* using log directory 'd:/Rcompile/CRANpkg/local/4.2/clustermole.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* checking for file 'clustermole/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'clustermole' version '1.1.0'
* 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 whether package 'clustermole' can be installed ... OK
* 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 R 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 loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... [29s] OK
* checking Rd files ... [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 LazyData ... NOTE
  'LazyData' is specified without a 'data' directory
* checking R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [19s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [28s] ERROR
  Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clustermole)
  > 
  > test_check("clustermole")
  [ FAIL 5 | WARN 7 | SKIP 0 | PASS 29 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-enrichment.R:30:3'): clustermole_enrichment() human input default method ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─clustermole::clustermole_enrichment(expr_mat = log_cpm_mat, species = "hs") at test-enrichment.R:30:3
    2.   └─clustermole:::get_scores(...)
    3.     ├─GSVA::gsva(...)
    4.     └─GSVA::gsva(...)
    5.       └─GSVA (local) .local(expr, gset.idx.list, ...)
    6.         └─GSVA:::.filterFeatures(expr, method)
    7.           ├─DelayedMatrixStats::rowSds(expr)
    8.           └─DelayedMatrixStats::rowSds(expr)
    9.             └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
   10.               └─matrixStats::rowSds(...)
   11.                 └─matrixStats::rowVars(...)
   12.                   └─matrixStats:::deprecatedUseNamesNA()
   13.                     └─base::.Defunct(...)
  ── Error ('test-enrichment.R:38:3'): clustermole_enrichment() human input gsva method ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─clustermole::clustermole_enrichment(...) at test-enrichment.R:38:3
    2.   └─clustermole:::get_scores(...)
    3.     ├─GSVA::gsva(...)
    4.     └─GSVA::gsva(...)
    5.       └─GSVA (local) .local(expr, gset.idx.list, ...)
    6.         └─GSVA:::.filterFeatures(expr, method)
    7.           ├─DelayedMatrixStats::rowSds(expr)
    8.           └─DelayedMatrixStats::rowSds(expr)
    9.             └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
   10.               └─matrixStats::rowSds(...)
   11.                 └─matrixStats::rowVars(...)
   12.                   └─matrixStats:::deprecatedUseNamesNA()
   13.                     └─base::.Defunct(...)
  ── Error ('test-enrichment.R:46:3'): clustermole_enrichment() human input ssgsea method ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─clustermole::clustermole_enrichment(...) at test-enrichment.R:46:3
    2.   └─clustermole:::get_scores(...)
    3.     ├─GSVA::gsva(...)
    4.     └─GSVA::gsva(...)
    5.       └─GSVA (local) .local(expr, gset.idx.list, ...)
    6.         └─GSVA:::.filterFeatures(expr, method)
    7.           ├─DelayedMatrixStats::rowSds(expr)
    8.           └─DelayedMatrixStats::rowSds(expr)
    9.             └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
   10.               └─matrixStats::rowSds(...)
   11.                 └─matrixStats::rowVars(...)
   12.                   └─matrixStats:::deprecatedUseNamesNA()
   13.                     └─base::.Defunct(...)
  ── Error ('test-enrichment.R:62:3'): clustermole_enrichment() human input all combined method ──
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─clustermole::clustermole_enrichment(...) at test-enrichment.R:62:3
    2.   └─clustermole:::get_scores(...)
    3.     ├─GSVA::gsva(...)
    4.     └─GSVA::gsva(...)
    5.       └─GSVA (local) .local(expr, gset.idx.list, ...)
    6.         └─GSVA:::.filterFeatures(expr, method)
    7.           ├─DelayedMatrixStats::rowSds(expr)
    8.           └─DelayedMatrixStats::rowSds(expr)
    9.             └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
   10.               └─matrixStats::rowSds(...)
   11.                 └─matrixStats::rowVars(...)
   12.                   └─matrixStats:::deprecatedUseNamesNA()
   13.                     └─base::.Defunct(...)
  ── Error ('test-enrichment.R:76:3'): clustermole_enrichment() mouse input ──────
  <defunctError/error/condition>
  Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.
  Backtrace:
       ▆
    1. └─clustermole::clustermole_enrichment(expr_mat = log_cpm_mat, species = "mm") at test-enrichment.R:76:3
    2.   └─clustermole:::get_scores(...)
    3.     ├─GSVA::gsva(...)
    4.     └─GSVA::gsva(...)
    5.       └─GSVA (local) .local(expr, gset.idx.list, ...)
    6.         └─GSVA:::.filterFeatures(expr, method)
    7.           ├─DelayedMatrixStats::rowSds(expr)
    8.           └─DelayedMatrixStats::rowSds(expr)
    9.             └─MatrixGenerics (local) .local(x, rows, cols, na.rm, center, ..., useNames = useNames)
   10.               └─matrixStats::rowSds(...)
   11.                 └─matrixStats::rowVars(...)
   12.                   └─matrixStats:::deprecatedUseNamesNA()
   13.                     └─base::.Defunct(...)
  
  [ FAIL 5 | WARN 7 | SKIP 0 | PASS 29 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [14s] OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE