H5CX__pop_common: Assertion `head && *head' failed error with install SpatialExperiment package

[curtishongbio-blip]

Hi Developer,
I got the error with insatll the SpatialExperiment in R 4.2.3 in platform centos7.9.
The detail error lying below:
Installing package(s) 'SpatialExperiment'
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/SpatialExperiment_1.8.1.tar.gz'
Content type 'application/gzip' length 5390680 bytes (5.1 MB)

downloaded 5.1 MB

• installing source package ‘SpatialExperiment’ ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  sh: line 1: 128116 Aborted (core dumped) R_TESTS= '/public/syssoft/R-4.2.3/lib64/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/tmp/Rtmp3zuIcX/file1f46e57fae751'
  R: H5CX.c:3535: H5CX__pop_common: Assertion `head && *head' failed.
  ERROR: lazy loading failed for package ‘SpatialExperiment’
• removing ‘/public/syssoft/R-4.2.3/lib64/R/library/SpatialExperiment’
  The R info:

sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /public/syssoft/R-4.2.3/lib64/R/lib/libRblas.so
LAPACK: /public/syssoft/R-4.2.3/lib64/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
[1] BiocManager_1.30.21.1 compiler_4.2.3 tools_4.2.3

Any advice would be appreciated,
Best,
hanhuihong

[drighelli]

Hi hanhuihong (@curtishongbio-blip),

I think this is not directly related to the SpatialExperiment, but mostly to the HDF5 handling, that SpE inherits from other classes.

Are you able to load the rhdf5 library?

My guess is that your centos is missing some hdf5 handling libraries.

Dario