• 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 ... [33s/46s] OK See the install log 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 ... [11s/16s] OK
• checking whether the package can be loaded with stated dependencies ... [10s/14s] OK
• checking whether the package can be unloaded cleanly ... [10s/13s] OK
• checking whether the namespace can be loaded with stated dependencies ... [10s/12s] OK
• checking whether the namespace can be unloaded cleanly ... [11s/13s] OK
• checking loading without being on the library search path ... [11s/13s] 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 ... [19s/19s] 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 ... [8s/8s] 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 ... [17s/17s] 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/5s] OK
• DONE Status: 2 ERRORs
• using check arguments '--no-clean-on-error '