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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GOTHiC.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GOTHiC_1.47.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/GOTHiC.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘GOTHiC/DESCRIPTION’ ... OK
* this is package ‘GOTHiC’ version ‘1.47.0’
* 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 ‘GOTHiC’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘GOTHiC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GOTHiC
> ### Title: Genome Organisation Through HiC
> ### Aliases: GOTHiC
> ### Keywords: manip package
> 
> ### ** Examples
> 
> library(GOTHiC)
> dirPath <- system.file("extdata", package="HiCDataLymphoblast")
> fileName1 <- list.files(dirPath, full.names=TRUE)[1]
> fileName2 <- list.files(dirPath, full.names=TRUE)[2]
> binom=GOTHiC(fileName1, fileName2, sampleName='lymphoid_chr20', res=1000000, 
+ BSgenomeName='BSgenome.Hsapiens.UCSC.hg18', genome=BSgenome.Hsapiens.UCSC.hg18, 
+ restrictionSite='A^AGCTT', enzyme='HindIII',cistrans='all', filterdist=10000, 
+ DUPLICATETHRESHOLD=1, fileType='Table', parallel=FALSE, cores=NULL)
Pairing reads
Mapping reads to restriction sites
Bioconductor version 3.23 (BiocManager 1.30.27), R Under development (unstable)
  (2025-10-20 r88955)
Installing package(s) 'BiocVersion', 'BSgenome.Hsapiens.UCSC.hg18'
trying URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/BiocVersion_3.23.1.tar.gz'
trying URL 'https://bioconductor.org/packages/3.23/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz'
URL
  'https://bioconductor.org/packages/3.23/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz':
  Timeout of 600 seconds was reached
some files were not downloaded
download of package ‘BSgenome.Hsapiens.UCSC.hg18’ failed
* installing *source* package ‘BiocVersion’ ...
** this is package ‘BiocVersion’ version ‘3.23.1’
** using staged installation
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocVersion)

The downloaded source packages are in
	‘/tmp/Rtmp6AtezW/downloaded_packages’
Error in library(BSgenomeName, character.only = TRUE) : 
  there is no package called ‘BSgenome.Hsapiens.UCSC.hg18’
Calls: GOTHiC ... mapReadsToRestrictionSites -> .getRestrictionSitesFromBSgenome -> library
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/GOTHiC.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL GOTHiC
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘GOTHiC’ ...
** this is package ‘GOTHiC’ version ‘1.47.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GOTHiC)