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I installed the rhdf5 package with BiocManager and wanted to use the h5write function to write a dataframe to a hdf5 file. But with each function from this package I only get:

> rhdf5::h5write(df, file="test3.hdf5", name ="table")
Error: segfault from C stack overflow

same if I try to open a new file with

> h5createFile("test3.hdf5")
Error: segfault from C stack overflow

R version is 4.0.2.

I didn't found any other users with this problem, maybe somebody might know a reason for this behavior, otherwise the R is working fine...

Thanks to all and have a nice day. Max

JcGKitten
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  • And you have `Rhdf5lib` and `rhdf5filters` installed? – Chris Sep 08 '21 at 14:15
  • @Chris were would I need to install these packages? I'm not really sure if I have them, thanks for the hint :) – JcGKitten Sep 09 '21 at 15:12
  • Basically, if, on a whim I decide to install some new pkg, I do one of two things, or both, `install.packages('some_pkg', dependencies = TRUE)`, and/or go to the pkg info and read Description, Needs Compilation, System Requirements. Description gives me what it imports/depends, do I have? `library(help='depends') no pkg depends found, install depends. `library(help='Rhdf5lib') will tell you. System requirements tells if you need a lib installed to compile, seems that is taken care of by Rhdf5lib in this case. Filters is probably utilities of some sort. – Chris Sep 09 '21 at 15:47

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