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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RGSEA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RGSEA_1.40.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RGSEA.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘RGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RGSEA’ version ‘1.40.0’
* 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 ‘RGSEA’ 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 ... NOTE
Auto-generated content requiring editing in Rd file 'RGSEA-package.Rd':
  \details: ‘...o use the package, including the most important functions ~~’
  \references: ‘~~ Literature or other references for background information ~~’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘RGSEA.Rnw’ using knitr

Quitting from RGSEA.Rnw:83-87 [RGSEA-DOWNLOAD]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 'colnames': error in evaluating the argument 'object' in selecting a method for function 'Table': HTTP 404 Not Found.
---
Backtrace:
     x
  1. +-GEOquery::GDS2eSet(getGEO("GDS4100"))
  2. | +-base::grep("GSM", colnames(Table(GDS)))
  3. | | \-base::is.factor(x)
  4. | +-BiocGenerics::colnames(Table(GDS))
  5. | \-GEOquery::Table(GDS)
  6. +-GEOquery::getGEO("GDS4100")
  7. | \-GEOquery::getGEOfile(GEO, destdir = destdir, AnnotGPL = AnnotGPL)
  8. |   \-GEOquery:::downloadFile(myurl, destfile, mode)
  9. |     \-base::tryCatch(...)
 10. |       \-base (local) tryCatchList(expr, classes, parentenv, handlers)
 11. |         \-base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12. |           \-value[[3L]](cond)
 13. |             \-base::message(e)
 14. |               +-base::withRestarts(...)
 15. |               | \-base (local) withOneRestart(expr, restarts[[1L]])
 16. |               |   \-base (local) doWithOneRestart(return(expr), restart)
 17. |               \-base::signalCondition(cond)
 18. +-base (local) `<fn>`(`<ht2__404>`)
 19. \-base::.handleSimpleError(...)
 20.   \-base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RGSEA.Rnw' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'colnames': error in evaluating the argument 'object' in selecting a method for function 'Table': HTTP 404 Not Found.
--- failed re-building ‘RGSEA.Rnw’

SUMMARY: processing the following file failed:
  ‘RGSEA.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/RGSEA.Rcheck/00check.log’
for details.