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CHECK report for trackViewer on tokay1

This page was generated on 2019-04-13 11:23:30 -0400 (Sat, 13 Apr 2019).

Package 1576/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
trackViewer 1.18.3
Jianhong Ou
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/trackViewer
Branch: RELEASE_3_8
Last Commit: be07a8e
Last Changed Date: 2019-03-14 14:26:44 -0400 (Thu, 14 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  NA 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: trackViewer
Version: 1.18.3
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:trackViewer.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings trackViewer_1.18.3.tar.gz
StartedAt: 2019-04-13 05:58:56 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 06:09:51 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 655.4 seconds
RetCode: 0
Status:  OK  
CheckDir: trackViewer.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:trackViewer.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings trackViewer_1.18.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/trackViewer.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'trackViewer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'trackViewer' version '1.18.3'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'trackViewer' 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
trackViewer-package 18.69   0.03   18.79
viewTracks          13.25   0.00   13.25
parseWIG            12.57   0.02   12.72
browseTracks        11.80   0.18   12.56
geneModelFromTxdb    7.19   0.28    7.60
viewGene             5.92   0.19    6.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
trackViewer-package 19.03   0.03   19.07
viewTracks          15.51   0.02   15.54
browseTracks        10.88   0.06   10.94
parseWIG            10.89   0.04   10.94
geneModelFromTxdb    5.89   0.24    6.12
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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: OK


Installation output

trackViewer.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/trackViewer_1.18.3.tar.gz && rm -rf trackViewer.buildbin-libdir && mkdir trackViewer.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=trackViewer.buildbin-libdir trackViewer_1.18.3.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL trackViewer_1.18.3.zip && rm trackViewer_1.18.3.tar.gz trackViewer_1.18.3.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
100  233k  100  233k    0     0  2749k      0 --:--:-- --:--:-- --:--:-- 2888k

install for i386

* installing *source* package 'trackViewer' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'trackViewer'
    finding HTML links ... done
    GRoperator                              html  
    addArrowMark                            html  
    addGuideLine                            html  
    browseTracks                            html  
    coverageGR                              html  
    dandelion.plot                          html  
    geneModelFromTxdb                       html  
    geneTrack                               html  
    getCurTrackViewport                     html  
    getLocation                             html  
    gieStain                                html  
    gridPlot                                html  
    ideogramPlot                            html  
    importBam                               html  
    importData                              html  
    importScore                             html  
    loadIdeogram                            html  
    lolliplot                               html  
    optimizeStyle                           html  
    parse2GRanges                           html  
    parseWIG                                html  
    plotGInteractions                       html  
    plotGRanges                             html  
    plotIdeo                                html  
    plotOneIdeo                             html  
    pos-class                               html  
    trackList-class                         html  
    trackStyle-class                        html  
    trackViewer-package                     html  
    trackViewerStyle-class                  html  
    viewGene                                html  
    viewTracks                              html  
    xscale-class                            html  
    yaxisStyle-class                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'trackViewer' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'trackViewer' as trackViewer_1.18.3.zip
* DONE (trackViewer)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'trackViewer' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

trackViewer.Rcheck/tests_i386/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> require("trackViewer") || stop("unable to load Package:trackViewer")
Loading required package: trackViewer
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, colMeans, colSums, colnames,
    dirname, 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: 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
Loading required package: grid
[1] TRUE
> require("RUnit") || stop("unable to load Package:RUnit")
Loading required package: RUnit
[1] TRUE
> BiocGenerics:::testPackage("trackViewer")


RUNIT TEST PROTOCOL -- Sat Apr 13 06:09:29 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
trackViewer RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  13.18    1.09   14.26 

trackViewer.Rcheck/tests_x64/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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.

> require("trackViewer") || stop("unable to load Package:trackViewer")
Loading required package: trackViewer
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, colMeans, colSums, colnames,
    dirname, 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: 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
Loading required package: grid
[1] TRUE
> require("RUnit") || stop("unable to load Package:RUnit")
Loading required package: RUnit
[1] TRUE
> BiocGenerics:::testPackage("trackViewer")


RUNIT TEST PROTOCOL -- Sat Apr 13 06:09:43 2019 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
trackViewer RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  12.93    0.46   13.39 

Example timings

trackViewer.Rcheck/examples_i386/trackViewer-Ex.timings

nameusersystemelapsed
GRoperator2.970.723.68
addArrowMark0.020.000.01
addGuideLine000
browseTracks11.80 0.1812.56
coverageGR0.270.000.26
dandelion.plot1.670.041.72
geneModelFromTxdb7.190.287.60
geneTrack0.290.020.31
getCurTrackViewport000
getLocation1.180.191.36
gieStain0.010.000.01
ideogramPlot000
importBam0.440.000.44
importData2.080.012.10
importScore0.800.000.89
loadIdeogram000
lolliplot0.690.000.69
optimizeStyle0.670.000.69
parse2GRanges0.010.000.01
parseWIG12.57 0.0212.72
plotGInteractions1.810.091.92
plotGRanges1.220.051.27
plotIdeo000
plotOneIdeo000
trackStyle-class0.030.000.03
trackViewer-package18.69 0.0318.79
trackViewerStyle-class000
viewGene5.920.196.11
viewTracks13.25 0.0013.25

trackViewer.Rcheck/examples_x64/trackViewer-Ex.timings

nameusersystemelapsed
GRoperator2.390.082.46
addArrowMark0.010.000.02
addGuideLine000
browseTracks10.88 0.0610.94
coverageGR0.160.000.15
dandelion.plot1.510.001.52
geneModelFromTxdb5.890.246.12
geneTrack0.250.010.27
getCurTrackViewport000
getLocation1.040.021.06
gieStain0.020.000.01
ideogramPlot000
importBam0.270.000.27
importData2.260.002.26
importScore0.520.050.57
loadIdeogram000
lolliplot0.670.000.67
optimizeStyle0.70.00.7
parse2GRanges0.020.000.02
parseWIG10.89 0.0410.94
plotGInteractions1.250.001.25
plotGRanges1.190.021.20
plotIdeo000
plotOneIdeo000
trackStyle-class0.030.000.04
trackViewer-package19.03 0.0319.07
trackViewerStyle-class000
viewGene4.770.124.89
viewTracks15.51 0.0215.54