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This page was generated on 2022-01-24 13:06:22 -0500 (Mon, 24 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" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 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 844/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Gviz 1.38.3  (landing page)
Robert Ivanek
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/Gviz
git_branch: RELEASE_3_14
git_last_commit: c4b352a
git_last_commit_date: 2022-01-21 10:31:49 -0500 (Fri, 21 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: Gviz
Version: 1.38.3
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Gviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Gviz_1.38.3.tar.gz
StartedAt: 2022-01-23 20:31:29 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 20:46:45 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 916.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Gviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Gviz.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Gviz_1.38.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Gviz.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 'Gviz/DESCRIPTION' ... OK
* this is package 'Gviz' version '1.38.3'
* 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  7.1Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    extdata   2.5Mb
    help      1.2Mb
* 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 17.22   2.06   20.81
SequenceTrack-class   14.78   0.58   16.73
AnnotationTrack-class  7.73   0.28    8.01
GeneRegionTrack-class  7.89   0.01    7.91
GenomeAxisTrack-class  5.23   0.00    5.24
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
AlignmentsTrack-class 13.25   0.78   14.03
SequenceTrack-class    9.77   0.51   10.28
GeneRegionTrack-class  7.34   0.14    7.55
AnnotationTrack-class  6.83   0.14    6.97
plotTracks             5.25   0.00    5.25
* 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/Gviz.Rcheck/00check.log'
for details.



Installation output

Gviz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Gviz_1.38.3.tar.gz && rm -rf Gviz.buildbin-libdir && mkdir Gviz.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Gviz.buildbin-libdir Gviz_1.38.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Gviz_1.38.3.zip && rm Gviz_1.38.3.tar.gz Gviz_1.38.3.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
 29 5246k   29 1555k    0     0  3819k      0  0:00:01 --:--:--  0:00:01 3821k
100 5246k  100 5246k    0     0  7019k      0 --:--:-- --:--:-- --:--:-- 7014k

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-3.14-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_1.38.3.zip
* DONE (Gviz)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Gviz' successfully unpacked and MD5 sums checked

Tests output

Gviz.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(Gviz)
Loading required package: S4Vectors
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


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 
 116.37    7.25  138.85 

Gviz.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(Gviz)
Loading required package: S4Vectors
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


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
Ensembl site unresponsive, trying asia mirror
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 299 ]
> 
> proc.time()
   user  system elapsed 
 102.37    5.79  129.82 

Example timings

Gviz.Rcheck/examples_i386/Gviz-Ex.timings

nameusersystemelapsed
AlignmentsTrack-class17.22 2.0620.81
AnnotationTrack-class7.730.288.01
BiomartGeneRegionTrack-class3.740.023.75
CustomTrack-class000
DataTrack-class2.220.002.22
DisplayPars-class0.010.000.02
GdObject-class0.530.000.53
GeneRegionTrack-class7.890.017.91
GenomeAxisTrack-class5.230.005.24
HighlightTrack-class0.240.000.23
IdeogramTrack-class1.370.021.39
OverlayTrack-class0.070.000.06
RangeTrack-class0.50.00.5
ReferenceTrack-class2.140.122.27
SequenceTrack-class14.78 0.5816.73
StackedTrack-class1.400.001.41
UcscTrack1.210.021.22
exportTracks0.110.000.11
plotTracks4.870.004.87
settings0.780.010.80

Gviz.Rcheck/examples_x64/Gviz-Ex.timings

nameusersystemelapsed
AlignmentsTrack-class13.25 0.7814.03
AnnotationTrack-class6.830.146.97
BiomartGeneRegionTrack-class3.350.003.34
CustomTrack-class0.010.000.02
DataTrack-class1.990.052.03
DisplayPars-class0.030.000.03
GdObject-class0.50.00.5
GeneRegionTrack-class7.340.147.55
GenomeAxisTrack-class3.930.013.93
HighlightTrack-class0.180.000.19
IdeogramTrack-class1.490.001.49
OverlayTrack-class0.060.000.06
RangeTrack-class0.530.000.53
ReferenceTrack-class2.310.192.50
SequenceTrack-class 9.77 0.5110.28
StackedTrack-class0.890.020.91
UcscTrack0.840.020.86
exportTracks0.130.000.12
plotTracks5.250.005.25
settings0.760.000.77