Michael Lawrence
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ggbio |
| Branch: master |
| Last Commit: a36c7b4 |
| Last Changed Date: 2019-03-19 13:36:35 -0400 (Tue, 19 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:31:37 -0400 (Tue, 09 Apr 2019).
| Package 666/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ggbio 1.31.2 Michael Lawrence
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: ggbio |
| Version: 1.31.2 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ggbio.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ggbio_1.31.2.tar.gz |
| StartedAt: 2019-04-09 00:51:54 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 01:03:20 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 686.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ggbio.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ggbio.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ggbio_1.31.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ggbio.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.31.2’
* 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 114.188 0.394 116.557
geom_alignment-method 46.940 0.235 47.658
tracks 34.569 0.020 34.969
layout_karyogram-method 23.030 0.013 23.082
plotRangesLinkedToData 14.382 0.064 14.523
geom_arrow-method 12.373 0.008 12.451
stat_reduce-method 11.180 0.056 11.277
ggplot-method 9.912 0.000 9.968
stat_aggregate-method 9.639 0.000 9.674
layout_circle-method 7.560 0.000 7.598
plotGrandLinear 6.389 0.004 6.418
stat_bin-method 6.274 0.004 6.289
geom_chevron-method 5.354 0.004 5.455
* 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-3.9-bioc/meat/ggbio.Rcheck/00check.log’
for details.
ggbio.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ggbio ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘ggbio’ ... ** using staged installation ** 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: 0x5600199b9b78>, 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: 0x5600199b9b78>, 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 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) (2019-03-18 r76245) -- "Unsuffered Consequences"
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, 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
16.185 0.499 16.850
ggbio.Rcheck/ggbio-Ex.timings
| name | user | system | elapsed | |
| arrangeGrobByParsingLegend | 4.210 | 0.091 | 4.420 | |
| autoplot-method | 114.188 | 0.394 | 116.557 | |
| geom_alignment-method | 46.940 | 0.235 | 47.658 | |
| geom_arch-method | 1.878 | 0.000 | 1.880 | |
| geom_arrow-method | 12.373 | 0.008 | 12.451 | |
| geom_arrowrect-method | 4.212 | 0.004 | 4.267 | |
| geom_bar-method | 1.462 | 0.000 | 1.473 | |
| geom_chevron-method | 5.354 | 0.004 | 5.455 | |
| geom_rect-method | 4.039 | 0.004 | 4.054 | |
| geom_segment-method | 3.817 | 0.008 | 3.825 | |
| ggbio-class | 0.008 | 0.000 | 0.008 | |
| ggplot-method | 9.912 | 0.000 | 9.968 | |
| layout_circle-method | 7.560 | 0.000 | 7.598 | |
| layout_karyogram-method | 23.030 | 0.013 | 23.082 | |
| plotFragLength | 0 | 0 | 0 | |
| plotGrandLinear | 6.389 | 0.004 | 6.418 | |
| plotRangesLinkedToData | 14.382 | 0.064 | 14.523 | |
| plotSingleChrom | 0 | 0 | 0 | |
| plotSpliceSum | 0 | 0 | 0 | |
| plotStackedOverview | 0.000 | 0.000 | 0.001 | |
| rescale-method | 0.159 | 0.000 | 0.160 | |
| scale_fill_fold_change | 0.569 | 0.000 | 0.569 | |
| scale_fill_giemsa | 3.575 | 0.000 | 3.718 | |
| scale_x_sequnit | 0.526 | 0.000 | 0.526 | |
| stat_aggregate-method | 9.639 | 0.000 | 9.674 | |
| stat_bin-method | 6.274 | 0.004 | 6.289 | |
| stat_coverage-method | 2.861 | 0.008 | 2.891 | |
| stat_gene-method | 0 | 0 | 0 | |
| stat_identity-method | 3.409 | 0.016 | 3.450 | |
| stat_reduce-method | 11.180 | 0.056 | 11.277 | |
| stat_slice-method | 4.511 | 0.004 | 4.583 | |
| stat_stepping-method | 3.148 | 0.000 | 3.152 | |
| stat_table-method | 2.059 | 0.000 | 2.061 | |
| theme | 2.243 | 0.004 | 2.250 | |
| tracks | 34.569 | 0.020 | 34.969 | |