BioC 3.4: CHECK report for ggbio on morelia

Package: ggbio

Version: 1.22.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggbio_1.22.4.tar.gz

StartedAt: 2017-04-15 02:54:43 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 03:06:02 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 678.8 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_1.22.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ggbio.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.22.4’
* 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 ‘/Users/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 sizes of PDF files under ‘inst/doc’ ... 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         106.692  2.032 110.280
tracks                   46.275  0.106  48.020
geom_alignment-method    41.815  0.931  42.799
layout_karyogram-method  28.485  0.087  32.214
geom_arrow-method        14.066  0.047  14.137
plotRangesLinkedToData   13.212  0.178  13.537
stat_aggregate-method    10.886  0.022  11.245
stat_reduce-method        9.874  0.232  10.744
ggplot-method             9.789  0.098   9.913
layout_circle-method      7.887  0.025   9.432
stat_bin-method           7.476  0.035   7.659
plotGrandLinear           6.483  0.039   6.953
geom_chevron-method       6.108  0.017   6.151
stat_slice-method         5.351  0.049   5.406
stat_identity-method      3.953  0.030   5.548
* 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
  ‘/Users/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	4.836	0.052	4.897
autoplot-method	106.692	2.032	110.280
geom_alignment-method	41.815	0.931	42.799
geom_arch-method	2.255	0.013	2.271
geom_arrow-method	14.066	0.047	14.137
geom_arrowrect-method	4.852	0.013	4.947
geom_bar-method	1.691	0.007	1.699
geom_chevron-method	6.108	0.017	6.151
geom_rect-method	4.654	0.013	4.692
geom_segment-method	3.967	0.025	4.007
ggbio-class	0.008	0.001	0.008
ggplot-method	9.789	0.098	9.913
layout_circle-method	7.887	0.025	9.432
layout_karyogram-method	28.485	0.087	32.214
plotFragLength	0.000	0.000	0.001
plotGrandLinear	6.483	0.039	6.953
plotRangesLinkedToData	13.212	0.178	13.537
plotSingleChrom	0.001	0.000	0.001
plotSpliceSum	0.001	0.000	0.001
plotStackedOverview	0.002	0.001	0.003
rescale-method	0.181	0.001	0.182
scale_fill_fold_change	0.632	0.007	0.641
scale_fill_giemsa	4.475	0.009	4.490
scale_x_sequnit	1.055	0.014	1.071
stat_aggregate-method	10.886	0.022	11.245
stat_bin-method	7.476	0.035	7.659
stat_coverage-method	3.686	0.026	3.716
stat_gene-method	0.001	0.000	0.001
stat_identity-method	3.953	0.030	5.548
stat_reduce-method	9.874	0.232	10.744
stat_slice-method	5.351	0.049	5.406
stat_stepping-method	3.322	0.010	3.339
stat_table-method	2.375	0.008	2.431
theme	3.453	0.009	3.467
tracks	46.275	0.106	48.020