Why can I open HDF5 files from local disk but not external disk using the rhdf5 R package?

Question

I am having an issue which I came across using the R package "sleuth" to analyze RNAseq data. The problem clearly depends on rhdf5, however. The issue boils down to this error, which I only get when trying to read a .h5 file from my external SSD but not from my local disk:

> library("rhdf5")

> H5Fopen("/pathway/to/external/SSD/abundance.h5")
#gives the following error:
Error in H5Fopen("/pathway/to/external/SSD/abundance.h5") : 
  HDF5. File accessibility. Unable to open file.

> H5Fopen("/Users/myname/Desktop/abundance.h5")
#this runs perfectly

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 13.0

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] rhdf5_2.38.1

loaded via a namespace (and not attached):
 [1] KEGGREST_1.34.0        progress_1.2.2         tidyselect_1.2.0      
 [4] xfun_0.36              vctrs_0.5.1            generics_0.1.3        
 [7] htmltools_0.5.4        stats4_4.1.3           BiocFileCache_2.2.1   
[10] yaml_2.3.6             utf8_1.2.2             blob_1.2.3            
[13] XML_3.99-0.13          rlang_1.0.6            pillar_1.8.1          
[16] glue_1.6.2             DBI_1.1.3              rappdirs_0.3.3        
[19] BiocGenerics_0.40.0    bit64_4.0.5            dbplyr_2.2.1          
[22] GenomeInfoDbData_1.2.7 lifecycle_1.0.3        stringr_1.5.0         
[25] zlibbioc_1.40.0        Biostrings_2.62.0      memoise_2.0.1         
[28] evaluate_0.19          Biobase_2.54.0         knitr_1.41            
[31] IRanges_2.28.0         fastmap_1.1.0          biomaRt_2.50.3        
[34] GenomeInfoDb_1.30.1    curl_4.3.3             fansi_1.0.3           
[37] AnnotationDbi_1.56.2   Rcpp_1.0.9             filelock_1.0.2        
[40] cachem_1.0.6           S4Vectors_0.32.4       XVector_0.34.0        
[43] bit_4.0.5              hms_1.1.2              png_0.1-8             
[46] digest_0.6.31          stringi_1.7.8          dplyr_1.0.10          
[49] rhdf5filters_1.6.0     cli_3.5.0              tools_4.1.3           
[52] bitops_1.0-7           magrittr_2.0.3         tibble_3.1.8          
[55] RCurl_1.98-1.9         RSQLite_2.2.20         crayon_1.5.2          
[58] pkgconfig_2.0.3        ellipsis_0.3.2         xml2_1.3.3            
[61] prettyunits_1.1.1      assertthat_0.2.1       rmarkdown_2.19        
[64] httr_1.4.4             rstudioapi_0.14        Rhdf5lib_1.16.0       
[67] R6_2.5.1               compiler_4.1.3

Notably, the .h5 file was initially stored exclusively on the external SSD and I copied it to my Desktop here for demonstration purposes (the file is identical in the two locations and was copied from the external SSD to desktop today)

Can anyone help me understand this behaviour? It works a lot better for my workflow if I can keep the .h5 file stored on the external SSD.

I have tried toggling Sys.setenv(HDF5_USE_FILE_LOCKING = "FALSE") and Sys.setenv(RHDF5_USE_FILE_LOCKING = "FALSE") based on some github issues all to no avail.

Others have been experiencing this issue using the sleuth package here: https://github.com/pachterlab/sleuth/issues/274

And a similar issue has been asked about here: Reading .h5 file in R

But neither of these answer my question or solve my issue!

I appreciate any insight!

Why can I open HDF5 files from local disk but not external disk using the rhdf5 R package?

Answers (1)

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