Question: windows tximport fail
0
gravatar for rhart
10 weeks ago by
rhart0
rhart0 wrote:

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
rhdf5 tximport • 121 views
ADD COMMENTlink modified 10 weeks ago by Michael Love25k • written 10 weeks ago by rhart0

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.

ADD REPLYlink written 10 weeks ago by Mike Smith4.0k

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.

ADD REPLYlink written 10 weeks ago by rhart0
Answer: windows tximport fail
0
gravatar for Michael Love
10 weeks ago by
Michael Love25k
United States
Michael Love25k wrote:

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/

ADD COMMENTlink written 10 weeks ago by Michael Love25k
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