- using R version 4.6.1 Patched (2026-07-27 r90311)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-15 (Debian 15.3.0-1) 15.3.0
GNU Fortran (Debian 15.3.0-1) 15.3.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
* current time: 2026-07-29 03:13:51 UTC
- 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 executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking serialization versions ... OK
- checking whether package ‘BioUtils’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... 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/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/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 ... [4s/5s] OK
- checking Rd files ... [0s/1s] OK
- checking Rd metadata ... OK
- checking Rd line widths ... 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 ... [0s/1s] OK
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [54s/78s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘bioutils-case-study.Rmd’ using rmarkdown
--- 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 1030542 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 1030542 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 ... [5s/7s] OK
- checking HTML version of manual ... [2s/3s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR