* using log directory ‘/srv/hornik/tmp/CRAN/bbknnR.Rcheck’
* using R Under development (unstable) (2023-11-16 r85542)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.4 (1)
    Debian flang-new version 17.0.4 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘bbknnR/DESCRIPTION’ ... OK
* this is package ‘bbknnR’ version ‘1.1.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/4s] NOTE
Maintainer: ‘Yuchen Li <ycli1995@outlook.com>’

New maintainer:
  Yuchen Li <ycli1995@outlook.com>
Old maintainer(s):
  Yuchen Li <liyuchen_1995@outlook.com>

The Date field is over a month old.
* 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 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 ‘bbknnR’ can be installed ... [21s/21s] OK
* used C++ compiler: ‘Debian clang version 17.0.5 (1)’
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [15s/15s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [4s/4s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... 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 ... [5s/5s] ERROR
  Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bbknnR)
  > 
  > test_check("bbknnR")
  Running BBKNN using RcppAnnoy...
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_bbknn.R:5:5'): BBKNN with RcppAnnoy ────────────────────────────
  Error in `validObject(object = value)`: invalid class "Graph" object: superclass "mMatrix" not defined in the environment of the object's class
  Backtrace:
      ▆
   1. ├─bbknnR::RunBBKNN(panc8_small, "tech", approx = T, use_annoy = T) at test_bbknn.R:5:5
   2. └─bbknnR:::RunBBKNN.Seurat(panc8_small, "tech", approx = T, use_annoy = T)
   3.   ├─methods (local) `[[<-`(`*tmp*`, graph_name, value = `<Graph[,500]>`)
   4.   └─SeuratObject (local) `[[<-`(`*tmp*`, graph_name, value = `<Graph[,500]>`)
   5.     └─methods::validObject(object = value)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  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 ... [5s/5s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘bbknnR-tutorial.Rmd’ using rmarkdown

Quitting from lines 30-31 [runbbknn] (bbknnR-tutorial.Rmd)
Error: processing vignette 'bbknnR-tutorial.Rmd' failed with diagnostics:
invalid class "Graph" object: superclass "mMatrix" not defined in the environment of the object's class
--- failed re-building ‘bbknnR-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘bbknnR-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [3s/2s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs, 1 NOTE