##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:ExpressionAtlas.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ExpressionAtlas_2.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/ExpressionAtlas.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ExpressionAtlas/DESCRIPTION’ ... OK
* this is package ‘ExpressionAtlas’ version ‘2.1.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Depends: includes the non-default packages:
  'Biobase', 'SummarizedExperiment', 'limma', 'S4Vectors', 'xml2',
  'RCurl', 'jsonlite', 'BiocStyle'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘ExpressionAtlas’ 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 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 ... ERROR
Running examples in ‘ExpressionAtlas-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name:  searchAtlasExperiments 
> ### Title: Search for Expression Atlas experiments
> ### Aliases: ' searchAtlasExperiments '
> 
> ### ** Examples
> 
>     
>     # Search for experiments on salt in oryza (rice)
>     atlasRes <- searchAtlasExperiments( properties = "salt", species = "oryza"  )
Searching for Expression Atlas experiments matching your query ...
Query successful.
Found 8 experiments matching your query.
Retrieving information from 8 experiments...
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Could not connect to server [ftp.ebi.ac.uk]:
Failed to connect to ftp.ebi.ac.uk port 443 after 1174 ms: Could not connect to server
Calls: searchAtlasExperiments ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
getAtlasData       0.273  0.159 115.632
getAtlasExperiment 0.081  0.003   5.227
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/ExpressionAtlas.Rcheck/00check.log’
for details.