Michael Lawrence
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ggbio |
| Branch: RELEASE_3_6 |
| Last Commit: b4f4c89 |
| Last Changed Date: 2018-03-08 07:47:27 -0400 (Thu, 08 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:09:59 -0400 (Thu, 12 Apr 2018).
| Package 582/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ggbio 1.26.1 Michael Lawrence
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ggbio |
| Version: 1.26.1 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ggbio_1.26.1.tar.gz |
| StartedAt: 2018-04-11 23:54:49 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-12 00:03:54 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 544.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ggbio.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ggbio_1.26.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ggbio.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.26.1’
* 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
Unexported objects imported by ':::' calls:
'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion'
'ggplot2:::rename_aes' 'ggplot2:::rescale01'
'ggplot2:::set_last_plot'
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'
Ideogram: no visible binding for global variable 'cytobands'
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'
plotKaryogram: no visible binding for global variable 'cytobands'
plotStackedOverview: no visible binding for global variable 'cytobands'
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 cytobands 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
autoplot-method 90.136 0.444 92.675
geom_alignment-method 33.172 0.252 33.444
tracks 28.976 0.036 29.046
layout_karyogram-method 21.256 0.104 21.408
plotRangesLinkedToData 10.992 0.160 11.166
geom_arrow-method 9.460 0.008 9.485
stat_aggregate-method 8.608 0.004 8.619
stat_reduce-method 7.852 0.072 7.940
ggplot-method 7.348 0.016 7.377
layout_circle-method 6.068 0.000 6.077
plotGrandLinear 5.860 0.148 6.056
stat_bin-method 5.460 0.004 5.472
* 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 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/ggbio.Rcheck/00check.log’
for details.
ggbio.Rcheck/00install.out
* installing *source* package ‘ggbio’ ... ** R ** inst ** preparing 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 * DONE (ggbio)
ggbio.Rcheck/tests/test-all.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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, cbind, colMeans, colSums, colnames, 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
11.484 0.156 12.043
ggbio.Rcheck/ggbio-Ex.timings
| name | user | system | elapsed | |
| arrangeGrobByParsingLegend | 4.796 | 0.032 | 4.833 | |
| autoplot-method | 90.136 | 0.444 | 92.675 | |
| geom_alignment-method | 33.172 | 0.252 | 33.444 | |
| geom_arch-method | 1.664 | 0.004 | 1.668 | |
| geom_arrow-method | 9.460 | 0.008 | 9.485 | |
| geom_arrowrect-method | 3.220 | 0.000 | 3.222 | |
| geom_bar-method | 1.204 | 0.000 | 1.204 | |
| geom_chevron-method | 4.480 | 0.008 | 4.493 | |
| geom_rect-method | 2.992 | 0.000 | 2.996 | |
| geom_segment-method | 2.756 | 0.004 | 2.764 | |
| ggbio-class | 0.004 | 0.000 | 0.004 | |
| ggplot-method | 7.348 | 0.016 | 7.377 | |
| layout_circle-method | 6.068 | 0.000 | 6.077 | |
| layout_karyogram-method | 21.256 | 0.104 | 21.408 | |
| plotFragLength | 0.000 | 0.000 | 0.001 | |
| plotGrandLinear | 5.860 | 0.148 | 6.056 | |
| plotRangesLinkedToData | 10.992 | 0.160 | 11.166 | |
| plotSingleChrom | 0 | 0 | 0 | |
| plotSpliceSum | 0.000 | 0.000 | 0.001 | |
| plotStackedOverview | 0.000 | 0.000 | 0.001 | |
| rescale-method | 0.120 | 0.000 | 0.118 | |
| scale_fill_fold_change | 0.424 | 0.004 | 0.428 | |
| scale_fill_giemsa | 3.320 | 0.004 | 3.327 | |
| scale_x_sequnit | 0.432 | 0.000 | 0.431 | |
| stat_aggregate-method | 8.608 | 0.004 | 8.619 | |
| stat_bin-method | 5.460 | 0.004 | 5.472 | |
| stat_coverage-method | 2.460 | 0.004 | 2.465 | |
| stat_gene-method | 0.000 | 0.000 | 0.001 | |
| stat_identity-method | 3.264 | 0.016 | 3.284 | |
| stat_reduce-method | 7.852 | 0.072 | 7.940 | |
| stat_slice-method | 3.644 | 0.000 | 3.651 | |
| stat_stepping-method | 2.396 | 0.000 | 2.407 | |
| stat_table-method | 1.776 | 0.000 | 1.780 | |
| theme | 2.204 | 0.008 | 2.215 | |
| tracks | 28.976 | 0.036 | 29.046 | |