##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ExpressionAtlas.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ExpressionAtlas_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/ExpressionAtlas.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ExpressionAtlas/DESCRIPTION' ... OK
* this is package 'ExpressionAtlas' version '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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 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 R 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 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...
Warning in open.connection(con, "rb") :
  cannot open URL 'https://www.ebi.ac.uk/biostudies/api/v1/studies/E-GEOD-58603': HTTP status was '500 Internal Server Error'
Error in open.connection(con, "rb") : 
  cannot open the connection to 'http://www.ebi.ac.uk/biostudies/api/v1/studies/E-GEOD-58603'
Calls: searchAtlasExperiments ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc/meat/ExpressionAtlas.Rcheck/00check.log'
for details.