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CHECK report for Gviz on tokay1

This page was generated on 2020-04-15 12:20:28 -0400 (Wed, 15 Apr 2020).

Package 764/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Gviz 1.30.3
Robert Ivanek
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/Gviz
Branch: RELEASE_3_10
Last Commit: 01406e6
Last Changed Date: 2020-02-17 09:39:57 -0400 (Mon, 17 Feb 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
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: Gviz
Version: 1.30.3
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Gviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Gviz_1.30.3.tar.gz
StartedAt: 2020-04-15 03:48:05 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:58:51 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 645.8 seconds
RetCode: 0
Status:  OK  
CheckDir: Gviz.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Gviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings Gviz_1.30.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/Gviz.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Gviz/DESCRIPTION' ... OK
* this is package 'Gviz' version '1.30.3'
* package encoding: UTF-8
* 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 'Gviz' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   2.1Mb
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
AlignmentsTrack-class  16.90   1.50   21.40
SequenceTrack-class    14.79   0.45   15.25
AnnotationTrack-class   9.17   0.33    9.50
AlignedReadTrack-class  6.55   0.53    7.09
GeneRegionTrack-class   6.27   0.09    6.36
plotTracks              5.33   0.05    5.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
AlignmentsTrack-class 14.42   0.86   16.87
SequenceTrack-class   13.75   0.66   14.42
AnnotationTrack-class  8.00   0.14    8.31
GeneRegionTrack-class  7.94   0.11    8.04
plotTracks             5.53   0.05    8.30
* 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-3.10-bioc/meat/Gviz.Rcheck/00check.log'
for details.



Installation output

Gviz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/Gviz_1.30.3.tar.gz && rm -rf Gviz.buildbin-libdir && mkdir Gviz.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Gviz.buildbin-libdir Gviz_1.30.3.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL Gviz_1.30.3.zip && rm Gviz_1.30.3.tar.gz Gviz_1.30.3.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4759k  100 4759k    0     0  13.0M      0 --:--:-- --:--:-- --:--:-- 13.2M

install for i386

* installing *source* package 'Gviz' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Gviz'
    finding HTML links ... done
    AlignedReadTrack-class                  html  
    finding level-2 HTML links ... done

    AlignmentsTrack-class                   html  
    AnnotationTrack-class                   html  
    BiomartGeneRegionTrack-class            html  
    CustomTrack-class                       html  
    DataTrack-class                         html  
    DisplayPars-class                       html  
    GdObject-class                          html  
    GeneRegionTrack-class                   html  
    GenomeAxisTrack-class                   html  
    HighlightTrack-class                    html  
    IdeogramTrack-class                     html  
    ImageMap-class                          html  
    NumericTrack-class                      html  
    OverlayTrack-class                      html  
    RangeTrack-class                        html  
    ReferenceTrack-class                    html  
    SequenceTrack-class                     html  
    StackedTrack-class                      html  
    UcscTrack                               html  
    collapsing                              html  
    datasets                                html  
    exportTracks                            html  
    grouping                                html  
    plotTracks                              html  
    settings                                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 'Gviz' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Gviz' as Gviz_1.30.3.zip
* DONE (Gviz)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'Gviz' successfully unpacked and MD5 sums checked

Tests output

Gviz.Rcheck/tests_i386/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(Gviz)
Loading required package: S4Vectors
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


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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> 
> test_check("Gviz")
== testthat results  ===========================================================
[ OK: 29 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  14.18    1.73   16.06 

Gviz.Rcheck/tests_x64/testthat.Rout


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
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(Gviz)
Loading required package: S4Vectors
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


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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> 
> test_check("Gviz")
== testthat results  ===========================================================
[ OK: 29 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  14.26    0.79   15.09 

Example timings

Gviz.Rcheck/examples_i386/Gviz-Ex.timings

nameusersystemelapsed
AlignedReadTrack-class6.550.537.09
AlignmentsTrack-class16.9 1.521.4
AnnotationTrack-class9.170.339.50
BiomartGeneRegionTrack-class3.340.023.36
DataTrack-class0.600.000.59
DisplayPars-class0.010.000.02
GeneRegionTrack-class6.270.096.36
GenomeAxisTrack-class3.450.003.45
IdeogramTrack-class1.080.001.08
SequenceTrack-class14.79 0.4515.25
plotTracks5.330.055.42

Gviz.Rcheck/examples_x64/Gviz-Ex.timings

nameusersystemelapsed
AlignedReadTrack-class3.740.073.82
AlignmentsTrack-class14.42 0.8616.87
AnnotationTrack-class8.000.148.31
BiomartGeneRegionTrack-class4.100.004.09
DataTrack-class0.720.000.72
DisplayPars-class0.010.000.02
GeneRegionTrack-class7.940.118.04
GenomeAxisTrack-class4.860.004.96
IdeogramTrack-class1.750.001.75
SequenceTrack-class13.75 0.6614.42
plotTracks5.530.058.30