Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-09 11:38 -0400 (Thu, 09 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4832 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4613 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4554 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4585 |
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 866/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ggbio 1.56.1 (landing page) Michael Lawrence
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
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. |
Package: ggbio |
Version: 1.56.1 |
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_1.56.1.tar.gz |
StartedAt: 2025-10-07 04:20:54 -0400 (Tue, 07 Oct 2025) |
EndedAt: 2025-10-07 04:45:22 -0400 (Tue, 07 Oct 2025) |
EllapsedTime: 1467.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ggbio.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### 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_1.56.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/ggbio.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ggbio/DESCRIPTION’ ... OK * this is package ‘ggbio’ version ‘1.56.1’ * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 25 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 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' 'biovizBase:::.checkFacetsRestrict' 'biovizBase:::isFacetByOnlySeq' 'ggplot2:::add_ggplot' 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: autoplot-method.Rd: GRanges, ScanBamParam geom_alignment-method.Rd: GRanges-class, TxDb-class ggbio-class.Rd: ggplot ggplot-method.Rd: mold plotSingleChrom.Rd: getIdeogram plotSpliceSum.Rd: qplot stat_aggregate-method.Rd: Hits, IntegerList tracks.Rd: IRanges-class, GRanges-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 193.338 2.803 199.293 tracks 73.254 0.422 87.600 geom_alignment-method 63.879 0.923 66.292 layout_karyogram-method 46.440 0.253 47.235 plotRangesLinkedToData 25.594 0.262 26.266 ggplot-method 18.481 0.165 19.032 stat_aggregate-method 18.241 0.078 18.698 stat_reduce-method 15.824 0.241 16.342 layout_circle-method 15.588 0.088 15.849 geom_arrow-method 13.705 0.085 14.934 plotGrandLinear 13.347 0.203 13.758 geom_chevron-method 11.986 0.051 12.106 arrangeGrobByParsingLegend 11.305 0.287 11.681 stat_bin-method 10.683 0.061 10.883 geom_segment-method 9.158 0.085 9.527 geom_arrowrect-method 8.660 0.047 9.329 geom_rect-method 8.297 0.040 8.443 stat_slice-method 7.784 0.054 8.234 scale_fill_giemsa 7.522 0.041 7.657 stat_identity-method 7.168 0.125 7.731 stat_stepping-method 6.127 0.043 6.793 stat_coverage-method 5.722 0.051 5.880 theme 5.643 0.035 9.219 stat_table-method 4.177 0.030 7.243 * 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, 5 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/ggbio.Rcheck/00check.log’ for details.
ggbio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ggbio ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘ggbio’ ... ** this is package ‘ggbio’ version ‘1.56.1’ ** 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)
ggbio.Rcheck/tests/test-all.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 32.386 2.115 53.384
ggbio.Rcheck/ggbio-Ex.timings
name | user | system | elapsed | |
arrangeGrobByParsingLegend | 11.305 | 0.287 | 11.681 | |
autoplot-method | 193.338 | 2.803 | 199.293 | |
geom_alignment-method | 63.879 | 0.923 | 66.292 | |
geom_arch-method | 3.302 | 0.051 | 3.517 | |
geom_arrow-method | 13.705 | 0.085 | 14.934 | |
geom_arrowrect-method | 8.660 | 0.047 | 9.329 | |
geom_bar-method | 2.917 | 0.021 | 2.965 | |
geom_chevron-method | 11.986 | 0.051 | 12.106 | |
geom_rect-method | 8.297 | 0.040 | 8.443 | |
geom_segment-method | 9.158 | 0.085 | 9.527 | |
ggbio-class | 0.032 | 0.001 | 0.033 | |
ggplot-method | 18.481 | 0.165 | 19.032 | |
layout_circle-method | 15.588 | 0.088 | 15.849 | |
layout_karyogram-method | 46.440 | 0.253 | 47.235 | |
plotFragLength | 0.001 | 0.001 | 0.001 | |
plotGrandLinear | 13.347 | 0.203 | 13.758 | |
plotRangesLinkedToData | 25.594 | 0.262 | 26.266 | |
plotSingleChrom | 0.000 | 0.001 | 0.001 | |
plotSpliceSum | 0.000 | 0.001 | 0.002 | |
plotStackedOverview | 0.001 | 0.002 | 0.003 | |
rescale-method | 0.368 | 0.005 | 0.380 | |
scale_fill_fold_change | 1.224 | 0.022 | 1.347 | |
scale_fill_giemsa | 7.522 | 0.041 | 7.657 | |
scale_x_sequnit | 1.073 | 0.006 | 1.089 | |
stat_aggregate-method | 18.241 | 0.078 | 18.698 | |
stat_bin-method | 10.683 | 0.061 | 10.883 | |
stat_coverage-method | 5.722 | 0.051 | 5.880 | |
stat_gene-method | 0.000 | 0.001 | 0.001 | |
stat_identity-method | 7.168 | 0.125 | 7.731 | |
stat_reduce-method | 15.824 | 0.241 | 16.342 | |
stat_slice-method | 7.784 | 0.054 | 8.234 | |
stat_stepping-method | 6.127 | 0.043 | 6.793 | |
stat_table-method | 4.177 | 0.030 | 7.243 | |
theme | 5.643 | 0.035 | 9.219 | |
tracks | 73.254 | 0.422 | 87.600 | |