Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-17 11:07:25 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 riesling1


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 772/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggbio 1.43.0  (landing page)
Michael Lawrence
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/ggbio
git_branch: master
git_last_commit: 7f5f384
git_last_commit_date: 2021-11-05 14:03:26 -0500 (Fri, 05 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ggbio
Version: 1.43.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggbio.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ggbio_1.43.0.tar.gz
StartedAt: 2022-01-16 19:04:55 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 19:14:23 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 568.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ggbio.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggbio.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ggbio_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ggbio.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggbio/DESCRIPTION' ... OK
* this is package 'ggbio' version '1.43.0'
* 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 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
autoplot-method         80.09   2.76   90.83
geom_alignment-method   34.20   1.33   44.25
tracks                  24.97   0.03   25.17
layout_karyogram-method 20.89   0.13   22.18
stat_reduce-method       9.02   0.39    9.40
ggplot-method            7.89   0.21   11.47
plotRangesLinkedToData   7.30   0.22    7.52
stat_aggregate-method    6.27   0.03    6.30
layout_circle-method     5.90   0.04    7.27
plotGrandLinear          5.74   0.04    5.78
geom_arrow-method        5.47   0.03    9.69
geom_chevron-method      4.80   0.03    5.88
geom_rect-method         3.60   0.02    5.28
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/ggbio.Rcheck/00check.log'
for details.



Installation output

ggbio.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ggbio
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'ggbio'
    finding HTML links ... done
    Grob-class                              html  
    Plot-class                              html  
    Tracked-class                           html  
    arrangeGrobByParsingLegend              html  
    autoplot-method                         html  
    finding level-2 HTML links ... done

    geom_alignment-method                   html  
    geom_arch-method                        html  
    geom_arrow-method                       html  
    geom_arrowrect-method                   html  
    geom_bar-method                         html  
    geom_chevron-method                     html  
    geom_rect-method                        html  
    geom_segment-method                     html  
    ggbio-class                             html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-ggbio/00new/ggbio/help/GGbio.html
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-ggbio/00new/ggbio/help/ggbio-class.html
    ggplot-method                           html  
    ggsave                                  html  
    layout_circle-method                    html  
    layout_karyogram-method                 html  
    nav                                     html  
    plotFragLength                          html  
    plotGrandLinear                         html  
    plotRangesLinkedToData                  html  
    plotSingleChrom                         html  
    plotSpliceSum                           html  
    plotStackedOverview                     html  
    rescale-method                          html  
    scale_fill_fold_change                  html  
    scale_fill_giemsa                       html  
    scale_x_sequnit                         html  
    stat_aggregate-method                   html  
    stat_bin-method                         html  
    stat_coverage-method                    html  
    stat_gene-method                        html  
    stat_identity-method                    html  
    stat_mismatch-method                    html  
    stat_reduce-method                      html  
    stat_slice-method                       html  
    stat_stepping-method                    html  
    stat_table-method                       html  
    theme                                   html  
    tracks                                  html  
** 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)
Making 'packages.html' ... done

Tests output

ggbio.Rcheck/tests/test-all.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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 
  10.46    0.98   11.43 

Example timings

ggbio.Rcheck/ggbio-Ex.timings

nameusersystemelapsed
arrangeGrobByParsingLegend1.660.241.89
autoplot-method80.09 2.7690.83
geom_alignment-method34.20 1.3344.25
geom_arch-method1.610.031.93
geom_arrow-method5.470.039.69
geom_arrowrect-method3.790.034.08
geom_bar-method1.100.021.75
geom_chevron-method4.800.035.88
geom_rect-method3.600.025.28
geom_segment-method3.320.014.73
ggbio-class000
ggplot-method 7.89 0.2111.47
layout_circle-method5.900.047.27
layout_karyogram-method20.89 0.1322.18
plotFragLength000
plotGrandLinear5.740.045.78
plotRangesLinkedToData7.300.227.52
plotSingleChrom000
plotSpliceSum000
plotStackedOverview000
rescale-method0.070.000.08
scale_fill_fold_change0.320.020.36
scale_fill_giemsa3.430.003.43
scale_x_sequnit0.360.000.36
stat_aggregate-method6.270.036.30
stat_bin-method4.560.024.58
stat_coverage-method1.720.001.72
stat_gene-method000
stat_identity-method2.780.072.86
stat_reduce-method9.020.399.40
stat_slice-method3.140.043.17
stat_stepping-method2.410.032.44
stat_table-method1.860.011.87
theme1.830.001.83
tracks24.97 0.0325.17