Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:07 -0400 (Fri, 15 Oct 2021).

CHECK results for Gviz on tokay2

To the developers/maintainers of the Gviz package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Gviz.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 831/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Gviz 1.36.2  (landing page)
Robert Ivanek
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/Gviz
git_branch: RELEASE_3_13
git_last_commit: 742ed80
git_last_commit_date: 2021-07-02 05:34:16 -0400 (Fri, 02 Jul 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Gviz
Version: 1.36.2
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Gviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Gviz_1.36.2.tar.gz
StartedAt: 2021-10-15 00:12:40 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 00:27:56 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 915.4 seconds
RetCode: 0
Status:   OK  
CheckDir: Gviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Gviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings Gviz_1.36.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/Gviz.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 'Gviz/DESCRIPTION' ... OK
* this is package 'Gviz' version '1.36.2'
* 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  7.1Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   2.5Mb
    help      1.3Mb
* 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 (user + system) or elapsed time > 5s
                       user system elapsed
AlignmentsTrack-class 14.80   0.95   15.84
SequenceTrack-class   11.05   0.45   11.50
AnnotationTrack-class  6.76   0.25    7.02
GeneRegionTrack-class  6.35   0.03    6.39
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
AlignmentsTrack-class 13.79   0.61   14.40
SequenceTrack-class    9.87   0.46   10.34
AnnotationTrack-class  7.94   0.16    8.10
GeneRegionTrack-class  6.82   0.05    6.86
plotTracks             5.16   0.00    5.16
GenomeAxisTrack-class  4.36   0.00   13.59
* 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-3.13-bioc/meat/Gviz.Rcheck/00check.log'
for details.



Installation output

Gviz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/Gviz_1.36.2.tar.gz && rm -rf Gviz.buildbin-libdir && mkdir Gviz.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Gviz.buildbin-libdir Gviz_1.36.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL Gviz_1.36.2.zip && rm Gviz_1.36.2.tar.gz Gviz_1.36.2.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
  4 5247k    4  238k    0     0   674k      0  0:00:07 --:--:--  0:00:07  674k
 33 5247k   33 1746k    0     0  1283k      0  0:00:04  0:00:01  0:00:03 1283k
 81 5247k   81 4259k    0     0  1807k      0  0:00:02  0:00:02 --:--:-- 1807k
100 5247k  100 5247k    0     0  1975k      0  0:00:02  0:00:02 --:--:-- 1975k

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
    AlignmentsTrack-class                   html  
    finding level-2 HTML links ... done

    AnnotationTrack-class                   html  
    BiomartGeneRegionTrack-class            html  
    CustomTrack-class                       html  
    DataTrack-class                         html  
    DisplayPars-class                       html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/Gviz.buildbin-libdir/00LOCK-Gviz/00new/Gviz/help/displayPars.html
    GdObject-class                          html  
    GeneRegionTrack-class                   html  
    GenomeAxisTrack-class                   html  
    Gviz-defunct                            html  
    Gviz-deprecated                         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_1.36.2.zip
* DONE (Gviz)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'Gviz' successfully unpacked and MD5 sums checked

Tests output

Gviz.Rcheck/tests_i386/testthat.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)
> 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.max, which.min


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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> 
> test_check("Gviz")
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    pattern

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

    strsplit

Loading required package: rtracklayer
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 299 ]
> 
> proc.time()
   user  system elapsed 
 113.73    7.40  126.82 

Gviz.Rcheck/tests_x64/testthat.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)
> 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.max, which.min


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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
> 
> test_check("Gviz")
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    pattern

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

    strsplit

Loading required package: rtracklayer
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 299 ]
> 
> proc.time()
   user  system elapsed 
 114.82    5.39  138.04 

Example timings

Gviz.Rcheck/examples_i386/Gviz-Ex.timings

nameusersystemelapsed
AlignmentsTrack-class14.80 0.9515.84
AnnotationTrack-class6.760.257.02
BiomartGeneRegionTrack-class3.890.013.91
CustomTrack-class000
DataTrack-class1.750.041.78
DisplayPars-class0.000.010.02
GdObject-class0.50.00.5
GeneRegionTrack-class6.350.036.39
GenomeAxisTrack-class3.490.003.48
HighlightTrack-class0.160.000.16
IdeogramTrack-class1.090.001.09
OverlayTrack-class0.050.000.05
RangeTrack-class0.480.000.49
ReferenceTrack-class1.920.132.04
SequenceTrack-class11.05 0.4511.50
StackedTrack-class0.860.000.86
UcscTrack1.610.001.61
exportTracks0.110.000.11
plotTracks4.870.024.99
settings0.860.000.85

Gviz.Rcheck/examples_x64/Gviz-Ex.timings

nameusersystemelapsed
AlignmentsTrack-class13.79 0.6114.40
AnnotationTrack-class7.940.168.10
BiomartGeneRegionTrack-class3.780.003.79
CustomTrack-class000
DataTrack-class2.290.002.29
DisplayPars-class0.030.000.03
GdObject-class0.500.020.52
GeneRegionTrack-class6.820.056.86
GenomeAxisTrack-class 4.36 0.0013.59
HighlightTrack-class0.190.000.19
IdeogramTrack-class1.310.001.31
OverlayTrack-class0.050.000.05
RangeTrack-class0.510.000.52
ReferenceTrack-class2.130.082.20
SequenceTrack-class 9.87 0.4610.34
StackedTrack-class0.990.000.99
UcscTrack0.860.000.86
exportTracks0.090.000.09
plotTracks5.160.005.16
settings0.810.000.81