Back to Multiple platform build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-29 11:06:15 -0400 (Wed, 29 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" | 4547 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" | 4308 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" | 4301 |
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 |
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. |
Package 818/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ggbio 1.47.0 (landing page) Michael Lawrence
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
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: 2023-03-29 00:54:16 -0400 (Wed, 29 Mar 2023) |
EndedAt: 2023-03-29 01:22:02 -0400 (Wed, 29 Mar 2023) |
EllapsedTime: 1665.8 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_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ggbio.Rcheck’ * using R Under development (unstable) (2023-03-16 r83985) * using platform: x86_64-apple-darwin17.0 (64-bit) * R was compiled by Apple clang version 12.0.0 (clang-1200.0.32.29) GNU Fortran (GCC) 8.2.0 * running under: macOS Mojave 10.14.6 * 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 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: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 175.866 2.386 297.921 geom_alignment-method 62.691 0.822 82.291 tracks 47.566 0.248 62.640 layout_karyogram-method 37.319 0.222 49.655 plotRangesLinkedToData 21.803 0.215 29.360 stat_reduce-method 17.051 0.254 24.286 ggplot-method 15.892 0.113 21.641 stat_aggregate-method 14.952 0.070 20.948 layout_circle-method 14.159 0.072 18.894 geom_arrow-method 12.080 0.050 17.029 plotGrandLinear 11.979 0.112 16.558 geom_chevron-method 10.148 0.057 13.276 stat_bin-method 9.520 0.053 13.385 geom_arrowrect-method 7.448 0.035 9.876 geom_rect-method 6.890 0.057 9.229 geom_segment-method 6.693 0.034 9.633 scale_fill_giemsa 5.755 0.028 7.711 arrangeGrobByParsingLegend 5.460 0.255 7.739 stat_slice-method 5.624 0.045 8.106 stat_identity-method 5.453 0.075 7.826 stat_stepping-method 5.065 0.031 6.931 stat_coverage-method 4.556 0.031 6.360 * 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.
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)
ggbio.Rcheck/tests/test-all.Rout
R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" Copyright (C) 2023 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 30.638 1.207 42.818
ggbio.Rcheck/ggbio-Ex.timings
name | user | system | elapsed | |
arrangeGrobByParsingLegend | 5.460 | 0.255 | 7.739 | |
autoplot-method | 175.866 | 2.386 | 297.921 | |
geom_alignment-method | 62.691 | 0.822 | 82.291 | |
geom_arch-method | 2.653 | 0.042 | 3.559 | |
geom_arrow-method | 12.080 | 0.050 | 17.029 | |
geom_arrowrect-method | 7.448 | 0.035 | 9.876 | |
geom_bar-method | 2.213 | 0.021 | 2.872 | |
geom_chevron-method | 10.148 | 0.057 | 13.276 | |
geom_rect-method | 6.890 | 0.057 | 9.229 | |
geom_segment-method | 6.693 | 0.034 | 9.633 | |
ggbio-class | 0.024 | 0.000 | 0.033 | |
ggplot-method | 15.892 | 0.113 | 21.641 | |
layout_circle-method | 14.159 | 0.072 | 18.894 | |
layout_karyogram-method | 37.319 | 0.222 | 49.655 | |
plotFragLength | 0 | 0 | 0 | |
plotGrandLinear | 11.979 | 0.112 | 16.558 | |
plotRangesLinkedToData | 21.803 | 0.215 | 29.360 | |
plotSingleChrom | 0.000 | 0.000 | 0.001 | |
plotSpliceSum | 0.001 | 0.000 | 0.000 | |
plotStackedOverview | 0.000 | 0.001 | 0.000 | |
rescale-method | 0.246 | 0.002 | 0.317 | |
scale_fill_fold_change | 0.794 | 0.009 | 1.076 | |
scale_fill_giemsa | 5.755 | 0.028 | 7.711 | |
scale_x_sequnit | 0.678 | 0.007 | 0.910 | |
stat_aggregate-method | 14.952 | 0.070 | 20.948 | |
stat_bin-method | 9.520 | 0.053 | 13.385 | |
stat_coverage-method | 4.556 | 0.031 | 6.360 | |
stat_gene-method | 0.001 | 0.000 | 0.001 | |
stat_identity-method | 5.453 | 0.075 | 7.826 | |
stat_reduce-method | 17.051 | 0.254 | 24.286 | |
stat_slice-method | 5.624 | 0.045 | 8.106 | |
stat_stepping-method | 5.065 | 0.031 | 6.931 | |
stat_table-method | 3.202 | 0.021 | 4.318 | |
theme | 3.479 | 0.016 | 4.575 | |
tracks | 47.566 | 0.248 | 62.640 | |