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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings ArrayExpress_1.68.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/ArrayExpress.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘ArrayExpress/DESCRIPTION’ ... OK
* this is package ‘ArrayExpress’ version ‘1.68.0’
* 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 ‘ArrayExpress’ 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'ArrayExpress.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'ae2bioc.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'procset.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ‘ArrayExpress-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getAE
> ### Title: Download MAGE-TAB files from the ArrayExpress collection in a
> ###   specified directory
> ### Aliases: getAE
> ### Keywords: datasets
> 
> ### ** Examples
> 
> mexp21 = getAE("E-MEXP-21", type = "full")
Downloading file: 1203aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel'
Content type 'unknown' length 7317392 bytes (7.0 MB)
==================================================
Downloading file: E-MEXP-21-processed-data-2487199618.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt'
Content type 'unknown' length 1683750 bytes (1.6 MB)
==================================================
Downloading file: 1205aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel'
Content type 'unknown' length 7340006 bytes (7.0 MB)
==================================================
Downloading file: 1202aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel'
Content type 'unknown' length 7329097 bytes (7.0 MB)
==================================================
Downloading file: 1204aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel'
Content type 'unknown' length 7343156 bytes (7.0 MB)
==================================================
Downloading file: E-MEXP-21-processed-data-2487199618.txt

/home/biocbuild/bbs-3.21-bioc/meat/ArrayExpress.Rcheck/E-MEXP-21-processed-data-2487199618.txt already exists, skipping.
Downloading file: E-MEXP-21.idf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt'
Content type 'unknown' length 7299 bytes
==================================================
Downloading file: E-MEXP-21.sdrf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt': status was 'Failure when receiving data from the peer'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt'
Warning in getAE("E-MEXP-21", type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.sdrf.txt  does not exist or is empty. 

Downloading file: A-AFFY-32.adf.txt

trying URL 'https://www.ebi.ac.uk/biostudies/files/A-AFFY-32/A-AFFY-32.adf.txt'
Content type 'text/plain; charset=UTF-8' length 790789 bytes (772 KB)
==================================================
downloaded 772 KB

Unpacking data files
> 
> ## Build a an ExpressionSet from the raw data
> MEXP21raw = ae2bioc(mageFiles = mexp21)
Warning in file(file, "rt") :
  'raw = FALSE' but '/home/biocbuild/bbs-3.21-bioc/meat/ArrayExpress.Rcheck/' is not a regular file
Warning in file(file, "rt") :
  cannot open file '/home/biocbuild/bbs-3.21-bioc/meat/ArrayExpress.Rcheck/': it is a directory
Error in file(file, "rt") : cannot open the connection
Calls: ae2bioc -> read.delim -> read.table -> file
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
ArrayExpress 30.608  2.439  87.325
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL ArrayExpress
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘ArrayExpress’ ...
** this is package ‘ArrayExpress’ version ‘1.68.0’
** 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 (ArrayExpress)