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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scQTLtools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scQTLtools_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scQTLtools.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scQTLtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scQTLtools’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scQTLtools’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... OK
* checking Rd files ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
zinbModel       150.921  5.002 178.729
DESeq_normalize  17.994  2.362  24.496
callQTL          10.965  0.358  20.706
poissonModel      9.790  0.310  11.442
visualizeQTL      8.421  0.044   9.543
linearModel       6.413  0.279   7.896
TPM_normalize     4.061  1.886   6.981
CPM_normalize     3.274  1.873   6.483
log_normalize     3.257  1.820   5.893
limma_normalize   2.711  1.851   5.432
get_raw_data      1.152  3.373   5.285
createGeneLoc     4.191  0.224   9.473
createSNPsLoc     3.618  0.195   6.853
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-visualizeQTL.R:62:3'): visualizeQTL function behaves as expected ──
  Expected `is.list(plot5)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 49 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/scQTLtools.Rcheck/00check.log’
for details.