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grimbough / rhdf5

Package providing an interface between HDF5 and R
http://bioconductor.org/packages/rhdf5
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Segfault on HDF5 consortium example file #48

Closed louisaslett closed 4 years ago

louisaslett commented 4 years ago

Thanks for a very nice package. Minor bug report here on a standard example ...

The test file h5ex_g_traverse.h5 on the HDF consortium website causes h5ls() to crash.

library(rhdf5)
h5ls("h5ex_g_traverse.h5")

results in:

Error: segfault from C stack overflow

presumably due to an infinite loop in links not being detected?

The official example solution probably gives an indication how to rectify this h5ex_g_traverse.c.

grimbough commented 4 years ago

Thanks for the report, this should now be addressed in rhdf5 v2.33.5