Michael Lawrence
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/ggbio |
| git_branch: RELEASE_3_13 |
| git_last_commit: c084632 |
| git_last_commit_date: 2021-05-19 11:50:29 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:06 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the ggbio package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ggbio.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 764/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ggbio 1.40.0 (landing page) Michael Lawrence
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.40.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggbio.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ggbio_1.40.0.tar.gz |
| StartedAt: 2021-10-14 23:46:31 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-15 00:02:38 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 966.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ggbio.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ggbio.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ggbio_1.40.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/ggbio.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ggbio/DESCRIPTION' ... OK
* this is package 'ggbio' version '1.40.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'do.ggcall'
* 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'
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 coefs data eds fe fl gieStain
ideoCyto indexProbesProcessed midpoint mt name read se stepping sts
value variable x xend y 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 ... WARNING
Codoc mismatches from documentation object 'geom_alignment':
\S4method{geom_alignment}{GRanges}
Code: function(data, ..., xlab, ylab, main, facets = NULL, stat =
c("stepping", "identity"), range.geom = c("rect",
"arrowrect"), gap.geom = c("chevron", "arrow",
"segment"), rect.height = NULL, group.selfish = TRUE)
Docs: function(data, ..., xlab, ylab, main, facets = NULL, stat =
c("stepping", "identity"), range.geom = c("rect",
"arrowrect"), gap.geom = c("chevron", "arrow",
"segment"), rect.height = NULL, group.selfish = TRUE,
label = TRUE)
Argument names in docs not in code:
label
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
autoplot-method 100.24 2.64 103.31
geom_alignment-method 34.93 0.38 35.31
layout_karyogram-method 19.18 0.01 19.21
tracks 17.56 0.03 17.60
stat_reduce-method 11.36 0.08 11.44
plotRangesLinkedToData 9.80 0.22 10.01
stat_aggregate-method 7.57 0.01 7.59
ggplot-method 7.41 0.03 7.44
plotGrandLinear 6.36 0.00 6.36
layout_circle-method 6.34 0.00 6.34
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
autoplot-method 93.70 0.84 96.23
geom_alignment-method 33.30 0.60 33.89
layout_karyogram-method 21.56 0.06 21.72
tracks 18.64 0.05 18.69
plotRangesLinkedToData 10.22 0.13 10.35
stat_reduce-method 8.84 0.16 9.00
ggplot-method 8.27 0.03 8.31
plotGrandLinear 7.71 0.03 7.73
stat_aggregate-method 7.35 0.03 7.37
layout_circle-method 6.58 0.03 6.65
geom_arrow-method 5.44 0.01 5.46
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test-all.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.13-bioc/meat/ggbio.Rcheck/00check.log'
for details.
ggbio.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/ggbio_1.40.0.tar.gz && rm -rf ggbio.buildbin-libdir && mkdir ggbio.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ggbio.buildbin-libdir ggbio_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ggbio_1.40.0.zip && rm ggbio_1.40.0.tar.gz ggbio_1.40.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
48 1305k 48 636k 0 0 1132k 0 0:00:01 --:--:-- 0:00:01 1133k
100 1305k 100 1305k 0 0 1451k 0 --:--:-- --:--:-- --:--:-- 1451k
install for i386
* 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
converting help for package 'ggbio'
finding HTML links ... done
Grob-class html
Plot-class html
Tracked-class html
arrangeGrobByParsingLegend html
autoplot-method html
finding level-2 HTML links ... done
geom_alignment-method html
geom_arch-method html
geom_arrow-method html
geom_arrowrect-method html
geom_bar-method html
geom_chevron-method html
geom_rect-method html
geom_segment-method html
ggbio-class html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/ggbio.buildbin-libdir/00LOCK-ggbio/00new/ggbio/help/GGbio.html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/ggbio.buildbin-libdir/00LOCK-ggbio/00new/ggbio/help/ggbio-class.html
ggplot-method html
ggsave html
layout_circle-method html
layout_karyogram-method html
nav html
plotFragLength html
plotGrandLinear html
plotRangesLinkedToData html
plotSingleChrom html
plotSpliceSum html
plotStackedOverview html
rescale-method html
scale_fill_fold_change html
scale_fill_giemsa html
scale_x_sequnit html
stat_aggregate-method html
stat_bin-method html
stat_coverage-method html
stat_gene-method html
stat_identity-method html
stat_mismatch-method html
stat_reduce-method html
stat_slice-method html
stat_stepping-method html
stat_table-method html
theme html
tracks html
** 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
install for x64
* installing *source* package 'ggbio' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ggbio' as ggbio_1.40.0.zip
* DONE (ggbio)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'ggbio' successfully unpacked and MD5 sums checked
|
ggbio.Rcheck/tests_i386/test-all.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.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
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
>
> proc.time()
user system elapsed
13.51 1.28 14.78
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ggbio.Rcheck/tests_x64/test-all.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.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
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
>
> proc.time()
user system elapsed
14.67 0.79 15.46
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ggbio.Rcheck/examples_i386/ggbio-Ex.timings
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ggbio.Rcheck/examples_x64/ggbio-Ex.timings
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