* using log directory 'd:/Rcompile/CRANpkg/local/4.5/BioUtils.Rcheck'
* using R version 4.5.3 (2026-03-11 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'BioUtils/DESCRIPTION' ... OK
* this is package 'BioUtils' version '0.1.3'
* 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 'BioUtils' can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
* 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 ... [0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s] OK
* checking whether the package can be unloaded cleanly ... [0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [0s] OK
* checking use of S3 registration ... 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 ... [3s] OK
* checking Rd files ... [1s] 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [1s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [129s] ERROR
Error(s) in re-building vignettes:
--- re-building 'bioutils-case-study.Rmd' using rmarkdown
Warning: stack imbalance in '<-', 65 then 67
Warning: stack imbalance in 'withVisible', 59 then 61
--- finished re-building 'bioutils-case-study.Rmd'

--- re-building 'rcc-visual-analytics.Rmd' using rmarkdown

Quitting from rcc-visual-analytics.Rmd:153-162 [load]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/httr2_failure>
Error in `httr2::req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Transferred a partial file [ftp.ncbi.nlm.nih.gov]:
end of response with 1063310 bytes missing
---
Backtrace:
     ▆
  1. ├─BioUtils::extract.expression(...)
  2. └─BioUtils::load.geo.soft(accession = "GDS507", log.transform = TRUE)
  3.   └─GEOquery::getGEO(accession, destdir = tempdir(), GSEMatrix = FALSE)
  4.     └─GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL)
  5.       └─GEOquery:::downloadFile(myurl, destfile, mode)
  6.         ├─base::tryCatch(...)
  7.         │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  8.         │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9.         │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 10.         └─httr2::req_perform(req)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'rcc-visual-analytics.Rmd' failed with diagnostics:
Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Transferred a partial file [ftp.ncbi.nlm.nih.gov]:
end of response with 1063310 bytes missing
--- failed re-building 'rcc-visual-analytics.Rmd'

SUMMARY: processing the following file failed:
  'rcc-visual-analytics.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [16s] OK
* checking HTML version of manual ... [4s] OK
* DONE
Status: 1 ERROR