Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-12 17:39 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 90/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpress 1.64.0  (landing page)
Jose Marugan
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/ArrayExpress
git_branch: RELEASE_3_19
git_last_commit: d95a2bf
git_last_commit_date: 2024-04-30 10:18:48 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD results for ArrayExpress on palomino7

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: 1.64.0
Command: chmod a+r ArrayExpress -R && E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data ArrayExpress
StartedAt: 2024-07-11 16:38:18 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 16:40:32 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 134.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r ArrayExpress -R && E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe 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, 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'
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

E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis/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'
Content type 'unknown' length 3791 bytes
==================================================
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
ArrayExpress: Reading pheno data from SDRF
ArrayExpress: Reading data files
Loading required package: pd.hu6800
Attempting to obtain 'pd.hu6800' from BioConductor website.
Checking to see if your internet connection works...
installing the source package 'pd.hu6800'

trying URL 'https://bioconductor.org/packages/3.19/data/annotation/src/contrib/pd.hu6800_3.12.0.tar.gz'
Content type 'application/x-gzip' length 4403663 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

* installing *source* package 'pd.hu6800' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (pd.hu6800)

The downloaded source packages are in
	'E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis\downloaded_packages'
Loading required package: pd.hu6800
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: RSQLite
Loading required package: oligoClasses
Welcome to oligoClasses version 1.66.0
Loading required package: oligo
================================================================================
Welcome to oligo version 1.68.2
================================================================================
Loading required package: DBI
Platform design info loaded.
Read 48 items

 E-MEXP-21  was successfully loaded into  ExpressionFeatureSet 

Warning in file.remove(file.path(path, basename(mageFiles$processedFiles),  :
  cannot remove file 'E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis\E-MEXP-21-processed-data-2487199618.txt', reason 'No such file or directory'
Warning in file.remove(file.path(path, basename(mageFiles$rawArchive), fsep = sep)) :
  cannot remove file 'E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis\1203aa.cel', reason 'No such file or directory'
Warning in file.remove(file.path(path, basename(mageFiles$rawArchive), fsep = sep)) :
  cannot remove file 'E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis\E-MEXP-21-processed-data-2487199618.txt', reason 'No such file or directory'
Warning in file.remove(file.path(path, basename(mageFiles$rawArchive), fsep = sep)) :
  cannot remove file 'E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis\1205aa.cel', reason 'No such file or directory'
Warning in file.remove(file.path(path, basename(mageFiles$rawArchive), fsep = sep)) :
  cannot remove file 'E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis\1202aa.cel', reason 'No such file or directory'
Warning in file.remove(file.path(path, basename(mageFiles$rawArchive), fsep = sep)) :
  cannot remove file 'E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis\1204aa.cel', reason 'No such file or directory'
Warning in file.remove(file.path(path, basename(mageFiles$processedArchive),  :
  cannot remove file 'E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis\E-MEXP-21-processed-data-2487199618.txt', reason 'No such file or directory'
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'
Content type 'unknown' length 5350610 bytes (5.1 MB)
==================================================
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)
==================================================
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 '421 Service not available, closing control connection'
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)
==================================================
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'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr': 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-MEXP-/870/E-MEXP-1870/Files/47_3_4.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/11_v4_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/11_v4_v3.gpr': 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-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'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr': 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-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/12_v4_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/12_v4_v3.gpr': 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-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)
==================================================
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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.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-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'
Warning 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.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-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/fire/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; charset=UTF-8' 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

E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis/30_v4_v4.gpr already exists, skipping.
Downloading file: 13_v3_v3.gpr

E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis/13_v3_v3.gpr already exists, skipping.
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 '421 Service not available, closing control connection'
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

E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis/45_4_4.gpr already exists, skipping.
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'
Warning 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': 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-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'
Warning in download.file(url, filedest) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr': 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-MEXP-/870/E-MEXP-1870/Files/46_3_3.gpr'
Warning in getAE(accession, path = path, type = "full") :
  ftp://ftp.ebi.ac.uk/biostudies/fire/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/fire/E-MEXP-/870/E-MEXP-1870/Files/12_v4_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/12_v4_v3.gpr': 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-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

E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis/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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/870/E-MEXP-1870/Files/E-MEXP-1870.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-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'
Warning 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.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-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/fire/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

E:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8m4Sis/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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1203aa.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-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)
==================================================
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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1205aa.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-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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1202aa.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-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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/1204aa.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-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

E:/biocbuild/bbs-3.19-bioc/tmpdir/Rtmp4eg5Zv/Rbuild2e9015dd6348/ArrayExpress/vignettes/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'
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.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-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) :
  cannot open URL 'ftp://ftp.ebi.ac.uk/biostudies/fire/E-MEXP-/021/E-MEXP-21/Files/E-MEXP-21.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-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

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