Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:54:52 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE ggbio PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 728/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ggbio 1.36.0 Michael Lawrence
| malbec2 | Linux (Ubuntu 18.04.4 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: 1.36.0 |
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ggbio.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ggbio_1.36.0.tar.gz |
StartedAt: 2020-10-17 01:47:37 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 01:59:11 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 694.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ggbio.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:ggbio.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings ggbio_1.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/ggbio.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ggbio/DESCRIPTION’ ... OK * this is package ‘ggbio’ version ‘1.36.0’ * 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 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. * 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' ScalePlot: no visible binding for global variable 'y' ScalePlot2: no visible binding for global variable 'breaks' ScalePlot2: no visible binding for global variable 'yend' ScalePlot2: no visible binding for global variable 'y.text' 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 breaks coefs data eds fe fl gieStain ideoCyto indexProbesProcessed midpoint mt name read se stepping sts value variable x xend y y.text 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 ... OK * 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 ... WARNING Found the following significant warnings: Warning: 'GenenameFilter' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. Examples with CPU (user + system) or elapsed time > 5s user system elapsed autoplot-method 96.952 0.440 98.915 geom_alignment-method 38.718 0.116 38.860 tracks 21.041 0.020 21.075 layout_karyogram-method 15.679 0.008 15.772 ggplot-method 9.855 0.016 9.872 plotRangesLinkedToData 9.632 0.052 9.683 stat_aggregate-method 9.056 0.015 9.074 stat_reduce-method 7.926 0.043 7.971 geom_arrow-method 7.248 0.004 7.253 plotGrandLinear 6.472 0.015 6.488 layout_circle-method 6.432 0.000 6.440 geom_arrowrect-method 6.229 0.004 6.233 * 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, 2 NOTEs See ‘/home/biocbuild/bbs-3.11-bioc/meat/ggbio.Rcheck/00check.log’ for details.
ggbio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL ggbio ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-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)
ggbio.Rcheck/tests/test-all.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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, 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 ══ testthat results ═══════════════════════════════════════════════════════════ [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ] > > proc.time() user system elapsed 19.184 0.532 22.405
ggbio.Rcheck/ggbio-Ex.timings
name | user | system | elapsed | |
arrangeGrobByParsingLegend | 2.565 | 0.096 | 2.661 | |
autoplot-method | 96.952 | 0.440 | 98.915 | |
geom_alignment-method | 38.718 | 0.116 | 38.860 | |
geom_arch-method | 1.256 | 0.012 | 1.269 | |
geom_arrow-method | 7.248 | 0.004 | 7.253 | |
geom_arrowrect-method | 6.229 | 0.004 | 6.233 | |
geom_bar-method | 0.849 | 0.000 | 0.849 | |
geom_chevron-method | 4.353 | 0.004 | 4.358 | |
geom_rect-method | 4.145 | 0.008 | 4.153 | |
geom_segment-method | 2.944 | 0.004 | 2.947 | |
ggbio-class | 0.005 | 0.000 | 0.006 | |
ggplot-method | 9.855 | 0.016 | 9.872 | |
layout_circle-method | 6.432 | 0.000 | 6.440 | |
layout_karyogram-method | 15.679 | 0.008 | 15.772 | |
plotFragLength | 0 | 0 | 0 | |
plotGrandLinear | 6.472 | 0.015 | 6.488 | |
plotRangesLinkedToData | 9.632 | 0.052 | 9.683 | |
plotSingleChrom | 0 | 0 | 0 | |
plotSpliceSum | 0.000 | 0.000 | 0.001 | |
plotStackedOverview | 0.001 | 0.000 | 0.000 | |
rescale-method | 0.088 | 0.000 | 0.087 | |
scale_fill_fold_change | 0.355 | 0.000 | 0.354 | |
scale_fill_giemsa | 2.523 | 0.003 | 2.527 | |
scale_x_sequnit | 0.416 | 0.000 | 0.415 | |
stat_aggregate-method | 9.056 | 0.015 | 9.074 | |
stat_bin-method | 4.786 | 0.001 | 4.786 | |
stat_coverage-method | 2.138 | 0.000 | 2.138 | |
stat_gene-method | 0.001 | 0.000 | 0.000 | |
stat_identity-method | 2.575 | 0.011 | 2.587 | |
stat_reduce-method | 7.926 | 0.043 | 7.971 | |
stat_slice-method | 2.926 | 0.001 | 2.927 | |
stat_stepping-method | 3.615 | 0.004 | 3.619 | |
stat_table-method | 3.188 | 0.007 | 3.195 | |
theme | 1.334 | 0.000 | 1.334 | |
tracks | 21.041 | 0.020 | 21.075 | |