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This page was generated on 2025-12-05 11:35 -0500 (Fri, 05 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" 4869
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" 4576
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 98/2331HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.71.0  (landing page)
Jose Marugan
Snapshot Date: 2025-12-04 13:40 -0500 (Thu, 04 Dec 2025)
git_url: https://git.bioconductor.org/packages/ArrayExpress
git_branch: devel
git_last_commit: 4a25159
git_last_commit_date: 2025-10-29 10:01:28 -0500 (Wed, 29 Oct 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for ArrayExpress on kjohnson3

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.
- 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: 1.71.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ArrayExpress
StartedAt: 2025-12-04 15:38:42 -0500 (Thu, 04 Dec 2025)
EndedAt: 2025-12-04 15:41:18 -0500 (Thu, 04 Dec 2025)
EllapsedTime: 155.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘ArrayExpress.Rnw’ using Sweave
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.cel': FTP status was '550 Requested action not taken; file unavailable'
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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21-processed-data-2487199618.txt': FTP status was '550 Requested action not taken; file unavailable'
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 '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/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'
Content type 'unknown' length 7329097 bytes (7.0 MB)

Warning in download.file(url, filedest) :
  downloaded length 0 != reported length 7329097
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 'Transferred a partial file'
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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.cel': FTP status was '550 Requested action not taken; file unavailable'
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'
Content type 'unknown' length 1683750 bytes (1.6 MB)
====================================
Warning in download.file(url, filedest) :
  downloaded length 1245184 != reported length 1683750
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 'Transferred a partial file'
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'
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'
Content type 'unknown' length 4096 bytes

Warning in download.file(url, filedest) :
  downloaded length 0 != reported length 4096
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 'Transferred a partial file'
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'
Warning in download.file(url, filedest) :
  downloaded length 0 != reported length 199
Warning in download.file(url, filedest) :
  cannot open URL 'https://ftp.ebi.ac.uk/biostudies/fire/A-AFFY-/032/A-AFFY-32/Files/A-AFFY-32.adf.txt': HTTP status was '403 Forbidden'
Error in download.file(url, filedest) : 
  cannot open URL 'https://www.ebi.ac.uk/biostudies/files/A-AFFY-32/A-AFFY-32.adf.txt'
Warning in getAE(accession, path = path, type = "full") :
  https://www.ebi.ac.uk/biostudies/files/A-AFFY-32/A-AFFY-32.adf.txt  does not exist or is empty. 

Unpacking data files
Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) : 
  ArrayExpress: Experiment has no raw files available. Consider using processed data instead by following procedure in the vignette
Downloading file: 30_v4_v4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr': 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-/870/E-MEXP-1870/Files/30_v4_v4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr': FTP status was '550 Requested action not taken; file unavailable'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr': FTP status was '550 Requested action not taken; file unavailable'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr': FTP status was '550 Requested action not taken; file unavailable'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr'
Content type 'unknown' length 5335570 bytes (5.1 MB)
==================================================
Downloading file: 11_v4_v3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr'
Content type 'unknown' length 5385618 bytes (5.1 MB)
========================================
Warning in download.file(url, filedest) :
  downloaded length 4333568 != reported length 5385618
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/11_v4_v3.gpr': status was 'Transferred a partial file'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr'
Content type 'unknown' length 5304968 bytes (5.1 MB)
==================================================
Downloading file: 12_v4_v3.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr'
Content type 'unknown' length 5358829 bytes (5.1 MB)
=
Warning in download.file(url, filedest) :
  downloaded length 131072 != reported length 5358829
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/12_v4_v3.gpr': status was 'Transferred a partial file'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr'
Content type 'unknown' length 5344579 bytes (5.1 MB)
================================================
Warning in download.file(url, filedest) :
  downloaded length 5181440 != reported length 5344579
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/29_v4_v4.gpr': status was 'Transferred a partial file'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt'
Content type 'unknown' length 17908 bytes (17 KB)

Warning in download.file(url, filedest) :
  downloaded length 0 != reported length 17908
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.idf.txt': status was 'Transferred a partial file'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.sdrf.txt'
Content type 'unknown' length 14207 bytes (13 KB)
==================================================
Downloading file: A-MEXP-1425.adf.txt

trying URL 'https://www.ebi.ac.uk/biostudies/files/A-MEXP-1425/A-MEXP-1425.adf.txt'
Warning in download.file(url, filedest) :
  downloaded length 0 != reported length 199
Warning in download.file(url, filedest) :
  cannot open URL 'https://ftp.ebi.ac.uk/biostudies/fire/A-MEXP-/425/A-MEXP-1425/Files/A-MEXP-1425.adf.txt': HTTP status was '403 Forbidden'
Error in download.file(url, filedest) : 
  cannot open URL 'https://www.ebi.ac.uk/biostudies/files/A-MEXP-1425/A-MEXP-1425.adf.txt'
Warning in getAE(accession, path = path, type = "full") :
  https://www.ebi.ac.uk/biostudies/files/A-MEXP-1425/A-MEXP-1425.adf.txt  does not exist or is empty. 

Unpacking data files
Duplicates found in SDRF file
Removed duplicates in SDRF file
ArrayExpress: Reading pheno data from SDRF
Warning: non-unique values when setting 'row.names': ‘11_v4_v3.gpr’, ‘12_v4_v3.gpr’, ‘13_v3_v3.gpr’, ‘29_v4_v4.gpr’, ‘30_v4_v4.gpr’, ‘31_v4_v4.gpr’, ‘45_4_4.gpr’, ‘46_3_3.gpr’, ‘47_3_4.gpr’
Error in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed
Downloading file: 30_v4_v4.gpr

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/30_v4_v4.gpr': FTP status was '550 Requested action not taken; file unavailable'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr'
Content type 'unknown' length 5277770 bytes (5.0 MB)
=
Warning in download.file(url, filedest) :
  downloaded length 196608 != reported length 5277770
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/13_v3_v3.gpr': status was 'Transferred a partial file'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr'
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/31_v4_v4.gpr': 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-/870/E-MEXP-1870/Files/31_v4_v4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr'
Content type 'unknown' length 5493312 bytes (5.2 MB)
==
Warning in download.file(url, filedest) :
  downloaded length 262144 != reported length 5493312
Warning in download.file(url, filedest) :
  URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr': status was 'Transferred a partial file'
Error in download.file(url, filedest) : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/45_4_4.gpr  does not exist or is empty. 

Downloading file: 47_3_4.gpr

/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpEdh6xH/47_3_4.gpr already exists, skipping.
Downloading file: 11_v4_v3.gpr

/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpEdh6xH/11_v4_v3.gpr already exists, skipping.
Downloading file: 46_3_3.gpr

/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpEdh6xH/46_3_3.gpr already exists, skipping.
Downloading file: 12_v4_v3.gpr

/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpEdh6xH/12_v4_v3.gpr already exists, skipping.
Downloading file: 29_v4_v4.gpr

/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpEdh6xH/29_v4_v4.gpr already exists, skipping.
Downloading file: E-MEXP-1870.idf.txt

trying URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.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-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/fire/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

/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpEdh6xH/E-MEXP-1870.sdrf.txt already exists, skipping.
Downloading file: A-MEXP-1425.adf.txt

trying URL 'https://www.ebi.ac.uk/biostudies/files/A-MEXP-1425/A-MEXP-1425.adf.txt'
Warning in download.file(url, filedest) :
  downloaded length 0 != reported length 199
Warning in download.file(url, filedest) :
  cannot open URL 'https://ftp.ebi.ac.uk/biostudies/fire/A-MEXP-/425/A-MEXP-1425/Files/A-MEXP-1425.adf.txt': HTTP status was '403 Forbidden'
Error in download.file(url, filedest) : 
  cannot open URL 'https://www.ebi.ac.uk/biostudies/files/A-MEXP-1425/A-MEXP-1425.adf.txt'
Warning in getAE(accession, path = path, type = "full") :
  https://www.ebi.ac.uk/biostudies/files/A-MEXP-1425/A-MEXP-1425.adf.txt  does not exist or is empty. 

Unpacking data files
Duplicates found in SDRF file
Removed duplicates in SDRF file
ArrayExpress: Reading pheno data from SDRF
Warning: non-unique values when setting 'row.names': ‘11_v4_v3.gpr’, ‘12_v4_v3.gpr’, ‘13_v3_v3.gpr’, ‘29_v4_v4.gpr’, ‘30_v4_v4.gpr’, ‘31_v4_v4.gpr’, ‘45_4_4.gpr’, ‘46_3_3.gpr’, ‘47_3_4.gpr’
Error in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed
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)
====
Warning in download.file(url, filedest) :
  downloaded length 724992 != reported length 7317392
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 'Transferred a partial file'
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'
Content type 'unknown' length 1683750 bytes (1.6 MB)

Warning in download.file(url, filedest) :
  downloaded length 0 != reported length 1683750
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 'Transferred a partial file'
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'
Content type 'unknown' length 7340006 bytes (7.0 MB)

Warning in download.file(url, filedest) :
  downloaded length 0 != reported length 7340006
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 'Transferred a partial file'
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'
Content type 'unknown' length 7329097 bytes (7.0 MB)
=======================
Warning in download.file(url, filedest) :
  downloaded length 3407872 != reported length 7329097
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 'Transferred a partial file'
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'
Content type 'unknown' length 7343156 bytes (7.0 MB)

Warning in download.file(url, filedest) :
  downloaded length 0 != reported length 7343156
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 'Transferred a partial file'
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'
Content type 'unknown' length 1683750 bytes (1.6 MB)
===
Warning in download.file(url, filedest) :
  downloaded length 131072 != reported length 1683750
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 'Transferred a partial file'
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'
Content type 'unknown' length 7299 bytes

Warning in download.file(url, filedest) :
  downloaded length 0 != reported length 7299
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 'Transferred a partial file'
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'
Content type 'unknown' length 4096 bytes

Warning in download.file(url, filedest) :
  downloaded length 0 != reported length 4096
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 'Transferred a partial file'
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'
Warning in download.file(url, filedest) :
  downloaded length 0 != reported length 199
Warning in download.file(url, filedest) :
  cannot open URL 'https://ftp.ebi.ac.uk/biostudies/fire/A-AFFY-/032/A-AFFY-32/Files/A-AFFY-32.adf.txt': HTTP status was '403 Forbidden'
Error in download.file(url, filedest) : 
  cannot open URL 'https://www.ebi.ac.uk/biostudies/files/A-AFFY-32/A-AFFY-32.adf.txt'
Warning in getAE("E-MEXP-21", type = "full") :
  https://www.ebi.ac.uk/biostudies/files/A-AFFY-32/A-AFFY-32.adf.txt  does not exist or is empty. 

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