Closing hdf5 file leaves open H5I_GENPROP_LST handle behind
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0
Entering edit mode
@dariuszratman-12169
Last seen 4.8 years ago

Hi,

I am having trouble with closing hdf5 file handles. The issue can be reproduced with a small code chunk below:

library(rhdf5)
file.name <- tempfile()
h5createFile(file.name)
fid <- H5Fopen(file.name)
H5Fclose(fid)
h5validObjects()

With rhdf5 v 2.16.0 the result is (as expected):

list()

but with v 2.18.0 I get:

[[1]]

HDF5 GENPROP_LST

Opening/closing each new hdf5 file leaves additional GENPROP_LST object behind. Does anyone know what does GENPROP_LST object represent and how to close it selectively w/o using H5close()?

Dariusz

Session info -------------------------------------------------------------------

 setting  value                       

 version  R version 3.3.2 (2016-10-31)

 system   x86_64, linux-gnu           

 ui       RStudio (1.0.27)            

 language (EN)                        

 collate  en_US.UTF-8                 

 tz       <NA>                        

 date     2017-01-13                  


Packages -----------------------------------------------------------------------

 package  * version date       source        

 devtools   1.12.0  2016-12-05 CRAN (R 3.3.2)

 digest     0.6.11  2017-01-03 CRAN (R 3.3.2)

 memoise    1.0.0   2016-01-29 CRAN (R 3.3.2)

 rhdf5    * 2.18.0  2017-01-07 Bioconductor  

 withr      1.0.2   2016-06-20 CRAN (R 3.3.2)

 zlibbioc   1.20.0  2017-01-07 Bioconductor  


 

 

 
rhdf5 • 681 views
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1
Entering edit mode
Mike Smith ★ 5.2k
@mike-smith
Last seen 51 minutes ago
EMBL Heidelberg / de.NBI

This has hopefully been fixed in rhdf5 version 2.21.3

A change was made between version 2.16.0 and 2.18.0 so that when H5Fcreate() was called a list of properties to be used during the file creation was generated. This list was never subsequently closed, hence why you would see these hanging around.

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