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This page was generated on 2023-10-13 11:32:17 -0400 (Fri, 13 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4346
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 88/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.60.0  (landing page)
Jose Marugan
Snapshot Date: 2023-10-08 14:00:07 -0400 (Sun, 08 Oct 2023)
git_url: https://git.bioconductor.org/packages/ArrayExpress
git_branch: RELEASE_3_17
git_last_commit: e1d39c3
git_last_commit_date: 2023-04-25 09:47:37 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    ERROR    OK  

CHECK results for ArrayExpress on kjohnson2


To the developers/maintainers of the ArrayExpress package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: ArrayExpress
Version: 1.60.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ArrayExpress_1.60.0.tar.gz
StartedAt: 2023-10-10 01:06:10 -0400 (Tue, 10 Oct 2023)
EndedAt: 2023-10-10 01:11:47 -0400 (Tue, 10 Oct 2023)
EllapsedTime: 337.1 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ArrayExpress.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ArrayExpress.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ArrayExpress_1.60.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ArrayExpress.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpress/DESCRIPTION’ ... OK
* this is package ‘ArrayExpress’ version ‘1.60.0’
* 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 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 sizes of PDF files under ‘inst/doc’ ... 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: 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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp7.CEL': FTP status was '421 Service not available, closing control connection'
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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp4.CEL': FTP status was '421 Service not available, closing control connection'
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'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx2.CEL': FTP status was '421 Service not available, closing control connection'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx2.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx2.CEL  does not exist or is empty. 

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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc2.CEL': FTP status was '421 Service not available, closing control connection'
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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc4.CEL': FTP status was '421 Service not available, closing control connection'
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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx1.CEL': FTP status was '421 Service not available, closing control connection'
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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp3.CEL': FTP status was '421 Service not available, closing control connection'
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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp6.CEL': FTP status was '421 Service not available, closing control connection'
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'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp5.CEL': FTP status was '421 Service not available, closing control connection'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp5.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp5.CEL  does not exist or is empty. 

Downloading file: cc6.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc6.CEL'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc6.CEL': FTP status was '421 Service not available, closing control connection'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc6.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc6.CEL  does not exist or is empty. 

Downloading file: cx4.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx4.CEL'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx4.CEL': FTP status was '421 Service not available, closing control connection'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx4.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx4.CEL  does not exist or is empty. 

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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp2.CEL': FTP status was '421 Service not available, closing control connection'
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'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc3.CEL': FTP status was '421 Service not available, closing control connection'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc3.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc3.CEL  does not exist or is empty. 

Downloading file: cp1.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp1.CEL'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp1.CEL': FTP status was '421 Service not available, closing control connection'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp1.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cp1.CEL  does not exist or is empty. 

Downloading file: cx3.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx3.CEL'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx3.CEL': FTP status was '421 Service not available, closing control connection'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx3.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx3.CEL  does not exist or is empty. 

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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc5.CEL': FTP status was '421 Service not available, closing control connection'
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'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx5.CEL': FTP status was '421 Service not available, closing control connection'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx5.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cx5.CEL  does not exist or is empty. 

Downloading file: cc1.CEL

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc1.CEL'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc1.CEL': FTP status was '421 Service not available, closing control connection'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc1.CEL'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/cc1.CEL  does not exist or is empty. 

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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.idf.txt': FTP status was '421 Service not available, closing control connection'
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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-TABM-/025/E-TABM-25/Files/E-TABM-25.sdrf.txt': FTP status was '421 Service not available, closing control connection'
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 in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘sampleNames’ for signature ‘"NULL"’
Calls: sampleNames -> <Anonymous>
Execution halted
* 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
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ArrayExpress.Rcheck/00check.log’
for details.

Installation output

ArrayExpress.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ArrayExpress
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘ArrayExpress’ ...
** 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)

Tests output

Example timings

ArrayExpress.Rcheck/ArrayExpress-Ex.timings

nameusersystemelapsed