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 13:02:54 -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: /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_1.31.2.tar.gz |
| StartedAt: 2019-04-09 02:21:01 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:36:23 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 921.1 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_1.31.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ggbio.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... 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 147.638 4.357 154.208
geom_alignment-method 47.072 1.723 48.806
tracks 45.658 0.186 46.333
layout_karyogram-method 30.850 0.122 30.984
plotRangesLinkedToData 16.140 0.408 16.551
geom_arrow-method 14.269 0.052 14.355
stat_reduce-method 12.810 0.515 13.439
ggplot-method 11.852 0.185 12.594
stat_aggregate-method 11.932 0.030 11.965
layout_circle-method 10.715 0.050 10.767
plotGrandLinear 9.409 0.124 9.540
stat_bin-method 8.234 0.100 8.338
geom_chevron-method 7.690 0.027 7.722
arrangeGrobByParsingLegend 5.777 0.380 6.158
geom_arrowrect-method 6.004 0.032 6.641
stat_slice-method 5.529 0.050 5.616
geom_rect-method 5.512 0.054 5.568
geom_segment-method 5.237 0.019 5.260
* 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
‘/Users/biocbuild/bbs-3.9-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/3.6/Resources/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: 0x7f8d461b9348>, 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: 0x7f8d461b9348>, 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-apple-darwin15.6.0 (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, 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
19.584 1.578 21.113
ggbio.Rcheck/ggbio-Ex.timings
| name | user | system | elapsed | |
| arrangeGrobByParsingLegend | 5.777 | 0.380 | 6.158 | |
| autoplot-method | 147.638 | 4.357 | 154.208 | |
| geom_alignment-method | 47.072 | 1.723 | 48.806 | |
| geom_arch-method | 2.458 | 0.039 | 2.498 | |
| geom_arrow-method | 14.269 | 0.052 | 14.355 | |
| geom_arrowrect-method | 6.004 | 0.032 | 6.641 | |
| geom_bar-method | 1.799 | 0.012 | 1.812 | |
| geom_chevron-method | 7.690 | 0.027 | 7.722 | |
| geom_rect-method | 5.512 | 0.054 | 5.568 | |
| geom_segment-method | 5.237 | 0.019 | 5.260 | |
| ggbio-class | 0.01 | 0.00 | 0.01 | |
| ggplot-method | 11.852 | 0.185 | 12.594 | |
| layout_circle-method | 10.715 | 0.050 | 10.767 | |
| layout_karyogram-method | 30.850 | 0.122 | 30.984 | |
| plotFragLength | 0.000 | 0.000 | 0.001 | |
| plotGrandLinear | 9.409 | 0.124 | 9.540 | |
| plotRangesLinkedToData | 16.140 | 0.408 | 16.551 | |
| plotSingleChrom | 0.000 | 0.000 | 0.001 | |
| plotSpliceSum | 0.001 | 0.000 | 0.001 | |
| plotStackedOverview | 0.000 | 0.001 | 0.001 | |
| rescale-method | 0.188 | 0.003 | 0.191 | |
| scale_fill_fold_change | 0.628 | 0.009 | 0.637 | |
| scale_fill_giemsa | 4.193 | 0.017 | 4.210 | |
| scale_x_sequnit | 0.524 | 0.006 | 0.531 | |
| stat_aggregate-method | 11.932 | 0.030 | 11.965 | |
| stat_bin-method | 8.234 | 0.100 | 8.338 | |
| stat_coverage-method | 3.751 | 0.024 | 3.777 | |
| stat_gene-method | 0.001 | 0.000 | 0.000 | |
| stat_identity-method | 4.359 | 0.116 | 4.479 | |
| stat_reduce-method | 12.810 | 0.515 | 13.439 | |
| stat_slice-method | 5.529 | 0.050 | 5.616 | |
| stat_stepping-method | 3.586 | 0.015 | 3.601 | |
| stat_table-method | 2.768 | 0.012 | 2.780 | |
| theme | 3.08 | 0.01 | 3.09 | |
| tracks | 45.658 | 0.186 | 46.333 | |