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### Running command:
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###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BSgenomeForge.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BSgenomeForge_1.5.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/BSgenomeForge.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BSgenomeForge/DESCRIPTION' ... OK
* this is package 'BSgenomeForge' version '1.5.0'
* 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 whether package 'BSgenomeForge' 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/extdata/seeds/BSgenome.Creinhardtii.JGI.v5.6-tools/CITATION
Most likely 'inst/CITATION' should be used instead.
* 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'BSgenomeForge-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: downloadGenomicSequencesFromUCSC
> ### Title: Download genomic sequences from UCSC
> ### Aliases: downloadGenomicSequencesFromUCSC
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## Download the 2bit file for UCSC genome sacCer1:
> downloadGenomicSequencesFromUCSC("sacCer1")
trying URL 'https://hgdownload.soe.ucsc.edu/goldenPath/sacCer1/bigZips/sacCer1.2bit'
Content type 'unknown' length 3039530 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

> 
> ## Use the 'destdir' argument to specify the directory where to
> ## download the file:
> downloadGenomicSequencesFromUCSC("sacCer1", destdir=tempdir())
trying URL 'https://hgdownload.soe.ucsc.edu/goldenPath/sacCer1/bigZips/sacCer1.2bit'
Content type 'unknown' length 3039530 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

> 
> ## Download and import the file in R as a DNAStringSet object:
> filepath <- downloadGenomicSequencesFromUCSC("sacCer1", destdir=tempdir())
trying URL 'https://hgdownload.soe.ucsc.edu/goldenPath/sacCer1/bigZips/sacCer1.2bit'
Content type 'unknown' length 3039530 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

> genomic_sequences <- import(filepath)
Warning in .seqlengths_TwoBitFile(con) : End of file reading 4 bytes
Error in .seqlengths_TwoBitFile(con) : UCSC library operation failed
Calls: import ... import -> import -> .local -> .seqlengths_TwoBitFile
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/BSgenomeForge.Rcheck/00check.log'
for details.