Hi Christian,

thanks for the quick response.
This is a foolish error and I didn't pay enough attention. Sorry.

I took your advice and updated to R 3.0.1.
Now I have a different problem (which I think has something to do with
root, but I can't interpret it correctly).

This is what I do:
library(xps)
libdir <- "/Users/ayeroslaviz/Documents/Annotations/xps"
anndir <-
"/Users/ayeroslaviz/Documents/Annotations/xps/MoGene1.0_Annotations"
scmdir <- "/Users/ayeroslaviz/Documents/Annotations/xps"
#MoGene-1_0-st-v1.r4: used as exon array

scheme.mogene10stv1.na33 <- import.exon.scheme("mogene10stv1", filedir =
file.path(scmdir, "na33"),
        file.path(libdir, "MoGene1_0_libFiles", "MoGene-1_0-st-v1.r4.clf"),
        file.path(libdir, "MoGene1_0_libFiles", "MoGene-1_0-st-v1.r4.pgf"),
        file.path(anndir, "MoGene-1_0-st-v1.na33.2.mm9.probeset.csv"),
        file.path(anndir, "MoGene-1_0-st-v1.na33.2.mm9.transcript.csv"))


and this is what I get as an error:
Creating new file
</Users/ayeroslaviz/Documents/Annotations/xps/na33/mogene10stv1.root>...
Importing
</Users/ayeroslaviz/Documents/Annotations/xps/MoGene1_0_libFiles/MoGene-1_0-st-v1.r4.clf>
as <MoGene-1_0-st-v1.cxy>...
   <1102500> records imported...Finished

 *** Break *** segmentation violation
tr: Illegal byte sequence



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================

Thread 1 (process 54446):
#0  0x00007fff830ec168 in wait4 ()
#1  0x00007fff8e91a5f5 in system ()
#2  0x0000000137a0b2f9 in TUnixSystem::StackTrace ()
#3  0x0000000137a08e54 in TUnixSystem::DispatchSignals ()
#4  <signal handler called>
#5  0x00000001379d9674 in TClass::GetStreamerInfo ()
#6  0x0000000138925777 in TBufferFile::WriteClones ()
#7  0x0000000138923d0a in TBufferFile::WriteObjectClass ()
#8  0x0000000138923e26 in TBufferFile::WriteObjectAny ()
#9  0x00000001379c1099 in TList::Streamer ()
#10 0x0000000138923d0a in TBufferFile::WriteObjectClass ()
#11 0x0000000138923e26 in TBufferFile::WriteObjectAny ()
#12 0x0000000138923442 in TBufferFile::WriteFastArray ()
#13 0x0000000138a7dc2b in TStreamerInfo::WriteBufferAux<char**> ()
#14 0x000000013897d6eb in TStreamerInfoActions::GenericWriteAction ()
#15 0x00000001389260ed in TBufferFile::ApplySequence ()
#16 0x000000013892601d in TBufferFile::WriteClassBuffer ()
#17 0x000000013948f180 in TTree::Streamer ()
#18 0x0000000138960abc in TKey::TKey ()
#19 0x00000001389367db in TFile::CreateKey ()
#20 0x000000013892ea7e in TDirectoryFile::WriteTObject ()
#21 0x000000013795928b in TObject::Write ()
#22 0x00000001340266bf in XTreeSet::WriteTree ()
#23 0x000000013405b2cf in XGenomeChip::ImportLayout ()
#24 0x000000013403c9da in XDNAChip::Import ()
#25 0x00000001340238fe in XManager::Import ()
#26 0x000000013406956e in XSchemeManager::NewScheme ()
#27 0x00000001340f3702 in ImportExonSchemes ()
#28 0x0000000100064daa in do_dotCode (call=0x7fff5fbfd8e0, op=0x1313ffb20,
args=0x6c5130, env=0x7fff5fbfd8e0) at dotcode.c:1734
#29 0x0000000100096ef4 in Rf_eval (e=0x1327b2ee8, rho=0x136340298) at
eval.c:635
#30 0x00000001000a2176 in Rf_DispatchOrEval (call=0x7fff5fbfdc20,
op=0x7fff5fbfdc20, generic=0x7fff5fbfdc20
"pܿ_===========================================================


The lines below might hint at the cause of the crash.
If they do not help you then please submit a bug report at
http://root.cern.ch/bugs. Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#5  0x00000001379d9674 in TClass::GetStreamerInfo ()
#6  0x0000000138925777 in TBufferFile::WriteClones ()
#7  0x0000000138923d0a in TBufferFile::WriteObjectClass ()
#8  0x0000000138923e26 in TBufferFile::WriteObjectAny ()
#9  0x00000001379c1099 in TList::Streamer ()
#10 0x0000000138923d0a in TBufferFile::WriteObjectClass ()
#11 0x0000000138923e26 in TBufferFile::WriteObjectAny ()
#12 0x0000000138923442 in TBufferFile::WriteFastArray ()
#13 0x0000000138a7dc2b in TStreamerInfo::WriteBufferAux<char**> ()
#14 0x000000013897d6eb in TStreamerInfoActions::GenericWriteAction ()
#15 0x00000001389260ed in TBufferFile::ApplySequence ()
#16 0x000000013892601d in TBufferFile::WriteClassBuffer ()
#17 0x000000013948f180 in TTree::Streamer ()
#18 0x0000000138960abc in TKey::TKey ()
#19 0x00000001389367db in TFile::CreateKey ()
#20 0x000000013892ea7e in TDirectoryFile::WriteTObject ()
#21 0x000000013795928b in TObject::Write ()
#22 0x00000001340266bf in XTreeSet::WriteTree ()
#23 0x000000013405b2cf in XGenomeChip::ImportLayout ()
#24 0x000000013403c9da in XDNAChip::Import ()
#25 0x00000001340238fe in XManager::Import ()
#26 0x000000013406956e in XSchemeManager::NewScheme ()
#27 0x00000001340f3702 in ImportExonSchemes ()
#28 0x0000000100064daa in do_dotCode (call=0x7fff5fbfd8e0, op=0x1313ffb20,
args=0x6c5130, env=0x7fff5fbfd8e0) at dotcode.c:1734
#29 0x0000000100096ef4 in Rf_eval (e=0x1327b2ee8, rho=0x136340298) at
eval.c:635
===========================================================

Does anyone has any idea what that means?

Do I need to re-install root again?

Thanks
Assa



On Mon, Sep 23, 2013 at 3:46 PM, cstrato <cstrato@aon.at> wrote:

> Dear Assa,
>
> I assume that you get the error since you are mixing MoGene-1_0-st
> pgf-files with MoGene-2_0-st annotation files.
>
> For MoGene-2_0-st you need to do:
>
> scheme.mogene20st.na33 <- import.exon.scheme("**mogene20stv1", filedir =
> file.path(scmdir, "na33"),
>    file.path(libdir, "MoGene-2_0-st", "MoGene-2_0-st.clf"),
>    file.path(libdir, "MoGene-2_0-st", "MoGene-2_0-st.pgf"),
>
>    file.path(anndir, "MoGene-2_0-st-v1.na33.2.mm10.**probeset.csv"),
>    file.path(anndir, "MoGene-2_0-st-v1.na33.2.mm10.**transcript.csv"))
>
> For MoGene-1_0-st arrays you would need the MoGene-1_0-st annotation files.
>
> Furthermore, your version of xps is pretty old, even for R-2.15.x. I would
> suggest to update to the latest versions of R and xps.
>
> Best regards,
> Christian
> _._._._._._._._._._._._._._._.**_._._
> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
> V.i.e.n.n.a           A.u.s.t.r.i.a
> e.m.a.i.l:        cstrato at aon.at
> _._._._._._._._._._._._._._._.**_._._
>
>
>
> On 9/23/13 3:02 PM, Assa Yeroslaviz wrote:
>
>> Hi everybody,
>>
>> I am trying to work with the xps package on mouse transcript arrays but
>> having problem creating the root scheme.
>>
>> This is the command I am using to start with (taken from the scripts
>> given with the package)
>>
>> scheme.mogene10stv1.na33 <- import.exon.scheme("**mogene10stv1", filedir
>> =
>> file.path(scmdir, "na33"),
>>                              file.path(libdir, "MoGene1_0_libFiles",
>> "MoGene-1_0-st-v1.r4.clf"),
>>                              file.path(libdir, "MoGene1_0_libFiles",
>> "MoGene-1_0-st-v1.r4.pgf"),
>>                              file.path(anndir,
>> "MoGene-2_0-st-v1.na33.2.mm10.**probeset.csv"),
>>                              file.path(anndir,
>> "MoGene-2_0-st-v1.na33.2.mm10.**transcript.csv"))
>>
>> But when I am running this command I get the following error massage:
>> Creating new file
>> </Users/ayeroslaviz/Documents/**Annotations/xps//na33/**
>> mogene10stv1.root>...
>> Importing
>> </Users/ayeroslaviz/Documents/**Annotations/xps//MoGene1_0_**
>> libFiles/MoGene-1_0-st-v1.r4.**clf>
>> as <MoGene-1_0-st-v1.cxy>...
>>     <1102500> records imported...Finished
>> New dataset <MoGene-1_0-st-v1> is added to Content...
>> Importing
>> </Users/ayeroslaviz/Documents/**Annotations/xps/MoGene1.0_**
>> Annotations//MoGene-2_0-st-v1.**na33.2.mm10.probeset.csv>
>> as <MoGene-1_0-st-v1.anp>...
>> Note: The following header columns are missing or in wrong order:
>>     <mouse_fl>
>>     <mouse_mrna>
>>     Number of probesets is <269751>.
>>     <269751> records read...Finished
>>     <269049> records imported...Finished
>>     <215654> exon annotations imported.
>> Importing
>> </Users/ayeroslaviz/Documents/**Annotations/xps//MoGene1_0_**
>> libFiles/MoGene-1_0-st-v1.r4.**pgf>
>> as <MoGene-1_0-st-v1.scm>...
>>     Reading data from input file...
>>     Number of probesets is <241576>.
>>     Note: Number of annotated probesets <269751> is not equal to number
>> of probesets <241576>.
>>     <241576> records read...Finished
>>     Sorting data for probeset_type and position...
>>     Total number of controls is <45>
>>     Filling trees with data for probeset type: control->chip...
>>     Number of control->chip items is <0>.
>>     Filling trees with data for probeset type: control->bgp...
>>     Filling trees with data for probeset type: control->affx...
>>     Number of control->affx probesets is <21>.
>> *Error: Number of control->affx imported <21> is not equal to number of
>> annotated AFFX controls <167>.*
>> *Error: CDF with version/magic number
>> </Users/ayeroslaviz/Documents/**Annotations/xps//MoGene1_0_**
>> libFiles/MoGene-1_0-st-v1.r4.**pgf>
>> is not supported.*
>> *Error in import.exon.scheme("**mogene10stv1", filedir =
>> file.path(scmdir,  :
>>    error in function ‘ImportExonSchemes’*
>>
>>
>> I would like to know what I am doing wrong and how to do it right, so
>> that the scheme will be uploaded into R with the right annotation files.
>>
>> Thanks
>>
>> Assa
>>
>> I'm working on MacBook Pro 10.7.5
>> R session info -
>>  > sessionInfo()
>> R version 2.15.0 (2012-03-30)
>> Platform: x86_64-apple-darwin9.8.0/x86_**64 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.**UTF-8/C/en_US.UTF-8/en_US.UTF-**8
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] Biobase_2.16.0      BiocGenerics_0.2.0  xps_1.16.0
>> [4] BiocInstaller_1.4.9
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.15.0
>>
>

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