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This page was generated on 2023-04-12 10:55:33 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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BUILD results for ArrayExpress on nebbiolo2


To the developers/maintainers of the ArrayExpress package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ArrayExpress.git to reflect on this report. See Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 88/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.59.3  (landing page)
Jose Marugan
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/ArrayExpress
git_branch: devel
git_last_commit: e6b84e0
git_last_commit_date: 2023-03-20 05:57:29 -0400 (Mon, 20 Mar 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    ERROR  skipped

Summary

Package: ArrayExpress
Version: 1.59.3
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ArrayExpress
StartedAt: 2023-04-12 02:12:04 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 02:13:04 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 60.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data ArrayExpress
###
##############################################################################
##############################################################################


* checking for file ‘ArrayExpress/DESCRIPTION’ ... OK
* preparing ‘ArrayExpress’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘ArrayExpress.Rnw’ using Sweave
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Downloading file: 1203aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel  does not exist or is empty. 

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'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt': status was 'Couldn't connect to server'
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-processed-data-2487199618.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt  does not exist or is empty. 

Downloading file: 1205aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel  does not exist or is empty. 

Downloading file: 1202aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel  does not exist or is empty. 

Downloading file: 1204aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel  does not exist or is empty. 

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'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt': status was 'Couldn't connect to server'
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-processed-data-2487199618.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt  does not exist or is empty. 

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'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt': status was 'Couldn't connect to server'
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.idf.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt  does not exist or is empty. 

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 'Couldn't connect to server'
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(accession, path = path, 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' length 790789 bytes (772 KB)
==================================================
downloaded 772 KB

Unpacking data files
Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) : 
  No SDRF file found.
Downloading file: 30_v4_v4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr  does not exist or is empty. 

Downloading file: 13_v3_v3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr  does not exist or is empty. 

Downloading file: 31_v4_v4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr  does not exist or is empty. 

Downloading file: 45_4_4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr  does not exist or is empty. 

Downloading file: 47_3_4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr  does not exist or is empty. 

Downloading file: 11_v4_v3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr  does not exist or is empty. 

Downloading file: 46_3_3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr  does not exist or is empty. 

Downloading file: 12_v4_v3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr  does not exist or is empty. 

Downloading file: 29_v4_v4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr  does not exist or is empty. 

Downloading file: E-MEXP-1870.idf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt  does not exist or is empty. 

Downloading file: E-MEXP-1870.sdrf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt  does not exist or is empty. 

Downloading file: A-MEXP-1425.adf.txt

trying URL 'https://www.ebi.ac.uk/biostudies/files/A-MEXP-1425/A-MEXP-1425.adf.txt'
Content type 'text/plain' length 768845 bytes (750 KB)
==================================================
downloaded 750 KB

Unpacking data files
Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) : 
  No SDRF file found.
Downloading file: 30_v4_v4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr  does not exist or is empty. 

Downloading file: 13_v3_v3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr  does not exist or is empty. 

Downloading file: 31_v4_v4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr  does not exist or is empty. 

Downloading file: 45_4_4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr  does not exist or is empty. 

Downloading file: 47_3_4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr  does not exist or is empty. 

Downloading file: 11_v4_v3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr  does not exist or is empty. 

Downloading file: 46_3_3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr  does not exist or is empty. 

Downloading file: 12_v4_v3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr  does not exist or is empty. 

Downloading file: 29_v4_v4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr  does not exist or is empty. 

Downloading file: E-MEXP-1870.idf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt  does not exist or is empty. 

Downloading file: E-MEXP-1870.sdrf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/nfs/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt  does not exist or is empty. 

Downloading file: A-MEXP-1425.adf.txt

/tmp/Rtmp3Bn6g7/A-MEXP-1425.adf.txt already exists, skipping.
Unpacking data files
Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) : 
  No SDRF file found.
Downloading file: 1203aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel'
Warning in getAE("E-MEXP-21", type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel  does not exist or is empty. 

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'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt': status was 'Couldn't connect to server'
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-processed-data-2487199618.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-processed-data-2487199618.txt  does not exist or is empty. 

Downloading file: 1205aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel'
Warning in getAE("E-MEXP-21", type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.cel  does not exist or is empty. 

Downloading file: 1202aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel'
Warning in getAE("E-MEXP-21", type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.cel  does not exist or is empty. 

Downloading file: 1204aa.cel

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel': status was 'Couldn't connect to server'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel'
Warning in getAE("E-MEXP-21", type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel  does not exist or is empty. 

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'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt': status was 'Couldn't connect to server'
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-processed-data-2487199618.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-processed-data-2487199618.txt  does not exist or is empty. 

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'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.idf.txt': status was 'Couldn't connect to server'
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.idf.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.idf.txt  does not exist or is empty. 

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 'Couldn't connect to server'
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' length 790789 bytes (772 KB)
==================================================
downloaded 772 KB

Unpacking data files

Error: processing vignette 'ArrayExpress.Rnw' failed with diagnostics:
 chunk 6 (label = ae2bioc-full) 
Error in ae2bioc(mageFiles = mexp1422) : No SDRF file found.

--- failed re-building ‘ArrayExpress.Rnw’

SUMMARY: processing the following file failed:
  ‘ArrayExpress.Rnw’

Error: Vignette re-building failed.
Execution halted