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This page was generated on 2022-01-21 13:06:32 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for karyoploteR on tokay2


To the developers/maintainers of the karyoploteR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/karyoploteR.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.

raw results

Package 975/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.20.3  (landing page)
Bernat Gel
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: RELEASE_3_14
git_last_commit: 1a34c68
git_last_commit_date: 2022-01-19 05:36:06 -0500 (Wed, 19 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  YES
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: karyoploteR
Version: 1.20.3
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:karyoploteR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings karyoploteR_1.20.3.tar.gz
StartedAt: 2022-01-20 21:58:53 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 22:14:04 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 910.9 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:karyoploteR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings karyoploteR_1.20.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/karyoploteR.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.20.3'
* 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     107.82   7.37  124.67
kpPlotGenes        24.69   0.41   25.09
kpPlotHorizon      20.83   0.03   20.86
mergeTranscripts   18.25   0.10   18.35
kpPlotRegions      14.07   0.08   14.17
kpPlotBAMCoverage   7.39   0.23    7.62
kpPlotTranscripts   7.12   0.00    7.12
kpPlotManhattan     6.86   0.03    6.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
kpPlotDensity     89.34   4.04   93.39
kpPlotGenes       26.05   0.30   26.34
kpPlotHorizon     24.95   0.02   24.97
mergeTranscripts  20.00   0.12   20.13
kpPlotRegions     14.78   0.00   14.78
kpPlotTranscripts  7.75   0.00    7.75
kpPlotManhattan    7.12   0.11    7.24
kpPlotBAMCoverage  6.33   0.33    6.65
* 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-3.14-bioc/meat/karyoploteR.Rcheck/00check.log'
for details.



Installation output

karyoploteR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/karyoploteR_1.20.3.tar.gz && rm -rf karyoploteR.buildbin-libdir && mkdir karyoploteR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=karyoploteR.buildbin-libdir karyoploteR_1.20.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL karyoploteR_1.20.3.zip && rm karyoploteR_1.20.3.tar.gz karyoploteR_1.20.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  295k  100  295k    0     0   537k      0 --:--:-- --:--:-- --:--:--  538k

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_1.20.3.zip
* DONE (karyoploteR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'karyoploteR' successfully unpacked and MD5 sums checked

Tests output

karyoploteR.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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)
> library(karyoploteR)
Loading required package: regioneR
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
> 
> test_check("karyoploteR")
== Skipped tests ===============================================================
* empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 181 ]
> 
> proc.time()
   user  system elapsed 
  15.23    1.73   16.95 

karyoploteR.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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)
> library(karyoploteR)
Loading required package: regioneR
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
> 
> test_check("karyoploteR")
== Skipped tests ===============================================================
* empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 181 ]
> 
> proc.time()
   user  system elapsed 
  17.96    0.85   18.81 

Example timings

karyoploteR.Rcheck/examples_i386/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames1.920.122.04
autotrack000
colByCategory000
colByChr0.470.080.55
colByRegion1.090.221.31
colByValue1.030.001.03
darker000
filterParams000
findIntersections0.160.000.16
getChromosomeNamesBoundingBox0.050.000.04
getColorSchemas000
getCytobandColors000
getCytobands000
getDataPanelBoundingBox0.050.000.05
getDefaultPlotParams0.080.000.07
getMainTitleBoundingBox0.030.000.04
getTextSize0.080.000.07
getVariantsColors000
horizonColors000
is.color000
kpAbline2.581.283.86
kpAddBaseNumbers0.340.000.35
kpAddChromosomeNames0.030.000.03
kpAddChromosomeSeparators0.380.000.37
kpAddColorRect0.140.000.14
kpAddCytobandLabels0.320.020.35
kpAddCytobands0.040.000.03
kpAddCytobandsAsLine0.070.000.08
kpAddLabels0.410.000.40
kpAddMainTitle0.050.000.05
kpArea0.360.000.36
kpArrows0.610.060.67
kpAxis0.260.000.27
kpBars0.190.000.18
kpDataBackground0.190.000.19
kpHeatmap0.140.020.16
kpLines0.280.000.28
kpPlotBAMCoverage7.390.237.62
kpPlotBAMDensity2.200.002.21
kpPlotBigWig000
kpPlotCoverage0.490.050.53
kpPlotDensity107.82 7.37124.67
kpPlotGenes24.69 0.4125.09
kpPlotHorizon20.83 0.0320.86
kpPlotLinks1.060.001.07
kpPlotLoess0.060.000.06
kpPlotManhattan6.860.036.89
kpPlotMarkers1.710.001.70
kpPlotNames0.140.000.14
kpPlotRainfall0.870.000.88
kpPlotRegions14.07 0.0814.17
kpPlotRibbon0.090.000.09
kpPlotTranscripts7.120.007.12
kpPoints0.30.00.3
kpPolygon0.240.000.24
kpRect0.870.000.87
kpSegments0.610.000.61
kpText0.310.000.31
lighter000
makeGenesDataFromTxDb3.360.043.42
mergeTranscripts18.25 0.1018.35
plotDefaultPlotParams0.160.000.15
plotKaryotype1.110.011.15
plotPalettes0.010.000.01
prepareParameters20.030.000.03
prepareParameters40.050.000.05
processClipping0.030.000.03
transparent000

karyoploteR.Rcheck/examples_x64/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames2.250.082.33
autotrack000
colByCategory0.020.000.02
colByChr0.480.020.50
colByRegion1.440.121.56
colByValue0.30.00.3
darker000
filterParams000
findIntersections0.20.00.2
getChromosomeNamesBoundingBox0.050.000.05
getColorSchemas000
getCytobandColors000
getCytobands000
getDataPanelBoundingBox0.050.000.05
getDefaultPlotParams0.090.020.11
getMainTitleBoundingBox0.080.030.11
getTextSize0.20.00.2
getVariantsColors000
horizonColors0.020.000.02
is.color000
kpAbline3.450.924.37
kpAddBaseNumbers0.380.010.39
kpAddChromosomeNames0.030.000.03
kpAddChromosomeSeparators0.440.000.44
kpAddColorRect0.150.000.16
kpAddCytobandLabels0.350.000.34
kpAddCytobands0.040.000.05
kpAddCytobandsAsLine0.080.000.08
kpAddLabels0.440.020.45
kpAddMainTitle0.050.000.05
kpArea0.360.000.36
kpArrows0.670.030.70
kpAxis0.370.000.37
kpBars0.350.000.35
kpDataBackground0.280.000.28
kpHeatmap0.150.000.15
kpLines0.330.000.33
kpPlotBAMCoverage6.330.336.65
kpPlotBAMDensity2.110.032.15
kpPlotBigWig0.010.000.01
kpPlotCoverage0.520.000.52
kpPlotDensity89.34 4.0493.39
kpPlotGenes26.05 0.3026.34
kpPlotHorizon24.95 0.0224.97
kpPlotLinks1.280.001.28
kpPlotLoess0.080.000.07
kpPlotManhattan7.120.117.24
kpPlotMarkers1.80.01.8
kpPlotNames0.190.000.18
kpPlotRainfall1.120.001.13
kpPlotRegions14.78 0.0014.78
kpPlotRibbon0.150.000.14
kpPlotTranscripts7.750.007.75
kpPoints0.290.000.30
kpPolygon0.300.000.29
kpRect1.250.001.25
kpSegments0.830.000.83
kpText0.330.000.33
lighter000
makeGenesDataFromTxDb3.660.063.71
mergeTranscripts20.00 0.1220.13
plotDefaultPlotParams0.150.000.16
plotKaryotype1.360.021.37
plotPalettes0.030.000.03
prepareParameters20.050.000.05
prepareParameters40.060.000.06
processClipping0.050.000.05
transparent000