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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 850/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ggbio 1.54.0  (landing page)
Michael Lawrence
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/ggbio
git_branch: RELEASE_3_20
git_last_commit: f8a48fa
git_last_commit_date: 2024-10-29 09:39:07 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for ggbio on palomino8

To the developers/maintainers of the ggbio package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: ggbio
Version: 1.54.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggbio.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ggbio_1.54.0.tar.gz
StartedAt: 2024-12-20 02:01:35 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 02:14:17 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 762.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ggbio.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ggbio.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings ggbio_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/ggbio.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ggbio/DESCRIPTION' ... OK
* this is package 'ggbio' version '1.54.0'
* 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 code 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 whether startup messages can be suppressed ... 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:353-355: Lost braces in \itemize; meant \describe ?
checkRd: (-1) autoplot-method.Rd:357-360: Lost braces in \itemize; meant \describe ?
checkRd: (-1) autoplot-method.Rd:442-448: Lost braces in \itemize; meant \describe ?
checkRd: (-1) autoplot-method.Rd:445: Escaped LaTeX specials: \~
checkRd: (-1) autoplot-method.Rd:449-455: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_arch-method.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_arch-method.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) geom_arch-method.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ggplot-method.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ggplot-method.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ggplot-method.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tracks.Rd:295-302: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tracks.Rd:303-306: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tracks.Rd:307-309: Lost braces in \itemize; meant \describe ?
* 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 Rd file 'geom_alignment-method.Rd':
\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 Rd file 'ggsave.Rd':
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 ... NOTE
Argument items with no description in Rd file 'autoplot-method.Rd':
  'rotate'
* 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         97.00   2.63  104.08
geom_alignment-method   33.97   0.89   34.82
tracks                  24.74   0.54   25.47
layout_karyogram-method 20.70   0.29   21.00
plotRangesLinkedToData  11.78   0.32   12.11
stat_reduce-method       8.51   0.31    8.82
stat_aggregate-method    8.70   0.06    8.76
ggplot-method            7.80   0.28    8.06
plotGrandLinear          6.72   0.21    6.92
layout_circle-method     6.59   0.10    6.69
stat_bin-method          5.99   0.05    6.03
geom_arrow-method        5.50   0.08    5.58
geom_chevron-method      5.00   0.11    5.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test-all.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 4 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/ggbio.Rcheck/00check.log'
for details.


Installation output

ggbio.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL ggbio
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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, saveRDS, setdiff, 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 
  19.34    1.40   20.73 

Example timings

ggbio.Rcheck/ggbio-Ex.timings

nameusersystemelapsed
arrangeGrobByParsingLegend4.790.084.87
autoplot-method 97.00 2.63104.08
geom_alignment-method33.97 0.8934.82
geom_arch-method1.680.011.70
geom_arrow-method5.500.085.58
geom_arrowrect-method4.490.034.51
geom_bar-method1.000.061.07
geom_chevron-method5.000.115.11
geom_rect-method3.540.083.62
geom_segment-method3.750.003.75
ggbio-class000
ggplot-method7.800.288.06
layout_circle-method6.590.106.69
layout_karyogram-method20.70 0.2921.00
plotFragLength000
plotGrandLinear6.720.216.92
plotRangesLinkedToData11.78 0.3212.11
plotSingleChrom000
plotSpliceSum000
plotStackedOverview000
rescale-method0.090.000.10
scale_fill_fold_change0.350.000.34
scale_fill_giemsa3.280.053.33
scale_x_sequnit0.420.000.42
stat_aggregate-method8.700.068.76
stat_bin-method5.990.056.03
stat_coverage-method2.400.092.50
stat_gene-method000
stat_identity-method3.410.083.48
stat_reduce-method8.510.318.82
stat_slice-method3.990.064.04
stat_stepping-method3.980.254.22
stat_table-method1.890.031.92
theme1.730.041.78
tracks24.74 0.5425.47