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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:TMExplorer.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings TMExplorer_1.21.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-data-experiment/meat/TMExplorer.Rcheck’
* using R Under development (unstable) (2025-12-22 r89219)
* 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 ‘TMExplorer/DESCRIPTION’ ... OK
* this is package ‘TMExplorer’ version ‘1.21.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘TMExplorer’ 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘TMExplorer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: queryTME
> ### Title: A function to query TME datasets available in this package
> ### Aliases: queryTME
> ### Keywords: tumour
> 
> ### ** Examples
> 
> 
> ## Retrieve the metadata table to see what data is available
> res <- queryTME(metadata_only = TRUE)
> 
> ## Retrieve a filtered metadata table that only shows datasets with 
> ## cell type annotations and cell type gene signatures
> res <- queryTME(has_truth = TRUE, has_signatures = TRUE, metadata_only = TRUE)
> 
> ## Retrieve a single dataset identified from the table
> res <- queryTME(geo_accession = "GSE72056")
Warning: download failed
  web resource path: ‘https://ndownloader.figshare.com/files/27622811?private_link=f3720f94a2a9e8f2eaa7’
  local file path: ‘/tmp/RtmpDBiaXI/file2413d5a97931a/2413d51a79a557_27622811%3Fprivate_link%3Df3720f94a2a9e8f2eaa7’
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Transferred a partial file [s3-eu-west-1.amazonaws.com]:
transfer closed with 31438992 bytes remaining to read
Warning: bfcadd() failed; resource removed
  rid: BFC1
  fpath: ‘https://ndownloader.figshare.com/files/27622811?private_link=f3720f94a2a9e8f2eaa7’
  reason: download failed
Error in .util_download(x, rid[i], proxy, progress, config, "bfcadd()",  : 
  bfcadd() failed; see warnings()
Calls: queryTME ... fetchTME -> downloadTME -> bfcadd -> bfcadd -> .util_download
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-data-experiment/meat/TMExplorer.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL TMExplorer
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘TMExplorer’ ...
** this is package ‘TMExplorer’ version ‘1.21.0’
** using staged installation
** R
** 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 (TMExplorer)