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This page was generated on 2023-06-05 11:04:07 -0400 (Mon, 05 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow" 4623
palomino3Windows Server 2022 Datacenterx644.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow" 4374
merida1macOS 12.6.4 Montereyx86_644.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow" 4332
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 motifbreakR on nebbiolo1


To the developers/maintainers of the motifbreakR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifbreakR.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1281/2229HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifbreakR 2.14.0  (landing page)
Simon Gert Coetzee
Snapshot Date: 2023-06-04 14:00:14 -0400 (Sun, 04 Jun 2023)
git_url: https://git.bioconductor.org/packages/motifbreakR
git_branch: RELEASE_3_17
git_last_commit: 5be1c08
git_last_commit_date: 2023-04-25 10:41:24 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    ERROR    NA  

Summary

Package: motifbreakR
Version: 2.14.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings motifbreakR_2.14.0.tar.gz
StartedAt: 2023-06-04 22:50:39 -0400 (Sun, 04 Jun 2023)
EndedAt: 2023-06-04 23:02:43 -0400 (Sun, 04 Jun 2023)
EllapsedTime: 724.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: motifbreakR.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings motifbreakR_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/motifbreakR.Rcheck’
* using R version 4.3.0 RC (2023-04-13 r84269)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘motifbreakR/DESCRIPTION’ ... OK
* this is package ‘motifbreakR’ version ‘2.14.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘motifbreakR’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'MotifDb'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
snps.from.file: no visible global function definition for
  'snpsByOverlaps'
Undefined global functions or variables:
  snpsByOverlaps
* 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 ... ERROR
Running examples in ‘motifbreakR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculatePvalue
> ### Title: Calculate the significance of the matches for the reference and
> ###   alternate alleles for the for their PWM
> ### Aliases: calculatePvalue
> 
> ### ** Examples
> 
> data(example.results)
> rs2661839 <- example.results[names(example.results) %in% "rs2661839"]
Error: object 'example.results' not found
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘motifbreakR-vignette.Rmd’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/motifbreakR.Rcheck/00check.log’
for details.


Installation output

motifbreakR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL motifbreakR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘motifbreakR’ ...
** using staged installation
** R
** data
** 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 (motifbreakR)

Tests output


Example timings

motifbreakR.Rcheck/motifbreakR-Ex.timings

nameusersystemelapsed