• using R Under development (unstable) (2025-01-24 r87627)
• using platform: x86_64-apple-darwin20
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
• running under: macOS Ventura 13.3.1
• using session charset: UTF-8
• checking for file ‘MARVEL/DESCRIPTION’ ... OK
• this is package ‘MARVEL’ version ‘1.4.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Packages suggested but not available for checking:   'BSgenome', 'BSgenome.Hsapiens.NCBI.GRCh38', 'factoextra',   'FactoMineR', 'org.Hs.eg.db', 'org.Mm.eg.db', 'wiggleplotr'
• 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 ‘MARVEL’ can be installed ... [14s/22s] OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... 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 code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [2s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] 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 ... [21s/36s] OK
• checking Rd files ... [1s/1s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [31s/54s] ERROR Running examples in ‘MARVEL-Ex.R’ failed The error most likely occurred in: > ### Name: RunPCA.Exp > ### Title: Principle component analysis for gene Data > ### Aliases: RunPCA.Exp > > ### ** Examples > > marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL")) > > # Define genes for analysis > gene_ids <- marvel.demo$Exp$gene_id > > # PCA > marvel.demo <- RunPCA.Exp(MarvelObject=marvel.demo, + sample.ids=marvel.demo$SplicePheno$sample.id, + cell.group.column="cell.type", + cell.group.order=c("iPSC", "Endoderm"), + min.cells=5, + features=gene_ids, + point.size=2 + ) Error in loadNamespace(x) : there is no package called ‘FactoMineR’ Calls: RunPCA.Exp ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [11s/20s] ERROR Error(s) in re-building vignettes: --- re-building ‘MARVEL.Rmd’ using rmarkdown Quitting from lines 60-71 [unnamed-chunk-4] (MARVEL.Rmd) Error: processing vignette 'MARVEL.Rmd' failed with diagnostics: there is no package called 'FactoMineR' --- failed re-building ‘MARVEL.Rmd’ SUMMARY: processing the following file failed:   ‘MARVEL.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [11s/19s] OK
• DONE Status: 2 ERRORs
• using check arguments '--no-clean-on-error '