* using log directory ‘/Volumes/Builds/packages/big-sur-arm64/results/4.3/conos.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.4
* using session charset: UTF-8
* checking for file ‘conos/DESCRIPTION’ ... OK
* this is package ‘conos’ version ‘1.5.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'conosPanel', 'p2data'
* 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 ‘conos’ can be installed ... [58s/66s] OK
See 'https://www.r-project.org/nosvn/R.check/r-oldrel-macos-arm64/conos-00install.html' for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
* checking package 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 ... [2s/3s] OK
* checking whether the package can be unloaded cleanly ... [2s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
* checking loading without being on the library search path ... [2s/3s] 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 ... [6s/6s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] 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 compiled code ... OK
* checking examples ... [2s/3s] ERROR
Running examples in ‘conos-Ex.R’ failed
The error most likely occurred in:

> ### Name: Conos
> ### Title: Conos R6 class
> ### Aliases: Conos
> 
> ### ** Examples
> 
> 
> ## ------------------------------------------------
> ## Method `Conos$new`
> ## ------------------------------------------------
> 
> con <- Conos$new(small_panel.preprocessed, n.cores=1)
> 
> 
> ## ------------------------------------------------
> ## Method `Conos$buildGraph`
> ## ------------------------------------------------
> 
> con <- Conos$new(small_panel.preprocessed, n.cores=1)
> con$buildGraph(k=10, k.self=5, space='PCA', ncomps=10, n.odgenes=20, matching.method='mNN',
+     metric='angular', score.component.variance=TRUE, verbose=TRUE)
found 0 out of 1 cached PCA space pairs ... 
running 1 additional PCA space pairs 
Error in irlba::irlba(x, nv = ncomps, nu = 0, center = cm, right_only = FALSE,  : 
  function 'as_cholmod_sparse' not provided by package 'Matrix'
Calls: <Anonymous> ... FUN -> quickPlainPCA -> lapply -> FUN -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [3s/3s] ERROR
  Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    1. ├─base::suppressWarnings(con$buildGraph(ncomps = 25)) at test_functions.R:15:1
    2. │ └─base::withCallingHandlers(...)
    3. └─con$buildGraph(ncomps = 25)
    4.   └─private$updatePairs(...)
    5.     └─sccore::plapply(...)
    6.       └─base::lapply(...)
    7.         └─conos (local) FUN(X[[i]], ...)
    8.           └─conos:::quickPlainPCA(...)
    9.             └─base::lapply(...)
   10.               └─conos (local) FUN(X[[i]], ...)
   11.                 └─irlba::irlba(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... [5s/5s] OK
* DONE
Status: 2 ERRORs, 2 NOTEs
* using check arguments '--no-clean-on-error '

* elapsed time (check, wall clock): 2:23