* 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 chm
ArrayExpress text html latex example chm
extract.zip text html latex chm
getAE text html latex example chm
getcolproc text html latex example chm
magetab2bioc text html latex example chm
procset text html latex example chm
queryAE text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.4-bioc\meat\ArrayExpress\chm\ArrayExpress.chm
Compile time: 0 minutes, 0 seconds
8 Topics
35 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.4-bioc\meat\ArrayExpress\chm\ArrayExpress.chm, 23,091 bytes
Compression decreased file by 3,516 bytes.
** building package indices ...
** MD5 sums
* 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
Error in file(file, "r") : cannot open the connection
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.
4: In file(file, "r") : cannot open file './': Permission denied
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
Error in file(file, "r") : cannot open the connection
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.
4: In file(file, "r") : cannot open file './': Permission denied
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
Error in file(file, "r") : cannot open the connection
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.
4: In file(file, "r") : cannot open file './': Permission denied
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
Error in file(file, "r") : cannot open the connection
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.
4: In file(file, "r") : cannot open file './': Permission denied
Error: processing vignette 'ArrayExpress.Rnw' failed with diagnostics:
chunk 7 (label=getcolproc)
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") : cannot open file './': Permission denied
Execution halted