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This page was generated on 2022-01-24 11:11:18 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 igvR on merida1


To the developers/maintainers of the igvR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/igvR.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 915/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
igvR 1.15.2  (landing page)
Paul Shannon
Snapshot Date: 2022-01-23 13:55:15 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/igvR
git_branch: master
git_last_commit: 20ba6be
git_last_commit_date: 2022-01-20 13:33:44 -0500 (Thu, 20 Jan 2022)
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: igvR
Version: 1.15.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:igvR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings igvR_1.15.2.tar.gz
StartedAt: 2022-01-24 01:56:58 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 02:06:01 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 543.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: igvR.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:igvR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings igvR_1.15.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/igvR.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘igvR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘igvR’ version ‘1.15.2’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘igvR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.6Mb
  sub-directories of 1Mb or more:
    browserCode  12.1Mb
    extdata       2.0Mb
* 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 ... WARNING
---- unloading
Error in .mergeMethodsTable(generic, mtable, tt, attach) : 
  trying to get slot "defined" from an object of a basic class ("environment") with no slots
Calls: unloadNamespace ... <Anonymous> -> .updateMethodsInTable -> .mergeMethodsTable
Execution halted
* 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 ... NOTE
setTrackHeight,igvR: no visible binding for global variable ‘igv’
Undefined global functions or variables:
  igv
* 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 include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘igvR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GWASTrack-class
> ### Title: Constructor for GWASTrack
> ### Aliases: GWASTrack-class .GWASTrack GWASTrack
> 
> ### ** Examples
> 
> 
>     #----------------------------
>     #  first, from a local file
>     #----------------------------
> 
>   file <- system.file(package="igvR", "extdata", "tbl.mef2cGWAS.variants.RData")
>   tbl.gwas <- read.table(file, sep="\t", as.is=TRUE, header=TRUE)
Warning in read.table(file, sep = "\t", as.is = TRUE, header = TRUE) :
  line 3 appears to contain embedded nulls
Warning in read.table(file, sep = "\t", as.is = TRUE, header = TRUE) :
  line 4 appears to contain embedded nulls
Warning in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  EOF within quoted string
Warning in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  embedded nul(s) found in input
>   dim(tbl.gwas)  #  32 6
[1] 16  1
>   track <- GWASTrack("GWAS", tbl.gwas)
Error in .GWASTrack(DataFrameAnnotationTrack(trackName, table, color = color,  : 
  argument "chrom.col" is missing, with no default
Calls: GWASTrack -> .GWASTrack -> new -> initialize -> initialize
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
  Found ‘inst/doc/makefile’: should be ‘Makefile’ and will be ignored
* 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 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/igvR.Rcheck/00check.log’
for details.


Installation output

igvR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL igvR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘igvR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package keeps a record of temporary installation path
* DONE (igvR)

Tests output


Example timings

igvR.Rcheck/igvR-Ex.timings

nameusersystemelapsed
BedpeInteractionsTrack-class0.0210.0000.022
DataFrameAnnotationTrack-class0.0200.0000.021
DataFrameQuantitativeTrack-class0.0120.0010.012
GRangesAnnotationTrack-class0.0950.0000.096
GRangesQuantitativeTrack-class0.0470.0000.048