Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:37 -0400 (Fri, 15 Oct 2021).
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. |
Package 764/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ggbio 1.40.0 (landing page) Michael Lawrence
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: ggbio |
Version: 1.40.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ggbio.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ggbio_1.40.0.tar.gz |
StartedAt: 2021-10-14 19:32:47 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 19:45:52 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 785.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ggbio.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ggbio.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ggbio_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/ggbio.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘1.40.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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:::rename_aes' 'ggplot2:::rescale01' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'do.ggcall' * 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' plotInter: no visible binding for global variable 'fe' plotInter: no visible binding for global variable 'value' plotInter2: no visible binding for global variable 'fe' plotInter2: no visible binding for global variable 'value' 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 'y' layout_karyogram,GRanges: no visible binding for global variable 'xend' layout_karyogram,GRanges: no visible binding for global variable 'yend' 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 fe fl gieStain ideoCyto indexProbesProcessed midpoint mt name read se stepping sts value variable x xend y y2 yend 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 ... OK * 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 * 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 129.448 1.709 131.665 geom_alignment-method 47.121 0.677 47.890 layout_karyogram-method 30.257 0.120 30.402 tracks 27.443 0.128 27.655 plotRangesLinkedToData 14.401 0.118 14.535 stat_reduce-method 12.889 0.129 13.026 stat_aggregate-method 11.931 0.038 11.985 layout_circle-method 11.848 0.068 11.961 ggplot-method 10.981 0.071 11.071 plotGrandLinear 8.602 0.115 8.734 geom_arrow-method 8.541 0.026 8.576 geom_chevron-method 7.639 0.041 7.690 stat_bin-method 6.130 0.053 6.196 geom_arrowrect-method 5.535 0.020 5.560 geom_rect-method 5.265 0.023 5.295 scale_fill_giemsa 5.192 0.019 5.216 * 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: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/ggbio.Rcheck/00check.log’ for details.
ggbio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ggbio ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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 Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB 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 http://tengfei.github.com/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 18.522 0.809 19.347
ggbio.Rcheck/ggbio-Ex.timings
name | user | system | elapsed | |
arrangeGrobByParsingLegend | 3.015 | 0.231 | 3.259 | |
autoplot-method | 129.448 | 1.709 | 131.665 | |
geom_alignment-method | 47.121 | 0.677 | 47.890 | |
geom_arch-method | 1.949 | 0.023 | 1.975 | |
geom_arrow-method | 8.541 | 0.026 | 8.576 | |
geom_arrowrect-method | 5.535 | 0.020 | 5.560 | |
geom_bar-method | 1.508 | 0.011 | 1.522 | |
geom_chevron-method | 7.639 | 0.041 | 7.690 | |
geom_rect-method | 5.265 | 0.023 | 5.295 | |
geom_segment-method | 4.558 | 0.018 | 4.581 | |
ggbio-class | 0.006 | 0.001 | 0.007 | |
ggplot-method | 10.981 | 0.071 | 11.071 | |
layout_circle-method | 11.848 | 0.068 | 11.961 | |
layout_karyogram-method | 30.257 | 0.120 | 30.402 | |
plotFragLength | 0.000 | 0.000 | 0.001 | |
plotGrandLinear | 8.602 | 0.115 | 8.734 | |
plotRangesLinkedToData | 14.401 | 0.118 | 14.535 | |
plotSingleChrom | 0.000 | 0.001 | 0.000 | |
plotSpliceSum | 0.000 | 0.000 | 0.001 | |
plotStackedOverview | 0.000 | 0.001 | 0.001 | |
rescale-method | 0.117 | 0.002 | 0.118 | |
scale_fill_fold_change | 0.478 | 0.007 | 0.486 | |
scale_fill_giemsa | 5.192 | 0.019 | 5.216 | |
scale_x_sequnit | 0.328 | 0.002 | 0.332 | |
stat_aggregate-method | 11.931 | 0.038 | 11.985 | |
stat_bin-method | 6.130 | 0.053 | 6.196 | |
stat_coverage-method | 3.057 | 0.027 | 3.090 | |
stat_gene-method | 0.001 | 0.000 | 0.000 | |
stat_identity-method | 3.586 | 0.073 | 3.665 | |
stat_reduce-method | 12.889 | 0.129 | 13.026 | |
stat_slice-method | 3.858 | 0.028 | 3.931 | |
stat_stepping-method | 3.742 | 0.013 | 3.797 | |
stat_table-method | 2.264 | 0.016 | 2.286 | |
theme | 1.939 | 0.010 | 1.954 | |
tracks | 27.443 | 0.128 | 27.655 | |