############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiContacts ### ############################################################################## ############################################################################## * checking for file ‘HiContacts/DESCRIPTION’ ... OK * preparing ‘HiContacts’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘HiContacts.Rmd’ using rmarkdown Warning in for (i in seq_along(slots)) { : closing unused connection 4 (/home/biocbuild/.cache/R/ExperimentHub/37cbb2193e94e6_7751) Quitting from HiContacts.Rmd:120-127 [unnamed-chunk-8] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `h()`: ! error in evaluating the argument 'con' in selecting a method for function 'import': HDF5. File accessibility. Unable to open file. --- Backtrace: ▆ 1. ├─BiocIO::import(...) 2. ├─BiocIO::import(...) 3. │ ├─BiocIO::import(FileForFormat(con, format), ...) 4. │ └─BiocIO::FileForFormat(con, format) 5. │ └─get(constructorName, ns)(path) 6. │ └─HiCExperiment:::.check_cool_file(path) 7. │ └─HiCExperiment:::.is_cool(path) 8. │ └─HiCExperiment:::.lsCoolFiles(path) 9. │ ├─(function(x) {... 10. │ │ └─base::gsub("//", "/", x) 11. │ │ └─base::is.factor(x) 12. │ ├─base::unique(...) 13. │ ├─dplyr::pull(...) 14. │ ├─dplyr::mutate(rhdf5::h5ls(file), path = paste0(group, "/", name)) 15. │ └─rhdf5::h5ls(file) 16. │ └─rhdf5:::h5checktypeOrOpenLoc(...) 17. │ └─rhdf5::H5Fopen(file, flags = flags, fapl = fapl, native = native) 18. └─base::.handleSimpleError(...) 19. └─base (local) h(simpleError(msg, call)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'HiContacts.Rmd' failed with diagnostics: error in evaluating the argument 'con' in selecting a method for function 'import': HDF5. File accessibility. Unable to open file. --- failed re-building ‘HiContacts.Rmd’ SUMMARY: processing the following file failed: ‘HiContacts.Rmd’ Error: Vignette re-building failed. Execution halted