Running ‘testthat.R’ [170s/266s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(CRMetrics)
  > 
  > test_check("CRMetrics")
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  Running preprocessing using pagoda2...
  3000 cells, 10000 genes; normalizing ... 
  Using plain model 
  Winsorizing ... 
  log scale ... 
  done.
  
  calculating variance fit ...
   using gam 
  0 overdispersed genes ... 0
  persisting ... 
  done.
  running PCA using 3000 OD genes .
  .
  .
  .
   done
  
  creating space of type angular done
  adding data ... done
  building index ... done
  querying ... done
  3000 cells, 10000 genes; normalizing ... 
  Using plain model 
  Winsorizing ... 
  log scale ... 
  done.
  
  calculating variance fit ...
   using gam 
  0 overdispersed genes ... 0
  persisting ... 
  done.
  running PCA using 3000 OD genes .
  .
  .
  .
   done
  
  creating space of type angular done
  adding data ... done
  building index ... done
  querying ... done
  3000 cells, 10000 genes; normalizing ... 
  Using plain model 
  Winsorizing ... 
  log scale ... 
  done.
  
  calculating variance fit ...
   using gam 
  0 overdispersed genes ... 0
  persisting ... 
  done.
  running PCA using 3000 OD genes .
  .
  .
  .
   done
  
  creating space of type angular done
  adding data ... done
  building index ... done
  querying ... done
  3000 cells, 10000 genes; normalizing ... 
  Using plain model 
  Winsorizing ... 
  log scale ... 
  done.
  
  calculating variance fit ...
   using gam 
  0 overdispersed genes ... 0
  persisting ... 
  done.
  running PCA using 3000 OD genes .
  .
  .
  .
   done
  
  creating space of type angular done
  adding data ... done
  building index ... done
  querying ... done
  Preprocessing done!
  
  Creating Conos object... 
  Building graph... 
  found 0 out of 6 cached PCA space pairs ... 
  running 6 additional PCA space pairs 
  ...... done
  inter-sample links using mNN 
  ...... done
  local pairs 
  .
  .
  .
  .
   done
  
  building graph .
  .done
  Finding communities... 
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('tests.R:41:3'): Check embedding object ──────────────────────────────
  Error in `find_partition(graph, igraph::E(graph)$weight, resolution, n.iterations)`: REAL() can only be applied to a 'numeric', not a 'NULL'
  Backtrace:
      ▆
   1. └─crm$createEmbedding(arg.embedGraph = list(method = "largeVis")) at tests.R:41:2
   2.   ├─base::do.call(con$findCommunities, arg.findCommunities)
   3.   └─conos (local) `<fn>`(n.iterations = 1)
   4.     └─leidenAlg (local) method(self$graph, ...)
   5.       └─leidenAlg::find_partition(...)
  ── Failure ('tests.R:49:3'): Check depth vector ────────────────────────────────
  length(crm$getConosDepth()) (`actual`) not equal to 12000 (`expected`).
  
    `actual`:     0
  `expected`: 12000
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 3 ]
  Error: Test failures
  Execution halted