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Question: segfault when trying to convert hta20_Hs_ENSE_22.cdf to binary format
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gravatar for relathman
15 months ago by
relathman0
Germany
relathman0 wrote:

Hi,

I want to convert a HTA 2.0 CDF file in ASCII format to binary using affxparser::convertCdf() but run into repeated problems.

I have been trying this for hta20_Hs_ENSE_22.cdf (released on Jun 21, 2017) as well as for hta20_hs_ENSE_21.cdf (released on Nov 28, 2016) and the respective ENSG files from Brainarray but I always get the following error message: (Strangely, the conversion works fine for hta20_hs_ENSE_19.cdf, I haven't tried any other versions yet.)

Can someone reproduce this or do you have any idea what is going wrong here?

I would be very grateful for any help.

Kind regards

Rukeia

convertCdf("hta20_Hs_ENSE_22.cdf","hta20_Hs_ENSE_22,binary.cdf",verbose=TRUE)

Reading CDF header...
Reading CDF header...done
Reading CDF QC units...

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: .Call("R_affx_get_cdf_file_qc", filename, as.integer(units),     as.integer(verbose), returnIndices, returnXY, returnLength,     returnPMInfo, returnBackgroundInfo, returnType, returnQcNumbers)
 2: readCdfQc(filename)
 3: convertCdf("hta20_Hs_ENSE_22.cdf",     "hta20_Hs_ENSE_22,binary.cdf",     verbose = TRUE)

sessionInfo:

R version 3.4.0 (2017-04-21)

Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.12.so

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C            
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8   
 [5] LC_MONETARY=en_US.utf8    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] affxparser_1.48.0

loaded via a namespace (and not attached):
[1] compiler_3.4.0

This is the header for hta20_hs_ENSE_22.cdf:

[CDF]
Version=GC3.0
 
[Chip]
Name=HTA-2_0.r1.exon
Rows=2572
Cols=2680
NumberOfUnits=580656
MaxUnit=581999
NumQCUnits=0
ChipReference=
ADD COMMENTlink written 15 months ago by relathman0
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