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/
