Michael Lawrence
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ggbio |
| Branch: RELEASE_3_8 |
| Last Commit: 8b05258 |
| Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:49:25 -0400 (Tue, 16 Apr 2019).
| Package 644/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ggbio 1.30.0 Michael Lawrence
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: ggbio |
| Version: 1.30.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ggbio.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ggbio_1.30.0.tar.gz |
| StartedAt: 2019-04-16 00:16:53 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 00:28:24 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 690.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ggbio.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ggbio.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ggbio_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ggbio.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.30.0’
* 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 or elapsed time > 5s
user system elapsed
autoplot-method 121.440 0.564 124.292
geom_alignment-method 49.036 0.400 49.692
tracks 39.572 0.028 39.889
layout_karyogram-method 26.120 0.164 26.498
plotRangesLinkedToData 15.508 0.288 15.885
geom_arrow-method 12.552 0.008 12.719
stat_reduce-method 11.460 0.056 11.548
ggplot-method 10.560 0.012 10.642
stat_aggregate-method 9.684 0.008 9.761
layout_circle-method 8.712 0.000 8.765
plotGrandLinear 7.528 0.300 7.867
stat_bin-method 7.400 0.004 7.457
geom_chevron-method 6.268 0.028 6.386
* 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-3.8-bioc/meat/ggbio.Rcheck/00check.log’
for details.
ggbio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ggbio ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘ggbio’ ... ** R ** inst ** byte-compile and prepare package for lazy loading From .checkSubclasses(): subclass "GeneNameFilter" of class "AnnotationFilter" is not local and is not updated for new inheritance information currently; [where=<environment: 0x3f78598>, where2=<environment: namespace:ggbio>] From .checkSubclasses(): subclass "GeneNameFilter" of class "AnnotationFilter" is not local and is not updated for new inheritance information currently; [where=<environment: 0x3f78598>, where2=<environment: namespace:ggbio>] 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 * DONE (ggbio)
ggbio.Rcheck/tests/test-all.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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 FAILED: 0
>
> proc.time()
user system elapsed
16.748 0.436 17.267
ggbio.Rcheck/ggbio-Ex.timings
| name | user | system | elapsed | |
| arrangeGrobByParsingLegend | 4.524 | 0.128 | 4.678 | |
| autoplot-method | 121.440 | 0.564 | 124.292 | |
| geom_alignment-method | 49.036 | 0.400 | 49.692 | |
| geom_arch-method | 2.052 | 0.016 | 2.107 | |
| geom_arrow-method | 12.552 | 0.008 | 12.719 | |
| geom_arrowrect-method | 4.644 | 0.000 | 4.692 | |
| geom_bar-method | 1.424 | 0.000 | 1.431 | |
| geom_chevron-method | 6.268 | 0.028 | 6.386 | |
| geom_rect-method | 4.136 | 0.004 | 4.172 | |
| geom_segment-method | 4.292 | 0.000 | 4.323 | |
| ggbio-class | 0.008 | 0.000 | 0.009 | |
| ggplot-method | 10.560 | 0.012 | 10.642 | |
| layout_circle-method | 8.712 | 0.000 | 8.765 | |
| layout_karyogram-method | 26.120 | 0.164 | 26.498 | |
| plotFragLength | 0.000 | 0.000 | 0.001 | |
| plotGrandLinear | 7.528 | 0.300 | 7.867 | |
| plotRangesLinkedToData | 15.508 | 0.288 | 15.885 | |
| plotSingleChrom | 0 | 0 | 0 | |
| plotSpliceSum | 0 | 0 | 0 | |
| plotStackedOverview | 0.000 | 0.000 | 0.001 | |
| rescale-method | 0.132 | 0.000 | 0.133 | |
| scale_fill_fold_change | 0.512 | 0.000 | 0.513 | |
| scale_fill_giemsa | 3.532 | 0.004 | 3.556 | |
| scale_x_sequnit | 0.380 | 0.008 | 0.388 | |
| stat_aggregate-method | 9.684 | 0.008 | 9.761 | |
| stat_bin-method | 7.400 | 0.004 | 7.457 | |
| stat_coverage-method | 3.136 | 0.008 | 3.168 | |
| stat_gene-method | 0 | 0 | 0 | |
| stat_identity-method | 3.296 | 0.004 | 3.314 | |
| stat_reduce-method | 11.460 | 0.056 | 11.548 | |
| stat_slice-method | 4.232 | 0.000 | 4.261 | |
| stat_stepping-method | 3.208 | 0.012 | 3.223 | |
| stat_table-method | 2.052 | 0.004 | 2.061 | |
| theme | 2.456 | 0.004 | 2.468 | |
| tracks | 39.572 | 0.028 | 39.889 | |