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CHECK report for ggbio on merida2

This page was generated on 2019-04-09 13:26:38 -0400 (Tue, 09 Apr 2019).

Package 666/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggbio 1.31.2
Michael Lawrence
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/ggbio
Branch: master
Last Commit: a36c7b4
Last Changed Date: 2019-03-19 13:36:35 -0400 (Tue, 19 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK 

Summary

Package: ggbio
Version: 1.31.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ggbio.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ggbio_1.31.2.tar.gz
StartedAt: 2019-04-09 01:12:51 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:24:54 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 722.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ggbio.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ggbio.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ggbio_1.31.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ggbio.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggbio/DESCRIPTION’ ... OK
* this is package ‘ggbio’ version ‘1.31.2’
* 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 "GeneNameFilter" of class "AnnotationFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
See ‘/Users/biocbuild/bbs-3.9-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 ... OK
* 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
':::' call which should be '::': 'ggplot2:::set_last_plot'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion'
  'ggplot2:::rename_aes' 'ggplot2:::rescale01'
  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
.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'
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'
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: no visible binding for global variable 'name'
plotFragLength,character-GRanges: no visible binding for global
  variable '.fragLength'
plotSpliceSum,character-EnsDb: possible error in GRangesFilter(which,
  condition = "overlapping"): unused argument (condition =
  "overlapping")
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 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 ... OK
* 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 include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'GenenameFilter' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                           user system elapsed
autoplot-method         128.630  2.514 132.415
geom_alignment-method    43.878  0.902  45.366
tracks                   34.783  0.118  35.512
layout_karyogram-method  22.799  0.084  23.280
plotRangesLinkedToData   13.418  0.227  13.878
geom_arrow-method        11.612  0.036  12.068
stat_reduce-method       10.298  0.231  10.639
ggplot-method            10.211  0.115  10.529
stat_aggregate-method     9.592  0.023   9.791
layout_circle-method      8.152  0.034   8.288
stat_bin-method           6.629  0.048   6.923
plotGrandLinear           6.215  0.038   6.296
geom_chevron-method       5.538  0.017   5.638
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/ggbio.Rcheck/00check.log’
for details.



Installation output

ggbio.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ggbio
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ggbio’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: subclass "GeneNameFilter" of class "AnnotationFilter" is not local and cannot be updated for new inheritance information; consider setClassUnion()
Warning: subclass "GeneNameFilter" of class "AnnotationFilter" 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)

Tests output

ggbio.Rcheck/tests/test-all.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> test_check("ggbio")
Loading required package: ggbio
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: ggplot2
Need specific help about ggbio? try mailing 
 the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':

    geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
    xlim

══ testthat results  ═══════════════════════════════════════════════════════════
OK: 0 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 15.199   0.703  16.022 

Example timings

ggbio.Rcheck/ggbio-Ex.timings

nameusersystemelapsed
arrangeGrobByParsingLegend4.3980.1694.656
autoplot-method128.630 2.514132.415
geom_alignment-method43.878 0.90245.366
geom_arch-method2.1020.0182.147
geom_arrow-method11.612 0.03612.068
geom_arrowrect-method3.9020.0174.049
geom_bar-method1.2940.0071.309
geom_chevron-method5.5380.0175.638
geom_rect-method4.0630.0164.182
geom_segment-method3.3520.0123.443
ggbio-class0.0100.0010.009
ggplot-method10.211 0.11510.529
layout_circle-method8.1520.0348.288
layout_karyogram-method22.799 0.08423.280
plotFragLength000
plotGrandLinear6.2150.0386.296
plotRangesLinkedToData13.418 0.22713.878
plotSingleChrom000
plotSpliceSum000
plotStackedOverview0.0000.0000.001
rescale-method0.1520.0000.153
scale_fill_fold_change0.5360.0050.567
scale_fill_giemsa3.1940.0113.234
scale_x_sequnit0.4320.0020.440
stat_aggregate-method9.5920.0239.791
stat_bin-method6.6290.0486.923
stat_coverage-method2.8450.0122.890
stat_gene-method0.0010.0000.001
stat_identity-method3.3390.0333.406
stat_reduce-method10.298 0.23110.639
stat_slice-method4.0100.0254.062
stat_stepping-method2.7150.0102.745
stat_table-method1.9410.0071.959
theme2.3520.0092.381
tracks34.783 0.11835.512