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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:motifbreakR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings motifbreakR_2.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/motifbreakR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘motifbreakR/DESCRIPTION’ ... OK
* this is package ‘motifbreakR’ version ‘2.24.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calculatePvalue.Rd: TFMsc2pv
  findSupportingRemapPeaks.Rd: MotifDb, associateTranscriptionFactors
  motifbreakR.Rd: TFMPvalue-package, TFMsc2pv
  shiny_motifbreakR.Rd: shinyAppDir
  snps.from.file.Rd: useEnsembl
  snps.from.rsid.Rd: useEnsembl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
* 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
>  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)
Loading required package: GenomeInfoDb

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_failure_cnd(req, resp, error_call = error_call)
  7.             ├─rlang::catch_cnd(...)
  8.             │ ├─rlang::eval_bare(...)
  9.             │ ├─base::tryCatch(...)
 10.             │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.             │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.             │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 13.             │ └─base::force(expr)
 14.             └─rlang::abort(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
calculatePvalue 46.641  0.573  47.216
motifbreakR      9.939  0.257  10.197
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/motifbreakR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL motifbreakR
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘motifbreakR’ ...
** this is package ‘motifbreakR’ version ‘2.24.0’
** 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)