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Package 38/467HostnameOS / ArchBUILDCHECKBUILD BIN
ArrayExpress 1.12.1
Audrey Kauffmann
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/ArrayExpress
Last Changed Rev: 58517 / Revision: 59457
Last Changed Date: 2011-09-28 06:52:46 -0700 (Wed, 28 Sep 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  TIMEOUT  skipped 
liverpool Windows Server 2003 R2 (32-bit) / x64  ERROR  skipped  skipped 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386 [ ERROR ] skipped  skipped 

Summary

Package: ArrayExpress
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data ArrayExpress
StartedAt: 2011-10-20 11:35:51 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 11:40:07 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 255.2 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

* checking for file 'ArrayExpress/DESCRIPTION' ... OK
* preparing 'ArrayExpress':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: Biobase

Welcome to Bioconductor

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

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/xml/experiments?keywords=pneumonia&species=homo+sapiens'
Content type 'text/xml;charset=UTF-8' length unknown
opened URL
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .........
downloaded 189 Kb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/index.html'
Content type 'text/html;charset=UTF-8' length unknown
opened URL
........
downloaded 9015 bytes

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.raw.1.zip'
Content type 'application/zip' length 11986799 bytes (11.4 Mb)
opened URL
==================================================
downloaded 11.4 Mb

Read 1 item
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.sdrf.txt'
Content type 'text/plain' length 5084 bytes
opened URL
==================================================
downloaded 5084 bytes

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/A-AFFY-37/A-AFFY-37.adf.txt'
Content type 'text/plain' length 2685935 bytes (2.6 Mb)
opened URL
==================================================
downloaded 2.6 Mb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.idf.txt'
Content type 'text/plain' length 5379 bytes
opened URL
==================================================
downloaded 5379 bytes

Read 49 items

 The object containing experiment  E-MEXP-1422  has been built.

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1870/index.html'
Content type 'text/html;charset=UTF-8' length unknown
opened URL
........
downloaded 8363 bytes

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1870/E-MEXP-1870.raw.1.zip'
Content type 'application/zip' length 13223709 bytes (12.6 Mb)
opened URL
==================================================
downloaded 12.6 Mb

Read 82 items
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1870/E-MEXP-1870.sdrf.txt'
Content type 'text/plain' length 14207 bytes (13 Kb)
opened URL
==================================================
downloaded 13 Kb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/A-MEXP-1425/A-MEXP-1425.adf.txt'
Content type 'text/plain' length 1384856 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1870/E-MEXP-1870.idf.txt'
Content type 'text/plain' length 17908 bytes (17 Kb)
opened URL
==================================================
downloaded 17 Kb

Read 82 items
Error in nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) : 
  None of the columns names of the expression files is matching a valid known quantitation type.
Try to set the argument 'rawcol' by choosing among the following columns names: 
"ScanArray Express:% > B3+1SD" 
"ScanArray Express:% > B3+2SD" 
"ScanArray Express:% > B4+1SD" 
"ScanArray Express:% > B4+2SD" 
"ScanArray Express:% > B550+1SD" 
"ScanArray Express:% > B550+2SD" 
"ScanArray Express:% > B650+1SD" 
"ScanArray Express:% > B650+2SD" 
"ScanArray Express:B Pixels" 
"ScanArray Express:B3 Mean" 
"ScanArray Express:B3 Median" 
"ScanArray Express:B3 SD" 
"ScanArray Express:B4 Mean" 
"ScanArray Express:B4 Median" 
"ScanArray Express:B4 SD" 
"ScanArray Express:B550 Mean" 
"ScanArray Express:B550 Median" 
"ScanArray Express:B550 SD" 
"ScanArray Express:B650 Mean" 
"ScanArray Express:B650 Median" 
"ScanArray Express:B650 SD" 
"ScanArray Express:Dia." 
"ScanArray Express:F Pixels" 
"ScanArray Express:F3 % Sat." 
"ScanArray Express:F3 Mean" 
"ScanArray Express:F3 Mean - B3" 
"ScanArray Express:F3 Median" 
"ScanArray Express:F3 Median - B3" 
"ScanArray Express:F3 SD" 
"ScanArray Express:F4 % Sat." 
"ScanArray Express:F4 Mean" 
"ScanArray Express:F4 Mean - B4" 
"ScanArray Express:F4 Median" 
"ScanArray Express:F4 Median - B4" 
"ScanArray Express:F4 SD" 
"ScanArray Express:F550 % Sat." 
"ScanArray Express:F550 Mean" 
"ScanArray Express:F550 Mean - B550" 
"ScanArray Express:F550 Median" 
"ScanArray Express:F550 Median - B550" 
"ScanArray Express:F550 SD" 
"ScanArray Express:F650 % Sat." 
"ScanArray Express:F650 Mean" 
"ScanArray Express:F650 Mean - B650" 
"ScanArray Express:F650 Median" 
"ScanArray Express:F650 Median - B650" 
"ScanArray Express:F650 SD" 
"ScanArray Express:Flags" 
"ScanArray Express:ID" 
"ScanArray Express:Log Ratio (650/550)" 
"ScanArray Express:Log Ratio (Ratio/2)" 
"ScanArray Express:Log Ratio (Ratio/3)" 
"ScanArray Express:Mean of Ratios (650/550)" 
"ScanArray Express:Mean of Ratios (Ratio/2)" 
"ScanArray Express:Mean of Ratios (Ratio/3)" 
"ScanArray Express:Median of Ratios (650/550)" 
"ScanArray Express:Median of Ratios (Ratio/2)" 
"ScanArray Express:Median of Ratios (Ratio/3)" 
"ScanArray Express:Name" 
"ScanArray Express:Normalize" 
"ScanArray Express:Ratio of Means (650/550)" 
"ScanArray Express:Ratio of Means (Ratio/2)" 
"ScanArray Express:Ratio of Means (Ratio/3)" 
"ScanArray Express:Ratio of Medians (650/550)" 
"ScanArray Express:Ratio of Medians (Ratio/2)" 
"ScanArray Express:Ratio of Medians (Ratio/3)" 
"ScanArray Express:Ratios SD (650/550)" 
"ScanArray Express:Ratios SD (Ratio/2)" 
"ScanArray Express:Ratios SD (Ratio/3)" 
"ScanArray Express:Rgn Ratio (650/550)" 
"ScanArray Express:Rgn Ratio (Ratio/2)" 
"ScanArray Express:Rgn Ratio (Ratio/3)" 
"ScanArray Express:Rgn R? (650/550)" 
"ScanArray Express:Rgn R? (Ratio/2)" 
"ScanArray Express:Rgn R? (Ratio/3)" 
"ScanArray Express:Sum of Means" 
"ScanArray Express:Sum of Medians" 

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1870/index.html'
Content type 'text/html;charset=UTF-8' length unknown
opened URL
........
downloaded 8363 bytes

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1870/E-MEXP-1870.raw.1.zip'
Content type 'application/zip' length 13223709 bytes (12.6 Mb)
opened URL
==================================================
downloaded 12.6 Mb

Read 82 items
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1870/E-MEXP-1870.sdrf.txt'
Content type 'text/plain' length 14207 bytes (13 Kb)
opened URL
==================================================
downloaded 13 Kb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/A-MEXP-1425/A-MEXP-1425.adf.txt'
Content type 'text/plain' length 1384856 bytes (1.3 Mb)
opened URL
==================================================
downloaded 1.3 Mb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1870/E-MEXP-1870.idf.txt'
Content type 'text/plain' length 17908 bytes (17 Kb)
opened URL
==================================================
downloaded 17 Kb

Read 82 items
Read 49 items
Error in Ops.factor(adff2[, ri1], fn[, ri2]) : 
  level sets of factors are different
Warning in nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) :
  Cannot attach featureData

 The object containing experiment  E-MEXP-1870  has been built.

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/index.html'
Content type 'text/html;charset=UTF-8' length unknown
opened URL
........
downloaded 9015 bytes

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.raw.1.zip'
Content type 'application/zip' length 11986799 bytes (11.4 Mb)
opened URL
==================================================
downloaded 11.4 Mb

Read 1 item
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.processed.1.zip'
Content type 'application/zip' length 857419 bytes (837 Kb)
opened URL
==================================================
downloaded 837 Kb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.sdrf.txt'
Content type 'text/plain' length 5084 bytes
opened URL
==================================================
downloaded 5084 bytes

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/A-AFFY-37/A-AFFY-37.adf.txt'
Content type 'text/plain' length 2685935 bytes (2.6 Mb)
opened URL
==================================================
downloaded 2.6 Mb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.idf.txt'
Content type 'text/plain' length 5379 bytes
opened URL
==================================================
downloaded 5379 bytes

Read 49 items
Read 13 items
Read 49 items
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1416/index.html'
Content type 'text/html;charset=UTF-8' length unknown
opened URL
........
downloaded 8830 bytes

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1416/E-MEXP-1416.raw.1.zip'
Content type 'application/zip' length 126669334 bytes (120.8 Mb)
opened URL
=========
downloaded 23.7 Mb

Warning in download.file(paste(exp, ".raw.", i, ".zip", sep = ""), rawdata[[i]],  :
  downloaded length 24884653 != reported length 126669334
Warning in unzip(zipfile = file.path(path[i], topic[i]), exdir = extractpath) :
  error 1 in extracting from zip file

Error: processing vignette 'ArrayExpress.Rnw' failed with diagnostics:
 chunk 9 (label = import) 
Error in unzip(zipfile = file.path(path[i], topic[i]), list = TRUE, exdir = extractpath) : 
  zip file '/private/tmp/RtmpGr2edH/Rbuild2e317bb8/ArrayExpress/inst/doc/E-MEXP-1416.raw.1.zip' cannot be opened
Execution halted