004	3.944
geom_rect-method	3.076	0.000	3.078
geom_segment-method	2.816	0.000	2.819
ggbio-class	0.004	0.000	0.005
ggplot-method	7.244	0.004	7.253
layout_circle-method	6.388	0.000	6.394
layout_karyogram-method	22.120	0.100	22.248
plotFragLength	0.000	0.000	0.001
plotGrandLinear	4.720	0.136	4.865
plotRangesLinkedToData	10.812	0.132	10.951
plotSingleChrom	0.000	0.000	0.001
plotSpliceSum	0.000	0.000	0.001
plotStackedOverview	0.004	0.000	0.001
rescale-method	0.124	0.000	0.126
scale_fill_fold_change	0.412	0.004	0.417
scale_fill_giemsa	3.296	0.000	3.298
scale_x_sequnit	0.428	0.000	0.428
stat_aggregate-method	8.292	0.004	8.306
stat_bin-method	5.984	0.000	5.988
stat_coverage-method	2.584	0.004	2.589
stat_gene-method	0.000	0.000	0.002
stat_identity-method	3.336	0.000	3.339
stat_reduce-method	8.596	0.060	8.678
stat_slice-method	3.628	0.000	3.630
stat_stepping-method	2.536	0.000	2.542
stat_table-method	1.524	0.000	1.523
theme	2.660	0.008	2.670
tracks	32.328	0.016	32.377