rhdf5 segmentation error with vdata
1
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Entering edit mode
sa.cizmeli • 0
@sacizmeli-7430
Last seen 6.7 years ago

Hello,

I have hundreds of tabular data stored as vdata objects in hdf4 files I would like to programmatically import into R. I researched and to my great surprise, could not find any libraries to import into R tabular vdata  in hdf4... So I had the idea of converting the hdf4 file into hdf5 format using H4toh5 (http://www.hdfgroup.org/ftp/HDF5/tools/h4toh5/src/unpacked/doc/h4toh5lib_RM.html#Tools-h4toh5) and use rhdf5...

Source hdf4 file :  http://arctus.serveftp.net/x.hdf

Created hdf5 file :  http://arctus.serveftp.net/x.h5

library( rhdf5)
rhdf5::h5ls("x.h5")

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: .Call("_h5ls", loc$H5Identifier@ID, depth, di, index_type, order,     PACKAGE = "rhdf5")
 2: rhdf5::h5ls("x.h5")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

 

Any ideas ? 

thanks from advance

Servet

 

sessionInfo() 
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rhdf5_2.10.0

loaded via a namespace (and not attached):
[1] tools_3.1.2     zlibbioc_1.12.0

rhdf5 • 927 views
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2
Entering edit mode
Bernd Fischer ▴ 540
@bernd-fischer-5348
Last seen 4.8 years ago
Germany / Heidelberg / DKFZ

Dear Servet,

Your data contains a lot of uncommitted datatypes. Unfortunately, there was a bug when writing the type name of uncommitted datatypes. This bug is fixed in version 2.11.7 that will appear on the Bioc-developer site by tomorrow night.

Bernd

 

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