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This page was generated on 2021-10-15 15:05:41 -0400 (Fri, 15 Oct 2021).

CHECK results for ggbio on nebbiolo1

To the developers/maintainers of the ggbio package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ggbio.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 764/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggbio 1.40.0  (landing page)
Michael Lawrence
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/ggbio
git_branch: RELEASE_3_13
git_last_commit: c084632
git_last_commit_date: 2021-05-19 11:50:29 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ggbio
Version: 1.40.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ggbio.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ggbio_1.40.0.tar.gz
StartedAt: 2021-10-14 10:00:29 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 10:10:13 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 583.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ggbio.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ggbio.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ggbio_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ggbio.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.40.0’
* 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
':::' 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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'do.ggcall'
* 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'
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 coefs data eds fe fl gieStain
  ideoCyto indexProbesProcessed midpoint mt name read se stepping sts
  value variable x xend y 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 ... WARNING
Codoc mismatches from documentation object 'geom_alignment':
\S4method{geom_alignment}{GRanges}
  Code: function(data, ..., xlab, ylab, main, facets = NULL, stat =
                 c("stepping", "identity"), range.geom = c("rect",
                 "arrowrect"), gap.geom = c("chevron", "arrow",
                 "segment"), rect.height = NULL, group.selfish = TRUE)
  Docs: function(data, ..., xlab, ylab, main, facets = NULL, stat =
                 c("stepping", "identity"), range.geom = c("rect",
                 "arrowrect"), gap.geom = c("chevron", "arrow",
                 "segment"), rect.height = NULL, group.selfish = TRUE,
                 label = TRUE)
  Argument names in docs not in code:
    label

* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
autoplot-method         81.335  0.859  82.204
geom_alignment-method   31.467  0.220  31.693
tracks                  24.195  0.060  26.673
layout_karyogram-method 18.706  0.038  18.745
plotRangesLinkedToData  13.321  0.120  13.990
stat_reduce-method      12.552  0.152  13.053
stat_aggregate-method   11.350  0.004  12.848
ggplot-method           10.738  0.028  10.987
geom_arrow-method        6.697  0.020   6.955
geom_chevron-method      6.511  0.008   6.542
stat_bin-method          6.273  0.112   7.188
plotGrandLinear          6.277  0.028   6.305
layout_circle-method     5.721  0.020   5.741
geom_rect-method         5.549  0.004   5.680
stat_coverage-method     4.423  0.007   5.310
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/ggbio.Rcheck/00check.log’
for details.



Installation output

ggbio.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ggbio
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘ggbio’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggbio)

Tests output

ggbio.Rcheck/tests/test-all.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, 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

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
 15.388   0.767  16.141 

Example timings

ggbio.Rcheck/ggbio-Ex.timings

nameusersystemelapsed
arrangeGrobByParsingLegend1.8160.1561.972
autoplot-method81.335 0.85982.204
geom_alignment-method31.467 0.22031.693
geom_arch-method1.0830.0041.087
geom_arrow-method6.6970.0206.955
geom_arrowrect-method3.8260.0193.851
geom_bar-method1.0390.0001.040
geom_chevron-method6.5110.0086.542
geom_rect-method5.5490.0045.680
geom_segment-method4.1220.0084.468
ggbio-class0.0100.0000.011
ggplot-method10.738 0.02810.987
layout_circle-method5.7210.0205.741
layout_karyogram-method18.706 0.03818.745
plotFragLength0.0010.0000.001
plotGrandLinear6.2770.0286.305
plotRangesLinkedToData13.321 0.12013.990
plotSingleChrom0.0000.0000.001
plotSpliceSum0.0010.0000.001
plotStackedOverview0.0020.0000.002
rescale-method0.1580.0000.158
scale_fill_fold_change0.6910.0041.007
scale_fill_giemsa4.1960.0084.358
scale_x_sequnit0.2180.0000.218
stat_aggregate-method11.350 0.00412.848
stat_bin-method6.2730.1127.188
stat_coverage-method4.4230.0075.310
stat_gene-method0.0010.0000.000
stat_identity-method3.0550.0283.126
stat_reduce-method12.552 0.15213.053
stat_slice-method4.8640.0404.985
stat_stepping-method3.0400.0003.042
stat_table-method3.8370.0044.764
theme1.5080.0001.508
tracks24.195 0.06026.673