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BioC 3.2: CHECK report for ggbio on oaxaca

This page was generated on 2016-04-23 10:25:33 -0700 (Sat, 23 Apr 2016).

Package 438/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggbio 1.18.5
Tengfei Yin
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ggbio
Last Changed Rev: 113590 / Revision: 116712
Last Changed Date: 2016-02-12 11:55:15 -0800 (Fri, 12 Feb 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ggbio
Version: 1.18.5
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

Command output

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


* 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.


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’
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
arrangeGrobByParsingLegend3.6430.0383.741
autoplot-method67.971 1.79577.072
geom_alignment-method38.941 0.97541.213
geom_arch-method1.8170.0121.830
geom_arrow-method12.247 0.03712.912
geom_arrowrect-method4.8390.0385.043
geom_bar-method1.5270.0071.535
geom_chevron-method4.7860.0147.551
geom_rect-method3.5350.0123.738
geom_segment-method3.5040.0113.518
ggbio-class0.0070.0000.007
ggplot-method8.8960.1059.050
layout_circle-method 7.499 0.03210.300
layout_karyogram-method21.703 0.07430.441
plotFragLength0.0010.0000.001
plotGrandLinear6.3970.0497.551
plotRangesLinkedToData11.472 0.24611.806
plotSingleChrom0.0000.0000.001
plotSpliceSum0.0010.0000.001
plotStackedOverview0.0020.0000.002
rescale-method0.1860.0010.209
scale_fill_fold_change0.6110.0050.720
scale_fill_giemsa3.5780.0133.901
scale_x_sequnit0.4520.0020.470
stat_aggregate-method13.897 0.03114.761
stat_bin-method6.9800.0427.059
stat_coverage-method3.7400.0153.822
stat_gene-method0.0020.0000.001
stat_identity-method3.6860.0344.440
stat_reduce-method8.7130.2579.128
stat_slice-method3.7820.0274.281
stat_stepping-method2.6530.0153.889
stat_table-method1.5630.0071.629
theme2.4610.0082.535
tracks34.569 0.10836.169