Bernat Gel
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/karyoploteR |
| Branch: RELEASE_3_11 |
| Last Commit: 33faf71 |
| Last Changed Date: 2020-09-09 11:02:07 -0400 (Wed, 09 Sep 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:55 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE karyoploteR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 915/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| karyoploteR 1.14.1 Bernat Gel
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: karyoploteR |
| Version: 1.14.1 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:karyoploteR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings karyoploteR_1.14.1.tar.gz |
| StartedAt: 2020-10-17 05:26:14 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 05:45:42 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 1167.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: karyoploteR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:karyoploteR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings karyoploteR_1.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/karyoploteR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'karyoploteR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'karyoploteR' version '1.14.1'
* 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 whether package 'karyoploteR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
'regioneR' 'GenomicRanges'
A package should be listed in only one of these fields.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 R/sysdata.rda ... 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
kpPlotDensity 119.48 7.16 140.23
kpPlotGenes 32.32 0.28 33.62
mergeTranscripts 24.96 0.09 25.05
kpPlotHorizon 21.26 0.01 21.29
kpPlotCoverage 16.50 0.05 16.55
kpPlotRegions 16.17 0.00 16.17
kpPlotTranscripts 12.00 0.00 12.00
kpPlotManhattan 9.15 0.09 9.25
kpPlotBAMCoverage 7.40 0.33 7.72
getCytobands 1.15 0.01 16.57
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
kpPlotDensity 104.14 5.26 109.43
kpPlotGenes 33.70 0.32 34.01
kpPlotHorizon 22.11 0.00 22.11
mergeTranscripts 21.11 0.15 21.25
kpPlotCoverage 13.66 0.03 13.68
kpPlotRegions 12.34 0.00 12.34
kpPlotTranscripts 9.78 0.12 9.91
kpPlotBAMCoverage 7.94 0.33 8.51
kpPlotManhattan 6.88 0.10 6.99
getCytobands 1.21 0.02 18.08
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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 NOTE
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/karyoploteR.Rcheck/00check.log'
for details.
karyoploteR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/karyoploteR_1.14.1.tar.gz && rm -rf karyoploteR.buildbin-libdir && mkdir karyoploteR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=karyoploteR.buildbin-libdir karyoploteR_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL karyoploteR_1.14.1.zip && rm karyoploteR_1.14.1.tar.gz karyoploteR_1.14.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 298k 100 298k 0 0 4541k 0 --:--:-- --:--:-- --:--:-- 4982k
install for i386
* installing *source* package 'karyoploteR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'karyoploteR'
finding HTML links ... done
addGeneNames html
autotrack html
colByCategory html
colByChr html
colByRegion html
colByValue html
darker html
filterParams html
findIntersections html
getChromosomeNamesBoundingBox html
getColorSchemas html
getCytobandColors html
getCytobands html
finding level-2 HTML links ... done
getDataPanelBoundingBox html
getDefaultPlotParams html
getMainTitleBoundingBox html
getTextSize html
getVariantsColors html
horizonColors html
is.color html
kpAbline html
kpAddBaseNumbers html
kpAddChromosomeNames html
kpAddChromosomeSeparators html
kpAddColorRect html
kpAddCytobandLabels html
kpAddCytobands html
kpAddCytobandsAsLine html
kpAddLabels html
kpAddMainTitle html
kpArea html
kpArrows html
kpAxis html
kpBars html
kpDataBackground html
kpHeatmap html
kpLines html
kpPlotBAMCoverage html
kpPlotBAMDensity html
kpPlotBigWig html
kpPlotCoverage html
kpPlotDensity html
kpPlotGenes html
kpPlotHorizon html
kpPlotLinks html
kpPlotLoess html
kpPlotManhattan html
kpPlotMarkers html
kpPlotNames html
kpPlotRainfall html
kpPlotRegions html
kpPlotRibbon html
kpPlotTranscripts html
kpPoints html
kpPolygon html
kpRect html
kpSegments html
kpText html
lighter html
makeGenesDataFromTxDb html
mergeTranscripts html
plotDefaultPlotParams html
plotKaryotype html
plotPalettes html
prepareParameters2 html
prepareParameters4 html
processClipping html
transparent 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 'karyoploteR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'karyoploteR' as karyoploteR_1.14.1.zip
* DONE (karyoploteR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'karyoploteR' successfully unpacked and MD5 sums checked
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karyoploteR.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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)
> library(karyoploteR)
Loading required package: regioneR
Loading required package: GenomicRanges
Loading required package: stats4
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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
>
> test_check("karyoploteR")
== testthat results ===========================================================
[ OK: 181 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
20.56 1.79 25.56
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karyoploteR.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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)
> library(karyoploteR)
Loading required package: regioneR
Loading required package: GenomicRanges
Loading required package: stats4
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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomeInfoDb
>
> test_check("karyoploteR")
== testthat results ===========================================================
[ OK: 181 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
17.84 0.90 22.14
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karyoploteR.Rcheck/examples_i386/karyoploteR-Ex.timings
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karyoploteR.Rcheck/examples_x64/karyoploteR-Ex.timings
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