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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 1315/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifbreakR 2.20.0  (landing page)
Simon Gert Coetzee
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/motifbreakR
git_branch: RELEASE_3_20
git_last_commit: e8d5e57
git_last_commit_date: 2024-10-29 10:03:45 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  


CHECK results for motifbreakR on kunpeng2

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.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: motifbreakR
Version: 2.20.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings motifbreakR_2.20.0.tar.gz
StartedAt: 2024-11-20 10:06:02 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 10:20:47 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 884.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: motifbreakR.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings motifbreakR_2.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/motifbreakR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘motifbreakR/DESCRIPTION’ ... OK
* this is package ‘motifbreakR’ version ‘2.20.0’
* 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 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 code 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
biomartToGranges: no visible binding for global variable 'chr_name'
biomartToGranges: no visible binding for global variable 'chrom_start'
biomartToGranges: no visible binding for global variable 'chrom_end'
biomartToGranges: no visible binding for global variable 'SNP_id'
biomartToGranges: no visible binding for global variable 'REF'
biomartToGranges: no visible binding for global variable 'ALT'
calculatePvalue: no visible binding for global variable 'Refpvalue'
calculatePvalue: no visible binding for global variable 'Altpvalue'
convertPeakFile: no visible binding for global variable 'chr'
convertPeakFile: no visible binding for global variable 'name'
Undefined global functions or variables:
  ALT Altpvalue REF Refpvalue SNP_id chr chr_name chrom_end chrom_start
  name
* checking Rd files ... NOTE
checkRd: (-1) calculatePvalue.Rd:7: Lost braces
     7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices.
       |  ^
checkRd: (-1) calculatePvalue.Rd:7: Lost braces
     7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices.
       |        ^
checkRd: (-1) calculatePvalue.Rd:7: Lost braces
     7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices.
       |                                  ^
checkRd: (-1) calculatePvalue.Rd:7: Lost braces
     7 | H{\'e}l{\`e}ne Touzet and Jean-St{\'e}phane Varr{\'e} (2007) Efficient and accurate P-value computation for Position Weight Matrices.
       |                                                 ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  'example.pvalue'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... NOTE
  Note: found 12 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... 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: snps.from.rsid
> ### Title: Import SNPs from rsid for use in motifbreakR
> ### Aliases: snps.from.rsid
> 
> ### ** Examples
> 
>  library(BSgenome.Hsapiens.UCSC.hg19)
Loading required package: BSgenome
Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

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

    FileForFormat

>  library(SNPlocs.Hsapiens.dbSNP155.GRCh37)
>  snps.file <- system.file("extdata", "pca.enhancer.snps", package = "motifbreakR")
>  snps <- as.character(read.table(snps.file)[,1])
>  snps.mb <- snps.from.rsid(snps[1],
+                            dbSNP = SNPlocs.Hsapiens.dbSNP155.GRCh37,
+                            search.genome = BSgenome.Hsapiens.UCSC.hg19)
> 
>  ## alternatively using biomaRt
> 
>  library(biomaRt)
>  library(BSgenome.Hsapiens.UCSC.hg38)

Attaching package: 'BSgenome.Hsapiens.UCSC.hg38'

The following object is masked from 'package:BSgenome.Hsapiens.UCSC.hg19':

    Hsapiens

>  ensembl_snp <- useEnsembl(biomart = "snps",
+                            dataset = "hsapiens_snp",
+                            version = "112")
Error in `req_perform()`:
! HTTP 500 Internal Server Error.
Backtrace:
    ▆
 1. └─biomaRt::useEnsembl(...)
 2.   └─biomaRt:::.listMarts(...)
 3.     └─biomaRt:::bmRequest(...)
 4.       └─httr2::req_perform(request)
 5.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 6.           └─httr2:::resp_abort(resp, req, body, call = error_call)
 7.             └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘SNPlocs.Hsapiens.dbSNP142.GRCh37’
* checking package vignettes ... 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, 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/motifbreakR.Rcheck/00check.log’
for details.


Installation output

motifbreakR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL motifbreakR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/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
calculatePvalue58.667 0.44359.217
encodemotif0.0710.0000.071
example.results0.1030.0040.107
exportMBbed0.0640.0040.067
exportMBtable0.0670.0000.067
factorbook0.0140.0000.013
findSupportingRemapPeaks0.0190.0000.019
hocomoco0.0250.0000.025
homer0.0130.0040.017
motifbreakR14.223 0.18714.446
motifbreakR_motif0.0820.0040.087
plotMB0.0680.0000.068
shiny_motifbreakR0.1960.0200.220
snps.from.file2.3740.0602.459