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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings motifbreakR_2.20.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/motifbreakR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 5 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/motifbreakR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL motifbreakR
###
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* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-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)