===============================
R CMD BUILD
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* checking for file ‘GXwasR/DESCRIPTION’ ... OK
* preparing ‘GXwasR’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to process help pages)
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building ‘GXwasR_in_action.Rmd’ using rmarkdown
Quitting from GXwasR_in_action.Rmd:142-145 [filter_variants]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/FilterAllele_error>
Error in `value[[3L]]()`:
! PLINK binary not found.
✖ Attempted to locate the 'PLINK_PATH' environment variable and 'plink' in system PATH.
i Ensure PLINK is available and executable (bioinformatics version).
i You can permanently set the path to 'plink' by running:
usethis::edit_r_environ() # then add a line like: PLINK_PATH=/full/path/to/plink
---
Backtrace:
▆
1. └─GXwasR::FilterAllele(DataDir, ResultDir, finput, foutput)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. ├─base (local) tryCatchOne(...)
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─base (local) tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
7. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
8. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GXwasR_in_action.Rmd' failed with diagnostics:
PLINK binary not found.
✖ Attempted to locate the 'PLINK_PATH' environment variable and 'plink' in system PATH.
i Ensure PLINK is available and executable (bioinformatics version).
i You can permanently set the path to 'plink' by running:
usethis::edit_r_environ() # then add a line like: PLINK_PATH=/full/path/to/plink
--- failed re-building ‘GXwasR_in_action.Rmd’
SUMMARY: processing the following file failed:
‘GXwasR_in_action.Rmd’
Error: Vignette re-building failed.
Execution halted