It worked!!!!!!! :)
Thank you very much!
Martina
Il giorno mercoledì 26 settembre 2012 22:09:28 UTC+2, Henrik Bengtsson ha
scritto:
>
> Hi, sorry about the affxparser mess.
>
> See if the following
>
> source("http://aroma-project.org/affxparser.R";);
> installAffxparser();
>
> solves your problems. The above will run tests to make sure
> everything works fine and if it says that is the case, you're read to
> rock'n'roll.
>
> Please report back and let me know if it works, because then I'll
> include the above as part of the default installation.
>
> /Henrik
>
> On Wed, Sep 26, 2012 at 7:12 AM, Martina Dori
> <martin...@gmail.com<javascript:>>
> wrote:
> > Hi Henrik,
> > I'm working on OS X 10.8.2 and
> >
> >> sessionInfo()
> >
> > R version 2.15.0 (2012-03-30)
> >
> > Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> >
> >
> > I followed the instruction you gave and uninstalled the affxparser I had
> and
> > re-installed the previous version.
> > It gave me this warning:
> >
> > Warning messages:
> >
> > 1: In packageDescription(pkg) : no package 'affxparser' was found
> >
> > 2: package ‘R.utils’ was built under R version 2.15.1
> >
> > 3: package ‘R.oo’ was built under R version 2.15.1
> >
> > 4: package ‘R.methodsS3’ was built under R version 2.15.1
> >
> >
> > So I checked if it was installed
> >
> >> packageDescription("affxparser")$Packaged
> >
> > [1] "2011-11-20 16:44:36 UTC; khansen"
> >
> >
> > Because it seemed to be installed, I tried to check my CDF file
> > (GenomeWideSNP_6,Full.cdf) as you mentioned as test but it returned me
> as
> > follows
> >
> > *** caught segfault ***
> >
> > address 0xfffffffc, cause 'memory not mapped'
> >
> >
> > Traceback:
> >
> > 1: .Call("R_affx_get_cdf_file_header", filename, PACKAGE =
> "affxparser")
> >
> > 2:
> >
> readCdfHeader("annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf")
>
>
> >
> >
> > Possible actions:
> >
> > 1: abort (with core dump, if enabled)
> >
> > 2: normal R exit
> >
> > 3: exit R without saving workspace
> >
> > 4: exit R saving workspace
> >
> > R(2155,0xacadaa28) malloc: *** error for object 0xbfffe730: pointer
> being
> > freed was not allocated
> >
> > *** set a breakpoint in malloc_error_break to debug
> >
> >
> > I loaded the aroma.affymetrix library and because it didn't find the
> > affxparser R automatically installed the latest version.
> >
> > What should I do?
> >
> > Thank you very much for any help
> >
> > Martina
> >
> >
> > Il giorno sabato 31 marzo 2012 02:31:50 UTC+2, Jorge Melendez ha
> scritto:
> >>
> >> Hi Henrik
> >> worked ok
> >>
> >> > library("affxparser");
> >>
> >> >
> >> >
> readCdfHeader("annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf");
>
>
> >>
> >> $ncols
> >>
> >> [1] 2560
> >>
> >>
> >> $nrows
> >>
> >> [1] 2560
> >>
> >>
> >> $nunits
> >>
> >> [1] 262338
> >>
> >>
> >> $nqcunits
> >>
> >> [1] 6
> >>
> >>
> >> $refseq
> >>
> >> [1] ""
> >>
> >>
> >> $chiptype
> >>
> >> [1] "Mapping250K_Nsp"
> >>
> >>
> >> $filename
> >>
> >> [1] "annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf"
> >>
> >>
> >> $rows
> >>
> >> [1] 2560
> >>
> >>
> >> $cols
> >>
> >> [1] 2560
> >>
> >>
> >> $probesets
> >>
> >> [1] 262338
> >>
> >>
> >> $qcprobesets
> >>
> >> [1] 6
> >>
> >>
> >> $reference
> >>
> >> [1] ""
> >>
> >>
> >> > sessionInfo()
> >>
> >> R version 2.14.2 (2012-02-29)
> >>
> >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> >>
> >>
> >> Thank you!
> >>
> >> ::::::::::::::::::::::::::::::::::::::::::::::::::
> >>
> >>
> >>> (*) If you have access to OSX 10.7 ("Lion"), could you please check
> >>> whether the patched version of affxparser on OSX or not, and report
> >>> back? Try the following:
> >>>
> >>> library("affxparser");
> >>>
> >>>
> readCdfHeader("annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf");
>
>
> >>>
> >>> It should not crash R, but return a list of CDF attributes. The above
> >>> CDF can be downloaded from:
> >>>
> >>>
> >>>
> http://www.aroma-project.org/data/annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf.gz
>
> >
> > --
> > 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-af...@googlegroups.com<javascript:>
> > 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/.
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