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Package 27/319HostnameOS / ArchBUILDCHECKBUILD BIN
ArrayExpress 1.4.3
Audrey Kauffmann
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/ArrayExpress
Last Changed Rev: 40278 / Revision: 42512
Last Changed Date: 2009-06-23 07:05:37 -0700 (Tue, 23 Jun 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  ERROR  skipped 
liverpool Windows Server 2003 R2 (32-bit) / x64  ERROR  skipped  skipped 
pitt Mac OS X Tiger (10.4.11) / i386 [ ERROR ] skipped  skipped 
pelham Mac OS X Leopard (10.5.8) / i386  ERROR  skipped  skipped 
Package: ArrayExpress
Version: 1.4.3
Command: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD build ArrayExpress
StartedAt: 2009-10-20 16:16:55 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 16:19:40 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 165.4 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
* Installing *source* package ‘ArrayExpress’ ...
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

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

** help
*** installing help indices
 >>> Building/Updating help pages for package 'ArrayExpress'
     Formats: text html latex example 
  ArrayExpress                      text    html    latex   example
  extract.zip                       text    html    latex
  getAE                             text    html    latex   example
  getcolproc                        text    html    latex   example
  magetab2bioc                      text    html    latex   example
  procset                           text    html    latex   example
  queryAE                           text    html    latex   example
** building package indices ...
* DONE (ArrayExpress)
* creating vignettes ... ERROR
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. 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=ISO-8859-1' length unknown
opened URL
.......... .......... .......... .......... ..........
.......... .......... ...
downloaded 73 Kb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.raw.zip'
Error in download.file(raw, rawdata, mode = "wb") : 
  cannot open URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.raw.zip'
In addition: Warning message:
In download.file(raw, rawdata, mode = "wb") :
  cannot open: HTTP status was '404 '
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.sdrf.txt'
Content type 'text/plain' length 6475 bytes
opened URL
==================================================
downloaded 6475 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 3590863 bytes (3.4 Mb)
opened URL
==================================================
downloaded 3.4 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 5378 bytes
opened URL
==================================================
downloaded 5378 bytes

Error : the following are not valid files:
    ./AF16.CEL
   ./AF7.CEL
   ./AF14.CEL
   ./AF8.CEL
   ./AF15.CEL
   ./AF6.CEL
In addition: Warning message:
In getAE(input, path, type = "raw") :
  http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.raw.zip  does not exist or is empty. 

Read 49 items
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "experimentData", for signature "try-error"
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "featureData<-", for signature "try-error", "AnnotatedDataFrame"
In addition: Warning message:
In AB(i = 1, files, path, ph, adr, adf, idf) : Cannot attach experimentData
Read 0 items
Error in nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) : 
  No scanner name is given. It is not possible to handle such a case. Try to set the argument 'rawcol' by choosing among the following columns names: 

In addition: There were 31 warnings (use warnings() to see them)
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-DKFZ-1/E-DKFZ-1.raw.zip'
Error in download.file(raw, rawdata, mode = "wb") : 
  cannot open URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-DKFZ-1/E-DKFZ-1.raw.zip'
In addition: Warning message:
In download.file(raw, rawdata, mode = "wb") :
  cannot open: HTTP status was '404 '
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-DKFZ-1/E-DKFZ-1.sdrf.txt'
Content type 'text/plain' length 77278 bytes (75 Kb)
opened URL
==================================================
downloaded 75 Kb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/A-RZPD-20/A-RZPD-20.adf.txt'
Content type 'text/plain' length 684951 bytes (668 Kb)
opened URL
==================================================
downloaded 668 Kb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-DKFZ-1/E-DKFZ-1.idf.txt'
Content type 'text/plain' length 3260 bytes
opened URL
==================================================
downloaded 3260 bytes

Error : the following are not valid files:
    ./E-DKFZ-1-raw-data-281733762.txt
   ./E-DKFZ-1-raw-data-281732763.txt
   ./E-DKFZ-1-raw-data-281733512.txt
   ./E-DKFZ-1-raw-data-281733326.txt
   ./E-DKFZ-1-raw-data-281732837.txt
   ./E-DKFZ-1-raw-data-281733535.txt
   ./E-DKFZ-1-raw-data-281733205.txt
   ./E-DKFZ-1-raw-data-281732741.txt
   ./E-DKFZ-1-raw-data-281733878.txt
   ./E-DKFZ-1-raw-data-281733468.txt
   ./E-DKFZ-1-raw-data-281733605.txt
   ./E-DKFZ-1-raw-data-281733116.txt
   ./E-DKFZ-1-raw-data-281732929.txt
   ./E-DKFZ-1-raw-data-281733673.txt
   ./E-DKFZ-1-raw-data-281733559.txt
   ./E-DKFZ-1-raw-data-281733740.txt
   ./E-DKFZ-1-raw-data-281734509.txt
   ./E-DKFZ-1-raw-data-281732952.txt
   ./E-DKFZ-1-raw-data-281734656.txt
   ./E-DKFZ-1-raw-data-281733372.txt
   ./E-DKFZ-1-raw-data-281733021.txt
   ./E-DKFZ-1-raw-data-281733093.txt
   ./E-DKFZ-1-raw-data-281733350.txt
   ./E-DKFZ-1-raw-data-281734753.txt
   ./E-DKFZ-1-raw-data-281733229.txt
   ./E-DKFZ-1-raw-data-281733253.txt
   ./E-DKFZ-1-raw-data-281733695.txt
   ./E-DKFZ-1-raw-data-281733070.txt
   ./E-DKFZ-1-raw-data-281734390.txt
   ./E-DKFZ-1-raw-data-281733855.txt
   ./E-DKFZ-1-raw-data-281733139.txt
   ./E-DKFZ-1-raw-data-281733045.txt
   ./E-DKFZ-1-raw-data-281732811.txt
   ./E-DKFZ-1-raw-data-281734604.txt
   ./E-DKFZ-1-raw-data-281734628.txt
   ./E-DKFZ-1-raw-data-281734580.txt
   ./E-DKFZ-1-raw-data-281732599.txt
   ./E-DKFZ-1-raw-data-281733301.txt
   ./E-DKFZ-1-raw-data-281733789.txt
   ./E-DKFZ-1-raw-data-281734437.txt
   ./E-DKFZ-1-raw-data-281734706.txt
   ./E-DKFZ-1-raw-data-281732998.txt
   ./E-DKFZ-1-raw-data-281734414.txt
   ./E-DKFZ-1-raw-data-281733717.txt
   ./E-DKFZ-1-raw-data-281734533.txt
   ./E-DKFZ-1-raw-data-281733811.txt
   ./E-DKFZ-1-raw-data-281732668.txt
   ./E-DKFZ-1-raw-data-281734683.txt
   ./E-DKFZ-1-raw-data-281733161.txt
   ./E-DKFZ-1-raw-data-281733277.txt
   ./E-DKFZ-1-raw-data-281732907.txt
   ./E-DKFZ-1-raw-data-281734557.txt
   ./E-DKFZ-1-raw-data-281734775.txt
   ./E-DKFZ-1-raw-data-281733446.txt
   ./E-DKFZ-1-raw-data-281734461.txt
   ./E-DKFZ-1-raw-data-281734728.txt
   ./E-DKFZ-1-raw-data-281733832.txt
   ./E-DKFZ-1-raw-data-281732694.txt
   ./E-DKFZ-1-raw-data-281732790.txt
   ./E-DKFZ-1-raw-data-281733181.txt
   ./E-DKFZ-1-raw-data-281732976.txt
   ./E-DKFZ-1-raw-data-281732556.txt
   ./E-DKFZ-1-raw-data-281733581.txt
   ./E-DKFZ-1-raw-data-281733420.txt
   ./E-DKFZ-1-raw-data-281732621.txt
   ./E-DKFZ-1-raw-data-281732861.txt
   ./E-DKFZ-1-raw-data-281732644.txt
   ./E-DKFZ-1-raw-data-281733396.txt
   ./E-DKFZ-1-raw-data-281733627.txt
   ./E-DKFZ-1-raw-data-281733649.txt
   ./E-DKFZ-1-raw-data-281732882.txt
   ./E-DKFZ-1-raw-data-281733490.txt
   ./E-DKFZ-1-raw-data-281734487.txt
   ./E-DKFZ-1-raw-data-281732718.txt
In addition: Warning message:
In getAE(input, path, type = "raw") :
  http://www.ebi.ac.uk/microarray-as/ae/files/E-DKFZ-1/E-DKFZ-1.raw.zip  does not exist or is empty. 

Read 48 items
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "experimentData", for signature "try-error"
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "featureData<-", for signature "try-error", "AnnotatedDataFrame"
In addition: Warning message:
In AB(i = 1, files, path, ph, adr, adf, idf) : Cannot attach experimentData
Read 0 items
Error in nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) : 
  No scanner name is given. It is not possible to handle such a case. Try to set the argument 'rawcol' by choosing among the following columns names: 

In addition: There were 31 warnings (use warnings() to see them)
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-DKFZ-1/E-DKFZ-1.raw.zip'
Error in download.file(raw, rawdata, mode = "wb") : 
  cannot open URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-DKFZ-1/E-DKFZ-1.raw.zip'
In addition: Warning message:
In download.file(raw, rawdata, mode = "wb") :
  cannot open: HTTP status was '404 '
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-DKFZ-1/E-DKFZ-1.sdrf.txt'
Content type 'text/plain' length 77278 bytes (75 Kb)
opened URL
==================================================
downloaded 75 Kb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/A-RZPD-20/A-RZPD-20.adf.txt'
Content type 'text/plain' length 684951 bytes (668 Kb)
opened URL
==================================================
downloaded 668 Kb

trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-DKFZ-1/E-DKFZ-1.idf.txt'
Content type 'text/plain' length 3260 bytes
opened URL
==================================================
downloaded 3260 bytes

Error : the following are not valid files:
    ./E-DKFZ-1-raw-data-281733762.txt
   ./E-DKFZ-1-raw-data-281732763.txt
   ./E-DKFZ-1-raw-data-281733512.txt
   ./E-DKFZ-1-raw-data-281733326.txt
   ./E-DKFZ-1-raw-data-281732837.txt
   ./E-DKFZ-1-raw-data-281733535.txt
   ./E-DKFZ-1-raw-data-281733205.txt
   ./E-DKFZ-1-raw-data-281732741.txt
   ./E-DKFZ-1-raw-data-281733878.txt
   ./E-DKFZ-1-raw-data-281733468.txt
   ./E-DKFZ-1-raw-data-281733605.txt
   ./E-DKFZ-1-raw-data-281733116.txt
   ./E-DKFZ-1-raw-data-281732929.txt
   ./E-DKFZ-1-raw-data-281733673.txt
   ./E-DKFZ-1-raw-data-281733559.txt
   ./E-DKFZ-1-raw-data-281733740.txt
   ./E-DKFZ-1-raw-data-281734509.txt
   ./E-DKFZ-1-raw-data-281732952.txt
   ./E-DKFZ-1-raw-data-281734656.txt
   ./E-DKFZ-1-raw-data-281733372.txt
   ./E-DKFZ-1-raw-data-281733021.txt
   ./E-DKFZ-1-raw-data-281733093.txt
   ./E-DKFZ-1-raw-data-281733350.txt
   ./E-DKFZ-1-raw-data-281734753.txt
   ./E-DKFZ-1-raw-data-281733229.txt
   ./E-DKFZ-1-raw-data-281733253.txt
   ./E-DKFZ-1-raw-data-281733695.txt
   ./E-DKFZ-1-raw-data-281733070.txt
   ./E-DKFZ-1-raw-data-281734390.txt
   ./E-DKFZ-1-raw-data-281733855.txt
   ./E-DKFZ-1-raw-data-281733139.txt
   ./E-DKFZ-1-raw-data-281733045.txt
   ./E-DKFZ-1-raw-data-281732811.txt
   ./E-DKFZ-1-raw-data-281734604.txt
   ./E-DKFZ-1-raw-data-281734628.txt
   ./E-DKFZ-1-raw-data-281734580.txt
   ./E-DKFZ-1-raw-data-281732599.txt
   ./E-DKFZ-1-raw-data-281733301.txt
   ./E-DKFZ-1-raw-data-281733789.txt
   ./E-DKFZ-1-raw-data-281734437.txt
   ./E-DKFZ-1-raw-data-281734706.txt
   ./E-DKFZ-1-raw-data-281732998.txt
   ./E-DKFZ-1-raw-data-281734414.txt
   ./E-DKFZ-1-raw-data-281733717.txt
   ./E-DKFZ-1-raw-data-281734533.txt
   ./E-DKFZ-1-raw-data-281733811.txt
   ./E-DKFZ-1-raw-data-281732668.txt
   ./E-DKFZ-1-raw-data-281734683.txt
   ./E-DKFZ-1-raw-data-281733161.txt
   ./E-DKFZ-1-raw-data-281733277.txt
   ./E-DKFZ-1-raw-data-281732907.txt
   ./E-DKFZ-1-raw-data-281734557.txt
   ./E-DKFZ-1-raw-data-281734775.txt
   ./E-DKFZ-1-raw-data-281733446.txt
   ./E-DKFZ-1-raw-data-281734461.txt
   ./E-DKFZ-1-raw-data-281734728.txt
   ./E-DKFZ-1-raw-data-281733832.txt
   ./E-DKFZ-1-raw-data-281732694.txt
   ./E-DKFZ-1-raw-data-281732790.txt
   ./E-DKFZ-1-raw-data-281733181.txt
   ./E-DKFZ-1-raw-data-281732976.txt
   ./E-DKFZ-1-raw-data-281732556.txt
   ./E-DKFZ-1-raw-data-281733581.txt
   ./E-DKFZ-1-raw-data-281733420.txt
   ./E-DKFZ-1-raw-data-281732621.txt
   ./E-DKFZ-1-raw-data-281732861.txt
   ./E-DKFZ-1-raw-data-281732644.txt
   ./E-DKFZ-1-raw-data-281733396.txt
   ./E-DKFZ-1-raw-data-281733627.txt
   ./E-DKFZ-1-raw-data-281733649.txt
   ./E-DKFZ-1-raw-data-281732882.txt
   ./E-DKFZ-1-raw-data-281733490.txt
   ./E-DKFZ-1-raw-data-281734487.txt
   ./E-DKFZ-1-raw-data-281732718.txt
In addition: Warning message:
In getAE(input, path, type = "raw") :
  http://www.ebi.ac.uk/microarray-as/ae/files/E-DKFZ-1/E-DKFZ-1.raw.zip  does not exist or is empty. 

Read 48 items
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "experimentData", for signature "try-error"
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "featureData<-", for signature "try-error", "AnnotatedDataFrame"
In addition: Warning message:
In AB(i = 1, files, path, ph, adr, adf, idf) : Cannot attach experimentData
Read 0 items
Error in read.maimages(files = unique(files), path = path, columns = rawcoln) : 
  Must specify input files
In addition: There were 31 warnings (use warnings() to see them)
Error in nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) : 
  Error in read.maimages: Error in read.maimages(files = unique(files), path = path, columns = rawcoln) : 
  Must specify input files
 The files have probably different columns header.
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.raw.zip'
Error in download.file(raw, rawdata, mode = "wb") : 
  cannot open URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.raw.zip'
In addition: Warning message:
In download.file(raw, rawdata, mode = "wb") :
  cannot open: HTTP status was '404 '
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.processed.zip'
Error in download.file(proc, procdata, mode = "wb") : 
  cannot open URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.processed.zip'
In addition: Warning messages:
1: In getAE("E-MEXP-1422", type = "full") :
  http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.raw.zip  does not exist or is empty. 

2: In download.file(proc, procdata, mode = "wb") :
  cannot open: HTTP status was '404 '
trying URL 'http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.sdrf.txt'
Content type 'text/plain' length 6475 bytes
opened URL
==================================================
downloaded 6475 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 3590863 bytes (3.4 Mb)
opened URL
==================================================
downloaded 3.4 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 5378 bytes
opened URL
==================================================
downloaded 5378 bytes

Error : the following are not valid files:
    ./AF16.CEL
   ./AF7.CEL
   ./AF14.CEL
   ./AF8.CEL
   ./AF15.CEL
   ./AF6.CEL
In addition: Warning message:
In getAE("E-MEXP-1422", type = "full") :
  http://www.ebi.ac.uk/microarray-as/ae/files/E-MEXP-1422/E-MEXP-1422.processed.zip  does not exist or is empty. 

Read 49 items
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "experimentData", for signature "try-error"
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "featureData<-", for signature "try-error", "AnnotatedDataFrame"
In addition: Warning message:
In AB(i = 1, files, path, ph, adr, adf, idf) : Cannot attach experimentData
Read 0 items
Error in nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) : 
  No scanner name is given. It is not possible to handle such a case. Try to set the argument 'rawcol' by choosing among the following columns names: 

In addition: There were 31 warnings (use warnings() to see them)

Error: processing vignette 'ArrayExpress.Rnw' failed with diagnostics:
 chunk 7 (label=getcolproc) 
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  no lines available in input
Execution halted