Hi, I can reproduce this in a fresh R session, but only when running outdated package versions. So, please update:
source("http://aroma-project.org/hbLite.R"); hbInstall("aroma.affymetrix"); DETAILS: > library("aroma.core"); > ufl <- AromaUflFile$byChipType("Mapping250K_Sty", tags="na31,HB20101007"); > raw <- readRawFooter(ufl)$raw; > xml <- rawToChar(raw); > xmlList <- XML::xmlToList(xml); Extra content at the end of the document Error: 1: Extra content at the end of the document Note how I had to to use the 'XML::' prefix. If I do the following and have aroma.core v2.3.0, it works: > xmlList <- xmlToList(xml); or equivalently > xmlList <- aroma.core::xmlToList(xml); It turns out that if you run an older aroma.core package prior to v2.3.0 and/or that hasn't been built on R v2.14.0, there will be a name clash for xmlToList() between the implementation in the aroma.core package and the one in the XML package. Lesson learned is to always make sure to run up-to-date versions of packages and preferably R itself too. /Henrik On Mon, Nov 14, 2011 at 3:59 AM, GermanL <glep...@gmail.com> wrote: > Hi Henrik, I've updated the XML now: > >> sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] BIASNP_0.5.2 XML_3.4-3 > RODBC_1.3-2 > [4] aroma.affymetrix_1.9.0 aroma.apd_0.1.7 > affxparser_1.22.1 > [7] R.huge_0.2.0 aroma.core_1.9.0 > aroma.light_1.18.2 > [10] matrixStats_0.2.2 R.rsp_0.4.1 > R.cache_0.3.0 > [13] R.filesets_0.9.1 digest_0.4.2 > R.utils_1.6.0 > [16] R.oo_1.7.4 R.methodsS3_1.2.1 > > If I try the readFooter command again, the error comes up still: > > ftr <- readFooter(ufl); > Extra content at the end of the document > Error: 1: Extra content at the end of the document > > the digest command works, giving me: > >> digest(raw) > [1] "ecfee3f93033dbbf4a25fd27195ff0e9" > > > > > On Nov 11, 5:18 pm, Henrik Bengtsson <henrik.bengts...@aroma- > project.org> wrote: >> Ok, so you have rather old versions running. Start by updating the XML >> package, retry and report back: >> >> http://cran.r-project.org/web/packages/XML/index.html >> >> Also, if it still gives and error, what does the following return: >> >> > digest(raw) >> >> [1] "ecfee3f93033dbbf4a25fd27195ff0e9" >> >> /Henrik >> >> On Fri, Nov 11, 2011 at 1:21 AM, GermanL <glep...@gmail.com> wrote: >> > Hi Henrik, >> >> > Thanks for your help in tracking the problem. >> >> > I tested your lines of code and it worked up until the point of the " >> > ftr <- readFooter(ufl); " command, here I paste the results below: >> >> >> 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>hb@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>" >> >> >> ftr <- readFooter(ufl); >> > Extra content at the end of the document >> > Error: 1: Extra content at the end of the document >> >> str(ftr); >> > Error in str(ftr) : object 'ftr' not found >> >> > and below is my sessionInfo(): >> >> >> print(sessionInfo()); >> > R version 2.12.1 (2010-12-16) >> > Platform: x86_64-unknown-linux-gnu (64-bit) >> >> > locale: >> > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C >> > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 >> > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 >> > [7] LC_PAPER=en_US.utf8 LC_NAME=C >> > [9] LC_ADDRESS=C LC_TELEPHONE=C >> > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >> >> > attached base packages: >> > [1] stats graphics grDevices utils datasets methods >> > base >> >> > other attached packages: >> > [1] BIASNP_0.5.2 XML_3.2-0 >> > RODBC_1.3-2 >> > [4] aroma.affymetrix_1.9.0 aroma.apd_0.1.7 >> > affxparser_1.22.1 >> > [7] R.huge_0.2.0 aroma.core_1.9.0 >> > aroma.light_1.18.2 >> > [10] matrixStats_0.2.2 R.rsp_0.4.1 >> > R.cache_0.3.0 >> > [13] R.filesets_0.9.1 digest_0.4.2 >> > R.utils_1.6.0 >> > [16] R.oo_1.7.4 R.methodsS3_1.2.1 >> >> > Kind Regards, >> > German >> >> > -- >> > 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 websitehttp://www.aroma-project.org/. >> > To post to this group, send email to aroma-affymetrix@googlegroups.com >> > To unsubscribe and other options, go tohttp://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/ > -- 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/