Rhdf5 C-library out of date
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channsoden • 0
@channsoden-16066
Last seen 3.3 years ago

I am trying to use a package that relies upon rhdf5 for reading hdf5 files. Unfortunately my install of rhdf5 2.25.3 links to the HDF5 1.8.19 C library and my hdf5 files were created using HDF5 1.10.1. Is there a way to update R's HDF5 library to 1.10.* so that the newer version of the files can be read?

> rhdf5::h5version()
This is Bioconductor rhdf5 2.25.3 linking to C-library HDF5 1.8.19
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /home/christopher/anaconda3/lib/R/lib/libRblas.so
LAPACK: /home/christopher/anaconda3/lib/R/lib/libRlapack.so

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] RevoUtils_10.0.8     RevoUtilsMath_10.0.1

loaded via a namespace (and not attached):
[1] compiler_3.4.3 rhdf5_2.25.3   Rhdf5lib_1.0.0

rhdf5 hdf5 • 506 views
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Mike Smith ★ 5.1k
@mike-smith
Last seen 10 hours ago
EMBL Heidelberg / de.NBI

I'm afraid the short answer is no.  At the moment rhdf5 is bundled with HDF5 1.8.19 and you can't override that.  This is a specific design decision so that anyone relying on rhdf5 does't have to worry about supporting a myriad of HDF5 versions across multiple platforms - which is the situation if you use system libraries.

 

However, if you're feeling adventurous, you can edit the configure and Makevars files in the source version of the package to ignore the bundled version and rely on a version of HDF5 in another location.  Feel free to contact me via the email address in the the package description and we can work that out together.

Out of interest which downstream package you you trying to use, and what type of data are you working with?  If HDF5 files only compatible with 1.10 are becoming common 'in the wild' then I will need to look more closely at updating the bundled version.

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The incompatibility is between two more-or-less interdependent tools for quantifying gene expression from RNA sequencing data. Kallisto uses system libraries (1.10 on my institution's cluster) to write the output of read pseudo-alignment while Sleuth uses rhdf5 to read the raw counts and build an expression model.

You can see my original issue for Sleuth here, and what looks like the same issue for Kallisto here. The second issue also indicates that there might be something R-version-dependent going on.

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I opened an issue at https://github.com/grimbough/rhdf5/issues/18 for the more technically minded...

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