windows tximport fail
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Entering edit mode
rhart • 0
@rhart-13682
Last seen 2.2 years ago

I've been using tximport with output from Kallisto. After recent updates, including R to 3.6.1, I now get the following error on Windows:

txi.kallisto=tximport(files,type="kallisto",txOut=T,ignoreTxVersion = T,countsFromAbundance = 'scaledTPM')
Error in rhdf5::h5ls(h5File) : HDF5. Object header. Can't open object.

Using R 3.6.1 in Linux I'm able to import without error from the same abundance.h5 files without an error.

If I try to diagnose the problem with h5read, I get this error:

k=rhdf5::h5read("results/S1/abundance.h5")
Error in H5Lexists(loc$H5Identifier, name) : 
  argument "name" is missing, with no default

Any idea why tximport gives an error?

Here's the sessionInfo()

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] tximport_1.12.3 rhdf5_2.28.0   

loaded via a namespace (and not attached):
[1] compiler_3.6.1 tools_3.6.1    Rhdf5lib_1.6.0
tximport rhdf5 • 462 views
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Entering edit mode

Your call to rhdf5::h5read() needs to you to specify the name of the dataset to extract via the name argument. That's the source of the error your getting there.

To try and recreate the tximport usage you want to try rhdf5::h5ls() which will grab the entire contents of the file.

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Entering edit mode

Thanks. h5lc() showed the contents of the file correctly.

Working backwards from that I am now able to import on Windows without error. Don't know what changed or if there was an error in my files vector.

In any case, problem solved and sorry to waste your time.

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Entering edit mode
@mikelove
Last seen 2 days ago
United States

Nothing in tximport has changed, so I wonder about the source of the error. tximport has unit tests for hdf5 import and its building ok on Windows on the Bioc machines:

http://bioconductor.org/checkResults/devel/bioc-LATEST/tximport/

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