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BioC 3.5: CHECK report for ggbio on malbec2

This page was generated on 2017-08-16 13:14:14 -0400 (Wed, 16 Aug 2017).

Package 558/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggbio 1.24.1
Michael Lawrence
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ggbio
Last Changed Rev: 130641 / Revision: 131943
Last Changed Date: 2017-06-23 13:52:53 -0400 (Fri, 23 Jun 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ggbio
Version: 1.24.1
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ggbio_1.24.1.tar.gz
StartedAt: 2017-08-15 23:27:44 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 23:36:53 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 549.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ggbio.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ggbio_1.24.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ggbio.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.24.1’
* 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 ... OK
* 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
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
.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'
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 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 ... 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 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         90.364  0.852  94.103
geom_alignment-method   32.908  0.284  33.214
tracks                  28.148  0.024  28.193
layout_karyogram-method 22.164  0.076  22.312
plotRangesLinkedToData  11.180  0.192  11.392
geom_arrow-method        8.832  0.004   8.839
stat_aggregate-method    8.688  0.004   8.699
ggplot-method            7.304  0.020   7.328
stat_reduce-method       7.004  0.024   7.032
layout_circle-method     5.516  0.000   5.520
stat_bin-method          5.312  0.004   5.317
* 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/ggbio.Rcheck/00check.log’
for details.


ggbio.Rcheck/00install.out:

* installing *source* package ‘ggbio’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
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
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (ggbio)

ggbio.Rcheck/ggbio-Ex.timings:

nameusersystemelapsed
arrangeGrobByParsingLegend4.2960.0124.310
autoplot-method90.364 0.85294.103
geom_alignment-method32.908 0.28433.214
geom_arch-method1.6400.0001.642
geom_arrow-method8.8320.0048.839
geom_arrowrect-method3.5160.0043.524
geom_bar-method1.2080.0001.209
geom_chevron-method4.1480.0044.156
geom_rect-method3.0440.0003.046
geom_segment-method2.9080.0082.915
ggbio-class0.0240.0000.025
ggplot-method7.3040.0207.328
layout_circle-method5.5160.0005.520
layout_karyogram-method22.164 0.07622.312
plotFragLength0.0000.0000.001
plotGrandLinear4.6000.1564.773
plotRangesLinkedToData11.180 0.19211.392
plotSingleChrom000
plotSpliceSum0.0000.0000.001
plotStackedOverview0.0000.0000.001
rescale-method0.140.000.14
scale_fill_fold_change0.3920.0000.390
scale_fill_giemsa2.9080.0002.911
scale_x_sequnit0.3840.0000.384
stat_aggregate-method8.6880.0048.699
stat_bin-method5.3120.0045.317
stat_coverage-method2.30.02.3
stat_gene-method0.0000.0040.001
stat_identity-method2.8080.0082.821
stat_reduce-method7.0040.0247.032
stat_slice-method3.7040.0003.712
stat_stepping-method2.1120.0042.118
stat_table-method1.8200.0041.827
theme2.0680.0042.072
tracks28.148 0.02428.193