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outdated package versions.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/
