* 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: Warning messages:
1: In AB(i = 1, files, path, ph, adr, adf, idf) :
Cannot attach featureData
2: In nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) :
Cannot find array data file names in the sdrf file. The object may not be built.
3: In nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) :
Cannot find array data file names in the sdrf file. The object may not be built.
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: Warning messages:
1: In AB(i = 1, files, path, ph, adr, adf, idf) :
Cannot attach featureData
2: In nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) :
Cannot find array data file names in the sdrf file. The object may not be built.
3: In nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) :
Cannot find array data file names in the sdrf file. The object may not be built.
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: Warning messages:
1: In AB(i = 1, files, path, ph, adr, adf, idf) :
Cannot attach featureData
2: In nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) :
Cannot find array data file names in the sdrf file. The object may not be built.
3: In nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) :
Cannot find array data file names in the sdrf file. The object may not be built.
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: Warning messages:
1: In AB(i = 1, files, path, ph, adr, adf, idf) :
Cannot attach featureData
2: In nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) :
Cannot find array data file names in the sdrf file. The object may not be built.
3: In nonAB(i = 1, files, path, ph, rawcol, adr, adf, idf) :
Cannot find array data file names in the sdrf file. The object may not be built.
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