##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:homosapienDEE2CellScore.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings homosapienDEE2CellScore_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/homosapienDEE2CellScore.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘homosapienDEE2CellScore/DESCRIPTION’ ... OK
* this is package ‘homosapienDEE2CellScore’ version ‘1.6.0’
* 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 ‘homosapienDEE2CellScore’ 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 whether startup messages can be suppressed ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘homosapienDEE2CellScore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: buildData
> ### Title: buildData builds the data included in this package
> ### Aliases: buildData
> 
> ### ** Examples
> 
> # To build the default, full dataset, and write it out to several csv files:
> #homosapienDEE2CellScore::buildData()
> 
> # To build a restricted set of data, with a cached metadata file,
> # only running deseq2 normalisation, to "data_PASS_deseq2.csv" and "data_WARN_deseq2.csv"
> metadata <- getDEE2::getDEE2Metadata("hsapiens", quiet=TRUE)
Warning in FUN(URL, ...) :
  downloaded length 59207938 != reported length 80467693
Warning in FUN(URL, ...) :
  URL 'https://dee2.io/metadata/hsapiens_metadata.tsv.cut': Timeout of 600 seconds was reached
Error in getURL(URL = metadataURL, FUN = download.file, N.TRIES = 1L,  : 
  'getURL()' failed:
  URL: http://dee2.io/metadata/hsapiens_metadata.tsv.cut
  error: download from 'http://dee2.io/metadata/hsapiens_metadata.tsv.cut' failed
Calls: <Anonymous> -> getURL
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-3.22-data-experiment/meat/homosapienDEE2CellScore.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL homosapienDEE2CellScore
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘homosapienDEE2CellScore’ ...
** this is package ‘homosapienDEE2CellScore’ version ‘1.6.0’
** using staged installation
** R
** inst
** 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 (homosapienDEE2CellScore)