* using log directory ‘/srv/hornik/tmp/CRAN/Platypus.Rcheck’ * using R Under development (unstable) (2023-11-17 r85545) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.5 (1) Debian flang-new version 17.0.5 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘Platypus/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Platypus’ version ‘3.5.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/7s] NOTE Maintainer: ‘Alexander Yermanos ’ New submission Package was archived on CRAN Possibly misspelled words in DESCRIPTION: immunogenomics (4:512) scSeq (4:174) transcriptional (4:318) CRAN repository db overrides: X-CRAN-Comment: Archived on 2023-06-15 as issues were not corrected in time. Found the following (possibly) invalid URLs: URL: https://github.com/alexyermanos/Platypus/blob/Functions/R/VDJ_GEX_matrix.R From: inst/doc/PlatypusV3_agedCNS.html Status: 404 Message: Not Found URL: https://github.com/alexyermanos/Platypus/tree/Functions/R From: inst/doc/PlatypusV3_agedCNS.html Status: 404 Message: Not Found * 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 ‘Platypus’ can be installed ... [16s/16s] 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] 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 ... [32s/32s] OK * checking Rd files ... [0s/0s] NOTE checkRd: (-1) VDJ_call_MIXCR.Rd:22: Lost braces; missing escapes or markup? 22 | \item{custom.cmd.call}{This function calls Mixcr via a terminal. The commands are build as follows: FOR DARWIN and LINUX machines: paste0(custom.cmd.call," ", mixcr.directory,"/mixcr.jar ... {mixcr parameters assembled by function}"). FOR WINDOWS machines: paste0(custom.cmd.call," mixcr.jar ... {mixcr parameters assembled by function}") custom.cmd.call defaults to "java -jar". In case different MIXCR installations, changing this to meet your systems requirements may be necessary.} | ^ checkRd: (-1) VDJ_call_MIXCR.Rd:22: Lost braces; missing escapes or markup? 22 | \item{custom.cmd.call}{This function calls Mixcr via a terminal. The commands are build as follows: FOR DARWIN and LINUX machines: paste0(custom.cmd.call," ", mixcr.directory,"/mixcr.jar ... {mixcr parameters assembled by function}"). FOR WINDOWS machines: paste0(custom.cmd.call," mixcr.jar ... {mixcr parameters assembled by function}") custom.cmd.call defaults to "java -jar". In case different MIXCR installations, changing this to meet your systems requirements may be necessary.} | ^ checkRd: (-1) VDJ_call_RECON.Rd:24: Lost braces; missing escapes or markup? 24 | \item{recon.directory}{directory containing recon executable. Defaults to {working directory}/Recon} | ^ * 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 ... [3s/3s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [8s/8s] ERROR Running examples in ‘Platypus-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: GEX_phenotype > ### Title: Assignment of cells to phenotypes based on selected markers > ### Aliases: GEX_phenotype > > ### ** Examples > > vgm.phenotyped <- GEX_phenotype(seurat.object = Platypus::small_vgm[[2]] + , default = TRUE) Error in `Idents<-`: ! 'value' must be a factor or vector Backtrace: ▆ 1. └─Platypus::GEX_phenotype(...) 2. ├─Seurat::`Idents<-`(object = `*tmp*`, value = seurat.object[["previous.ident"]]) 3. └─SeuratObject:::`Idents<-.Seurat`(object = `*tmp*`, value = seurat.object[["previous.ident"]]) 4. └─rlang::abort(message = "'value' must be a factor or vector") Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [1s/1s] OK * checking PDF version of manual ... [5s/5s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs