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 |
* 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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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