Hi.
What is your sessionInfo()? Start a fresh R session. Do you get the
same as I do below?
> library("aroma.affymetrix");
> ufl <- AromaUflFile$byChipType("Mapping250K_Sty", tags="na31,HB20101007");
> print(getFileSize(ufl));
[1] 477371
> print(getChecksum(ufl));
[1] "74ff2c698e623474fd89bf13c2c47972"
> raw <-readRawFooter(ufl)$raw;
> length(raw)
[1] 544
> print(rawToChar(raw));
[1] "<createdOn>20101007 15:15:44
PDT</createdOn>\n<platform>Affymetrix</platform>\n<chipType>Mapping250K_Sty</chipType>\n<createdBy>\n<fullname>Henrik
Bengtsson</fullname>\n<email>h...@aroma-project.org</email>\n</createdBy>\n<srcFiles>\n<srcFile1>\n<filename>Mapping250K_Sty.cdf</filename>\n<filesize>184371335</filesize>\n<checksum>8c7ffa88bb444d953214f601bb998e51</checksum>\n</srcFile1>\n<srcFile2>\n<filename>Mapping250K_Sty.na31.annot.csv</filename>\n<filesize>363323700</filesize>\n<checksum>f1ac266c6becac99d1a7d4d343eb2a73</checksum>\n</srcFile2>\n</srcFiles>"
Then, does this give the error?
> ftr <- readFooter(ufl);
> str(ftr);
List of 5 $ createdOn: chr "20101007 15:15:44 PDT" $ platform : chr
"Affymetrix" $ chipType : chr "Mapping250K_Sty" $ createdBy:List of 2
..$ fullname: chr "Henrik Bengtsson" ..$ email : chr
"h...@aroma-project.org" $ srcFiles :List of 2 ..$ srcFile1:List of 3
.. ..$ filename: chr "Mapping250K_Sty.cdf" .. ..$ filesize: chr
"184371335" .. ..$ checksum: chr "8c7ffa88bb444d953214f601bb998e51"
..$ srcFile2:List of 3 .. ..$ filename: chr
"Mapping250K_Sty.na31.annot.csv" .. ..$ filesize: chr "363323700" ..
..$ checksum: chr "f1ac266c6becac99d1a7d4d343eb2a73"
> print(sessionInfo());
/Henrik
On Thu, Nov 10, 2011 at 6:54 AM, GermanL <glep...@gmail.com> wrote:
>
> Dear Aroma community,
>
> I am running an perl wrapper that calls the Aroma package in R and my
> Aroma run is stopping always at a specific point, where it is trying
> to read in the annotation information for the SNPchip.
>
> This is the annotation data that I have:
>
> Mapping250K_Sty.cdf
> Mapping250K_Sty,HB20080710.acs
> Mapping250K_Sty,monocell.CDF
> Mapping250K_Sty,na31,HB20101007.ufl
> Mapping250K_Sty,na31,HB20101007.ugp
>
> The error stops with a traceback to what appears to be some XML
> related error (see below)
>
> The odd thing is that this script used to work and recently it stopped
> working. It has been suggested to me that perhaps the locale settings
> are wrong? This may affect certain aspects of the code - for example
> single quotes if they are used. My colleagues are using UTF8 while I
> was on a non-UTF8 locale setting. My question is has anybody out there
> had similar issues?
>
> Thanks for any help/suggestions/ideas to try out.
>
>
>
>
> <--- above output snipped---- >
> Identifying SNP and CN units...done
> Retrieving SNP information annotations...
> Error: 1: Extra content at the end of the document
> In addition: There were 50 or more warnings (use warnings() to see the
> first 50)
> Retrieving SNP information annotations...done
> Normalizing set for PCR fragment-length effects...done
> <---end of output -->
>
> ******* using warnings, I get:
>
> warnings()
> 1: In log(y, base = 2) : NaNs produced
> 2: In log(y, base = 2) : NaNs produced
> 3: In log(y, base = 2) : NaNs produced
> 4: In log(y, base = 2) : NaNs produced
>
> ******* using traceback, I get:
>
> traceback()
> 30: stop(e)
> 29: function (msg, ...)
> {
> if (length(grep("\\\n$", msg)) == 0)
> paste(msg, "\n", sep = "")
> if (immediate)
> cat(msg)
> if (length(msg) == 0) {
> e = simpleError(paste(1:length(messages), messages, sep = ": ",
> collapse = ""))
> class(e) = c(class, class(e))
> stop(e)
> }
> messages <<- c(messages, msg)
> }(character(0), NULL, NULL, NULL, NULL, NULL, NULL)
> 28: .Call("RS_XML_ParseTree", as.character(file), handlers,
> as.logical(ignoreBlanks),
> as.logical(replaceEntities), as.logical(asText), as.logical(trim),
> as.logical(validate), as.logical(getDTD), as.logical(isURL),
> as.logical(addAttributeNamespaces), as.logical(useInternalNodes),
> FALSE, as.logical(isSchema), as.logical(fullNamespaceInfo),
> as.character(encoding), as.logical(useDotNames), xinclude,
> error, PACKAGE = "XML")
> 27: xmlTreeParse(node)
> 26: xmlToList(xml)
> 25: readFooter.AromaTabularBinaryFile(this)
> 24: readFooter(this)
> 23: getChipType.AromaMicroarrayTabularBinaryFile(ufl, ...)
> 22: NextMethod("getChipType", ...)
> 21: getChipType.UnitAnnotationDataFile(ufl, ...)
> 20: getChipType(ufl, ...)
> 19: getChipType.UflSnpInformation(this)
> 18: getChipType(this)
> 17: sprintf("Chip type: %s", getChipType(this))
> 16: as.character.SnpInformation(x)
> 15: as.character(x)
> 14: print(as.character(x))
> 13: print.Object(...)
> 12: print(...)
> 11: eval.with.vis(expr, pf, NULL)
> 10: evalVis(expr)
> 9: capture.Verbose(this, print(...), level = level)
> 8: capture(this, print(...), level = level)
> 7: print.Verbose(verbose, si)
> 6: print(verbose, si)
> 5: process.FragmentLengthNormalization(fln, verbose = verbose)
> 4: process(fln, verbose = verbose)
> 3: .local(object, ...)
> 2: normalizeSNPData(aroma, alleles = TRUE, sequence = sequence,
> quantile = quantile, fragment = TRUE, model = normalize,
> ram = useram, shift = 0, verbose = verbose)
> 1: normalizeSNPData(aroma, alleles = TRUE, sequence = sequence,
> quantile = quantile, fragment = TRUE, model = normalize,
> ram = useram, shift = 0, verbose = verbose)
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
