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This page was generated on 2022-12-01 11:09:59 -0500 (Thu, 01 Dec 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-10-25 r83175) -- "Unsuffered Consequences" 4462
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-10-11 r83083 ucrt) -- "Unsuffered Consequences" 4203
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-13 r83342) -- "Unsuffered Consequences" 4231
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ggbio on merida1


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? 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 797/2154HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggbio 1.47.0  (landing page)
Michael Lawrence
Snapshot Date: 2022-11-30 14:00:15 -0500 (Wed, 30 Nov 2022)
git_url: https://git.bioconductor.org/packages/ggbio
git_branch: master
git_last_commit: 45abc27
git_last_commit_date: 2022-11-01 11:06:25 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'biovizBase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  NO, package depends on 'biovizBase' which is not available

Summary

Package: ggbio
Version: 1.47.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggbio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggbio_1.47.0.tar.gz
StartedAt: 2022-12-01 01:43:02 -0500 (Thu, 01 Dec 2022)
EndedAt: 2022-12-01 02:08:55 -0500 (Thu, 01 Dec 2022)
EllapsedTime: 1553.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ggbio.Rcheck
Warnings: 2

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ggbio.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ggbio_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ggbio.Rcheck’
* using R Under development (unstable) (2022-11-13 r83342)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ggbio/DESCRIPTION’ ... OK
* this is package ‘ggbio’ version ‘1.47.0’
* 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:::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'
getNR: no visible global function definition for 'se'
getNR: no visible global function definition for 'indexProbesProcessed'
getNR: no visible global function definition for 'coefs'
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 'xend'
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 fl gieStain
  ideoCyto indexProbesProcessed midpoint mt name read se stepping sts
  value variable x xend y2 yend2
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) autoplot-method.Rd:445: Escaped LaTeX specials: \~
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '+' and siglist 'Tracks,ANY'
  generic '+' and siglist 'Tracks,Tracks'
  generic '+' and siglist 'Tracks,cartesian'
  generic '+' and siglist 'Tracks,position_c'
  generic '+' and siglist 'Tracks,theme'
  generic '+' and siglist 'Tracks,zoom'
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 ... 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

Codoc mismatches from documentation object 'ggsave':
ggsave
  Code: function(filename, plot = last_plot(), device = NULL, path =
                 NULL, scale = 1, width = NA, height = NA, units =
                 c("in", "cm", "mm"), dpi = 300, limitsize = TRUE, ...)
  Docs: function(filename, plot = last_plot(), device =
                 default_device(filename), path = NULL, scale = 1,
                 width = par("din")[1], height = par("din")[2], units =
                 c("in", "cm", "mm"), dpi = 300, limitsize = TRUE, ...)
  Mismatches in argument default values:
    Name: 'device' Code: NULL Docs: default_device(filename)
    Name: 'width' Code: NA Docs: par("din")[1]
    Name: 'height' Code: NA Docs: par("din")[2]

* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
autoplot-method            171.331  2.305 226.228
geom_alignment-method       62.727  0.865 100.099
tracks                      46.820  0.216  61.920
layout_karyogram-method     36.723  0.178  72.595
plotRangesLinkedToData      20.419  0.192  29.182
stat_aggregate-method       15.806  0.062  23.133
ggplot-method               15.482  0.117  20.237
stat_reduce-method          15.273  0.229  22.323
layout_circle-method        13.587  0.077  24.942
plotGrandLinear             11.973  0.129  21.698
geom_arrow-method           11.179  0.041  14.772
stat_bin-method              9.933  0.048  13.327
geom_chevron-method          9.657  0.042  12.975
geom_arrowrect-method        7.032  0.027   9.567
stat_identity-method         6.773  0.082   9.179
geom_rect-method             6.591  0.034   8.472
geom_segment-method          6.220  0.024   8.104
scale_fill_giemsa            5.899  0.027   7.865
arrangeGrobByParsingLegend   5.418  0.221   6.988
stat_slice-method            5.527  0.036   7.501
stat_stepping-method         5.053  0.025   7.023
stat_coverage-method         4.543  0.029   6.035
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/ggbio.Rcheck/00check.log’
for details.



Installation output

ggbio.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/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 Under development (unstable) (2022-11-13 r83342) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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

Attaching package: 'BiocGenerics'

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, aperm, 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 https://lawremi.github.io/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 
 30.502   1.246  42.701 

Example timings

ggbio.Rcheck/ggbio-Ex.timings

nameusersystemelapsed
arrangeGrobByParsingLegend5.4180.2216.988
autoplot-method171.331 2.305226.228
geom_alignment-method 62.727 0.865100.099
geom_arch-method2.6000.0293.512
geom_arrow-method11.179 0.04114.772
geom_arrowrect-method7.0320.0279.567
geom_bar-method2.1280.0142.831
geom_chevron-method 9.657 0.04212.975
geom_rect-method6.5910.0348.472
geom_segment-method6.2200.0248.104
ggbio-class0.0230.0000.028
ggplot-method15.482 0.11720.237
layout_circle-method13.587 0.07724.942
layout_karyogram-method36.723 0.17872.595
plotFragLength000
plotGrandLinear11.973 0.12921.698
plotRangesLinkedToData20.419 0.19229.182
plotSingleChrom000
plotSpliceSum0.0000.0010.000
plotStackedOverview0.0010.0000.007
rescale-method0.2440.0020.331
scale_fill_fold_change0.7880.0070.959
scale_fill_giemsa5.8990.0277.865
scale_x_sequnit0.7830.0061.044
stat_aggregate-method15.806 0.06223.133
stat_bin-method 9.933 0.04813.327
stat_coverage-method4.5430.0296.035
stat_gene-method0.0010.0000.001
stat_identity-method6.7730.0829.179
stat_reduce-method15.273 0.22922.323
stat_slice-method5.5270.0367.501
stat_stepping-method5.0530.0257.023
stat_table-method3.2310.0204.330
theme3.4320.0134.519
tracks46.820 0.21661.920