##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ArrayExpress_1.71.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ArrayExpress.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘1.71.0’
* 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 sizes of PDF files under ‘inst/doc’ ...* 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: ArrayExpress
> ### Title: R objects from ArrayExpress collection
> ### Aliases: ArrayExpress
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ETABM25.affybatch = ArrayExpress("E-TABM-25")
Downloading file: cp7.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp7.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp7.CEL': 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-TABM-/025/E-TABM-25/Files/cp7.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp7.CEL  does not exist or is empty. 

Downloading file: cp4.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp4.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp4.CEL': 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-TABM-/025/E-TABM-25/Files/cp4.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp4.CEL  does not exist or is empty. 

Downloading file: cx2.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx2.CEL'
Content type 'unknown' length 9593339 bytes (9.1 MB)
==================================================
Downloading file: cc2.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc2.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc2.CEL': 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-TABM-/025/E-TABM-25/Files/cc2.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc2.CEL  does not exist or is empty. 

Downloading file: cc4.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc4.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc4.CEL': 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-TABM-/025/E-TABM-25/Files/cc4.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc4.CEL  does not exist or is empty. 

Downloading file: cx1.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx1.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx1.CEL': 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-TABM-/025/E-TABM-25/Files/cx1.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx1.CEL  does not exist or is empty. 

Downloading file: cp3.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp3.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp3.CEL': 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-TABM-/025/E-TABM-25/Files/cp3.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp3.CEL  does not exist or is empty. 

Downloading file: cp6.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp6.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp6.CEL': 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-TABM-/025/E-TABM-25/Files/cp6.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp6.CEL  does not exist or is empty. 

Downloading file: cp5.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp5.CEL'
Content type 'unknown' length 9608514 bytes (9.2 MB)
==================================================
Downloading file: cc6.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc6.CEL'
Content type 'unknown' length 9583909 bytes (9.1 MB)
==================================================
Downloading file: cx4.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx4.CEL'
Content type 'unknown' length 9566430 bytes (9.1 MB)
==================================================
Downloading file: cp2.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp2.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp2.CEL': 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-TABM-/025/E-TABM-25/Files/cp2.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp2.CEL  does not exist or is empty. 

Downloading file: cc3.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc3.CEL'
Content type 'unknown' length 9753457 bytes (9.3 MB)
==================================================
Downloading file: cp1.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp1.CEL'
Content type 'unknown' length 9594151 bytes (9.1 MB)
==================================================
Downloading file: cx3.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx3.CEL'
Content type 'unknown' length 9582638 bytes (9.1 MB)
==================================================
Downloading file: cc5.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc5.CEL'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc5.CEL': 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-TABM-/025/E-TABM-25/Files/cc5.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc5.CEL  does not exist or is empty. 

Downloading file: cx5.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx5.CEL'
Content type 'unknown' length 9593453 bytes (9.1 MB)
==================================================
Downloading file: cc1.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc1.CEL'
Content type 'unknown' length 9594808 bytes (9.2 MB)
==================================================
Downloading file: E-TABM-25.idf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.idf.txt'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.idf.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-TABM-/025/E-TABM-25/Files/E-TABM-25.idf.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.idf.txt  does not exist or is empty. 

Downloading file: E-TABM-25.sdrf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.sdrf.txt'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.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-TABM-/025/E-TABM-25/Files/E-TABM-25.sdrf.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.sdrf.txt  does not exist or is empty. 

Downloading file: A-AFFY-1.adf.txt

trying URL 'https://www.ebi.ac.uk/biostudies/files/A-AFFY-1/A-AFFY-1.adf.txt'
Content type 'text/plain; charset=UTF-8' length 1547751 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

Unpacking data files
Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) : 
  No SDRF file found.
> print(ETABM25.affybatch)
NULL
> sampleNames(ETABM25.affybatch)
Error: unable to find an inherited method for function ‘sampleNames’ for signature ‘object = "NULL"’
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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.