############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data ELViS ### ############################################################################## ############################################################################## * checking for file ‘ELViS/DESCRIPTION’ ... OK * preparing ‘ELViS’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘ELViS_Toy_Example.Rmd’ using rmarkdown Quitting from ELViS_Toy_Example.Rmd:168-199 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `.check_versions()`: ! versions must be explicitly specified for 'samtools' --- Backtrace: ▆ 1. ├─base::system.time(...) 2. └─ELViS::get_depth_matrix(...) 3. └─ELViS:::get_envs_samtools_basilisk(...) 4. └─basilisk::obtainEnvironmentPath(samtools_env) 5. └─basilisk::setupBasiliskEnv(...) 6. └─basilisk:::.check_versions(packages, "[^=<>]==[0-9]") ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'ELViS_Toy_Example.Rmd' failed with diagnostics: versions must be explicitly specified for 'samtools' --- failed re-building ‘ELViS_Toy_Example.Rmd’ SUMMARY: processing the following file failed: ‘ELViS_Toy_Example.Rmd’ Error: Vignette re-building failed. Execution halted