• using R Under development (unstable) (2025-12-24 r89227)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.8 (1)     Debian flang version 21.1.8 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘rADA/DESCRIPTION’ ... OK
• this is package ‘rADA’ version ‘1.1.9’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/1s] OK
• 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 ‘rADA’ can be installed ... OK See the install log for details.
• 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 code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [0s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/0s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
• checking loading without being on the library search path ... [0s/0s] 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 ... [4s/6s] 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 ... [0s/0s] 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 ... [7s/9s] ERROR Running examples in ‘rADA-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: scpForestPlot > ### Title: Generate forest plot of SCP values > ### Aliases: scpForestPlot scpForestPlot,ImmunoAssay-method > > ### ** Examples > > assay.obj <- importAssay(assay.df = lognormAssay, exp.name = 'Experiment1') > assay.obj <- scp(assay.obj, category = 'Experiment1', distrib = 'normal', + data.transf = TRUE, transf.method = 'log10', rm.out = FALSE) > scpForestPlot(assay.obj) Error in xtfrm.data.frame(list(mean = 23.0524633087061, upper = 23.5679826580867, :   cannot xtfrm data frames Calls: scpForestPlot ... prFpConvertMultidimArray -> xtfrm -> xtfrm.data.frame Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [13s/18s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘rada_vignette.Rmd’ using knitr Quitting from rada_vignette.Rmd:392-396 [unnamed-chunk-23] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `xtfrm.data.frame()`: ! cannot xtfrm data frames --- Backtrace:     ▆  1. ├─rADA::scpForestPlot(assay.obj)  2. └─rADA::scpForestPlot(assay.obj)  3. ├─forestplot::forestplot(...)  4. └─forestplot:::forestplot.default(...)  5. └─forestplot:::createEstimateArray(labeltext, lower, upper, mean)  6. └─forestplot:::prFpConvertMultidimArray(mean)  7. ├─base::xtfrm(`<df[,3]>`)  8. └─base::xtfrm.data.frame(`<df[,3]>`) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'rada_vignette.Rmd' failed with diagnostics: cannot xtfrm data frames --- failed re-building ‘rada_vignette.Rmd’ --- re-building ‘rada_vignette_supplemental.Rmd’ using knitr Quitting from rada_vignette_supplemental.Rmd:392-396 [unnamed-chunk-23] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `xtfrm.data.frame()`: ! cannot xtfrm data frames --- Backtrace:     ▆  1. ├─rADA::scpForestPlot(assay.obj)  2. └─rADA::scpForestPlot(assay.obj)  3. ├─forestplot::forestplot(...)  4. └─forestplot:::forestplot.default(...)  5. └─forestplot:::createEstimateArray(labeltext, lower, upper, mean)  6. └─forestplot:::prFpConvertMultidimArray(mean)  7. ├─base::xtfrm(`<df[,3]>`)  8. └─base::xtfrm.data.frame(`<df[,3]>`) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'rada_vignette_supplemental.Rmd' failed with diagnostics: cannot xtfrm data frames --- failed re-building ‘rada_vignette_supplemental.Rmd’ SUMMARY: processing the following files failed:   ‘rada_vignette.Rmd’ ‘rada_vignette_supplemental.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs