* 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 ’ * 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