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BioC 3.3: CHECK report for ggbio on morelia

This page was generated on 2016-04-21 13:23:00 -0700 (Thu, 21 Apr 2016).

Package 486/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggbio 1.19.13
Michael Lawrence
Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggbio
Last Changed Rev: 115641 / Revision: 116626
Last Changed Date: 2016-04-01 11:59:31 -0700 (Fri, 01 Apr 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ggbio
Version: 1.19.13
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggbio_1.19.13.tar.gz
StartedAt: 2016-04-21 03:11:44 -0700 (Thu, 21 Apr 2016)
EndedAt: 2016-04-21 03:24:14 -0700 (Thu, 21 Apr 2016)
EllapsedTime: 749.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ggbio.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ggbio_1.19.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ggbio.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.19.13’
* 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 ... [27s/27s] WARNING
Found the following significant warnings:
  Warning: subclass "ExonrankFilter" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
  Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
See ‘/Users/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:
  '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 ... [411s/431s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
autoplot-method         109.750  2.894 121.727
tracks                   50.223  0.120  53.378
geom_alignment-method    48.177  1.272  51.422
layout_karyogram-method  30.687  0.108  31.759
geom_arrow-method        15.271  0.052  15.564
plotRangesLinkedToData   14.271  0.281  14.794
stat_aggregate-method    13.592  0.035  14.194
stat_reduce-method       11.627  0.337  12.878
ggplot-method            10.931  0.140  11.299
layout_circle-method      9.873  0.056  10.128
stat_bin-method           8.371  0.044   8.764
plotGrandLinear           7.176  0.046   7.501
geom_chevron-method       6.993  0.026   7.334
stat_slice-method         5.367  0.028   5.492
geom_arrowrect-method     5.275  0.014   5.394
stat_identity-method      4.940  0.037   5.146
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [14s/16s]
 [15s/16s] 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-3.3-bioc/meat/ggbio.Rcheck/00check.log’
for details.

ggbio.Rcheck/00install.out:

* installing *source* package ‘ggbio’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
Warning: subclass "ExonrankFilter" of class "BasicFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "ExonrankFilter" 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 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)

ggbio.Rcheck/ggbio-Ex.timings:

nameusersystemelapsed
arrangeGrobByParsingLegend4.8920.0574.998
autoplot-method109.750 2.894121.727
geom_alignment-method48.177 1.27251.422
geom_arch-method2.6800.0192.787
geom_arrow-method15.271 0.05215.564
geom_arrowrect-method5.2750.0145.394
geom_bar-method1.9490.0081.978
geom_chevron-method6.9930.0267.334
geom_rect-method4.8800.0144.964
geom_segment-method4.8400.0244.948
ggbio-class0.0080.0000.010
ggplot-method10.931 0.14011.299
layout_circle-method 9.873 0.05610.128
layout_karyogram-method30.687 0.10831.759
plotFragLength0.0010.0010.001
plotGrandLinear7.1760.0467.501
plotRangesLinkedToData14.271 0.28114.794
plotSingleChrom0.0010.0000.001
plotSpliceSum0.0010.0000.001
plotStackedOverview0.0020.0010.002
rescale-method0.1990.0010.202
scale_fill_fold_change0.6930.0060.701
scale_fill_giemsa4.4590.0124.614
scale_x_sequnit0.6100.0020.615
stat_aggregate-method13.592 0.03514.194
stat_bin-method8.3710.0448.764
stat_coverage-method4.1510.0144.210
stat_gene-method0.0010.0010.002
stat_identity-method4.9400.0375.146
stat_reduce-method11.627 0.33712.878
stat_slice-method5.3670.0285.492
stat_stepping-method3.5920.0113.643
stat_table-method2.5880.0192.643
theme3.5150.0093.633
tracks50.223 0.12053.378