* using log directory ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/lisat.Rcheck’
* using R version 4.5.2 Patched (2026-01-31 r89382)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.3.1
* using session charset: UTF-8
* checking for file ‘lisat/DESCRIPTION’ ... OK
* this is package ‘lisat’ version ‘0.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘lisat’ can be installed ... [34s/52s] OK
See 'https://www.r-project.org/nosvn/R.check/r-oldrel-macos-x86_64/lisat-00install.html' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [10s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/17s] OK
* checking whether the package can be unloaded cleanly ... [11s/17s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/17s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/16s] OK
* checking loading without being on the library search path ... [11s/17s] OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [24s/31s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [9s/9s] ERROR
  Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lisat)
  > testthat::test_check("lisat")
  Saving _problems/test-functions-71.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-functions.R:71:1'): (code run outside of `test_that()`) ────────
  Error: Package "TxDb.Hsapiens.UCSC.hg38.knownGene" needed for this function to work. Please install it.
  Backtrace:
      ▆
   1. └─lisat::get_feature(IS_raw) at test-functions.R:71:1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [19s/19s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘lisat-intro.Rmd’ using rmarkdown

Quitting from lisat-intro.Rmd:107-111 [cis_analysis]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.frame`:
! undefined columns selected
---
Backtrace:
    ▆
 1. └─lisat::CIS(IS_raw = IS_raw, connect_distance = 50000)
 2.   ├─IS_raw[, c("Locus", "Chr", "nearest_gene_name")]
 3.   └─base::`[.data.frame`(IS_raw, , c("Locus", "Chr", "nearest_gene_name"))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'lisat-intro.Rmd' failed with diagnostics:
undefined columns selected
--- failed re-building ‘lisat-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘lisat-intro.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [5s/6s] OK
* DONE
Status: 2 ERRORs

* DONE
* Status: FAILURE
* using check arguments '--no-clean-on-error '
* elapsed time (check, wall clock): 5:56
* result classification: failed check, errors:yes, warnings:no, notes:no