I would like to run the example code from the Reading HDF5 Files In The Cloud vignette from the
rhdf5 Bioconductor package:
Executing the first example:
public_S3_url <- "https://rhdf5-public.s3.eu-central-1.amazonaws.com/h5ex_t_array.h5" h5ls(file = public_S3_url, s3 = TRUE)
raises an error, because the
Rhdf5lib package hasn't been compiled with support for S3:
Error in H5Pset_fapl_ros3(fapl, s3credentials) : Rhdf5lib was not compiled with support for the S3 VFD
Does anybody have pointers on how to add support for S3 VFD?
This is what I found so far:
- I found the vignette that documents how the authors of the
Rhdf5liblibrary created their HDF5 distribution. The details are beyond my understanding, unfortunately. The authors also state:
This is for record keeping only, users of the Rhdf5lib package are not expected to follow any of the steps detailed here.
- The hdf5 group provides information on how to include the
S3 VFDinto hdf5, e.g. by adding arguments to the
configurecommand. I tried to install the
Rhdf5liblibrary from source and included those arguments via the
configure.argsargument, but they weren't recognized.
BiocManager::install('Rhdf5lib', type = "source", configure.args = "-DHDF5_ENABLE_ROS3_VFD:BOOL=ON")
Any suggestions would be appreciated - I'd love to understand how to
Read HDF5 Files In The Cloud!
Thank you, Thomas
sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.7 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  rhdf5_2.34.0 loaded via a namespace (and not attached):  compiler_4.0.3 credentials_1.3.0 tools_4.0.3 curl_4.3  rhdf5filters_1.2.0 jsonlite_1.7.2 openssl_1.4.3 sys_3.4  Rhdf5lib_1.12.1 askpass_1.1