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This page was generated on 2022-01-17 11:07:25 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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 GenVisR on riesling1


To the developers/maintainers of the GenVisR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenVisR.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 759/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenVisR 1.27.0  (landing page)
Zachary Skidmore
Snapshot Date: 2022-01-16 13:55:18 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/GenVisR
git_branch: master
git_last_commit: dc30305
git_last_commit_date: 2021-10-26 12:24:58 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    ERROR  
riesling1Windows Server 2019 Standard / x64  OK    OK    ERROR    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: GenVisR
Version: 1.27.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenVisR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenVisR_1.27.0.tar.gz
StartedAt: 2022-01-16 19:04:01 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 19:13:52 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 590.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: GenVisR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenVisR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenVisR_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GenVisR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GenVisR/DESCRIPTION' ... OK
* this is package 'GenVisR' version '1.27.0'
* 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 'GenVisR' 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
* 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 ... NOTE
Namespace in Imports field not imported from: 'reshape2'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setTierTwo,data.table : a: no visible binding for global variable 'tmp'
toLolliplot,GMS: no visible binding for global variable 'missingINdex'
Undefined global functions or variables:
  missingINdex tmp
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
Lolliplot-class 24.22   1.46   79.94
lolliplot       12.45   0.21   24.26
genCov           6.09   0.45    6.61
geneViz          5.30   0.27    5.56
cnFreq           5.49   0.02    5.50
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(GenVisR)
  > 
  > test_check("GenVisR")
  == Skipped tests ===============================================================
  * On Bioconductor (54)
  
  == Failed tests ================================================================
  -- Failure (test-Lolliplot-class.R:526:5): setDomainHeights domains are nested correctly --
  `expected` not equivalent to `actual`.
  1/1 mismatches
  [1] 7 - 9 == -2
  
  [ FAIL 1 | WARN 18 | SKIP 54 | PASS 650 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/GenVisR.Rcheck/00check.log'
for details.


Installation output

GenVisR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GenVisR
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'GenVisR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GenVisR'
    finding HTML links ... done
    Clinical-class                          html  
    GMS-class                               html  
    GMS_Virtual-class                       html  
    GMS_v4-class                            html  
    GenVisR                                 html  
    HCC1395_Germline                        html  
    HCC1395_N                               html  
    HCC1395_T                               html  
    Lolliplot-class                         html  
    LucCNseg                                html  
    MutSpectra-class                        html  
    MutationAnnotationFormat-class          html  
    MutationAnnotationFormat_Virtual-class
                                            html  
    MutationAnnotationFormat_v1.0-class     html  
    MutationAnnotationFormat_v2.0-class     html  
    MutationAnnotationFormat_v2.1-class     html  
    MutationAnnotationFormat_v2.2-class     html  
    MutationAnnotationFormat_v2.3-class     html  
    MutationAnnotationFormat_v2.4-class     html  
    PIK3CA                                  html  
    Rainfall-class                          html  
    SNPloci                                 html  
    TvTi                                    html  
    VEP-class                               html  
    VEP_Virtual-class                       html  
    VEP_v88-class                           html  
    Waterfall-class                         html  
    brcaMAF                                 html  
    cnFreq                                  html  
    cnSpec                                  html  
    cnView                                  html  
    compIdent                               html  
    covBars                                 html  
    cytoGeno                                html  
    drawPlot-methods                        html  
    genCov                                  html  
    geneViz                                 html  
    getData-methods                         html  
    getDescription-methods                  html  
    getGrob-methods                         html  
    getHeader-methods                       html  
    getMeta-methods                         html  
    getMutation-methods                     html  
    getPath-methods                         html  
    getPosition-methods                     html  
    getSample-methods                       html  
    getVersion-methods                      html  
    hg19chr                                 html  
    ideoView                                html  
    lohSpec                                 html  
    lohView                                 html  
    lolliplot                               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GenVisR/00new/GenVisR/help/lolliplot.html
    lolliplot_AA2sidechain                  html  
    lolliplot_buildMain                     html  
    waterfall                               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-GenVisR/00new/GenVisR/help/waterfall.html
    writeData-methods                       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
* DONE (GenVisR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'epivizrChart' is missing or broken
 done

Tests output

GenVisR.Rcheck/tests/testthat.Rout.fail


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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(GenVisR)
> 
> test_check("GenVisR")
== Skipped tests ===============================================================
* On Bioconductor (54)

== Failed tests ================================================================
-- Failure (test-Lolliplot-class.R:526:5): setDomainHeights domains are nested correctly --
`expected` not equivalent to `actual`.
1/1 mismatches
[1] 7 - 9 == -2

[ FAIL 1 | WARN 18 | SKIP 54 | PASS 650 ]
Error: Test failures
Execution halted

Example timings

GenVisR.Rcheck/GenVisR-Ex.timings

nameusersystemelapsed
Lolliplot-class24.22 1.4679.94
TvTi1.190.011.20
Waterfall-class0.340.000.35
cnFreq5.490.025.50
cnSpec2.700.032.73
cnView1.530.081.73
compIdent1.160.141.30
covBars0.440.000.44
genCov6.090.456.61
geneViz5.300.275.56
ideoView1.170.001.17
lohSpec1.940.112.05
lohView1.380.011.39
lolliplot12.45 0.2124.26
waterfall0.620.000.63