* using log directory ‘/srv/hornik/tmp/CRAN/SPECK.Rcheck’
* using R Under development (unstable) (2023-11-15 r85536)
* 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 ‘SPECK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPECK’ version ‘1.0.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/5s] Note_to_CRAN_maintainers
Maintainer: ‘Azka Javaid <azka.javaid.gr@dartmouth.edu>’
* 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 serialization versions ... OK
* checking whether package ‘SPECK’ can be installed ... [12s/12s] OK
* 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 ... [13s/13s] 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 ... [1s/1s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] ERROR
Running examples in ‘SPECK-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ckmeansThreshold
> ### Title: Clustered thresholding of a vector.
> ### Aliases: ckmeansThreshold
> 
> ### ** Examples
> 
> library(SeuratObject)
Loading required package: sp
‘SeuratObject’ was built with package ‘Matrix’ 1.6.1.1 but the current
version is 1.6.3; it is recomended that you reinstall ‘SeuratObject’ as
the ABI for ‘Matrix’ may have changed

Attaching package: ‘SeuratObject’

The following objects are masked from ‘package:base’:

    %||%, intersect

> data.mat <- t(as.matrix(pbmc_small@assays$RNA@counts))
> rrr.object <- randomizedRRR(counts.matrix = data.mat, rank.range.end = 60,
+ min.consec.diff = 0.01, rep.consec.diff = 2,
+ manual.rank = NULL, seed.rsvd = 1)
Warning: Data is of class matrix. Coercing to dgCMatrix.
Error in validObject(.Object) : 
  invalid class “LogMap” object: superclass "mMatrix" not defined in the environment of the object's class
Calls: randomizedRRR ... initialize -> initialize -> initMatrix -> validObject
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 ‘SPECKVignette.Rmd’ using rmarkdown

Quitting from lines 48-69 [unnamed-chunk-4] (SPECKVignette.Rmd)
Error: processing vignette 'SPECKVignette.Rmd' failed with diagnostics:
invalid class "LogMap" object: superclass "mMatrix" not defined in the environment of the object's class
--- failed re-building ‘SPECKVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘SPECKVignette.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