* using log directory ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck’ * using R Under development (unstable) (2024-04-29 r86495) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 18.1.4 (1) Debian flang-new version 18.1.4 (1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘SCORPIUS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SCORPIUS’ version ‘1.0.9’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: ‘SingleCellExperiment’ * 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 ‘SCORPIUS’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/SCORPIUS-00install.html' 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 ... [4s/6s] OK * checking whether the package can be loaded with stated dependencies ... [4s/4s] OK * checking whether the package can be unloaded cleanly ... [4s/4s] OK * checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK * checking whether the namespace can be unloaded cleanly ... [4s/5s] OK * checking loading without being on the library search path ... [4s/5s] 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 ... [21s/26s] OK * checking Rd files ... [0s/1s] NOTE checkRd: (-1) reduce_dimensionality.Rd:19: Lost braces 19 | \item{ndim}{the maximum dimension of the space which the data are to be represented in; must be in {1, 2, \ldots, n-1}.} | ^ checkRd: (-1) ti_scorpius.Rd:18: Lost braces; missing escapes or markup? 18 | \item{distance_method}{A character string indicating which correlationcoefficient (or covariance) is to be computed. One of "pearson", "spearman" (default), or "cosine". Domain: {spearman, pearson, cosine}. Default: spearman. Format: character.} | ^ checkRd: (-1) ti_scorpius.Rd:30: Lost braces; missing escapes or markup? 30 | \item{smoother}{\code{principal_curve} parameter; choice of smoother. Domain: {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format: character.} | ^ * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [21s/24s] OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed draw_trajectory_plot 4.076 0.231 5.232 extract_modules 4.089 0.086 5.489 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [77s/79s] OK Running ‘testthat.R’ [76s/78s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [83s/82s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘anndata.Rmd’ using rmarkdown --- finished re-building ‘anndata.Rmd’ --- re-building ‘ginhoux.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/ginhoux_files/figure-html/show_dimred-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19199 bytes Input file size = 19301 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14187 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14187 Output IDAT size = 14187 bytes (5012 bytes decrease) Output file size = 14265 bytes (5036 bytes = 26.09% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/ginhoux_files/figure-html/plot_trajectory-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20139 bytes Input file size = 20241 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15180 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15180 Output IDAT size = 15180 bytes (4959 bytes decrease) Output file size = 15258 bytes (4983 bytes = 24.62% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/ginhoux_files/figure-html/visualise_tafs-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 15021 bytes Input file size = 15111 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11452 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11452 Output IDAT size = 11452 bytes (3569 bytes decrease) Output file size = 11530 bytes (3581 bytes = 23.70% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/ginhoux_files/figure-html/moduled_tafs-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 15692 bytes Input file size = 15782 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11492 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11492 Output IDAT size = 11492 bytes (4200 bytes decrease) Output file size = 11570 bytes (4212 bytes = 26.69% decrease) --- finished re-building ‘ginhoux.Rmd’ --- re-building ‘simulated-data.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/simulated-data_files/figure-html/show_dimred-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 18081 bytes Input file size = 18183 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13317 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13317 Output IDAT size = 13317 bytes (4764 bytes decrease) Output file size = 13395 bytes (4788 bytes = 26.33% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/simulated-data_files/figure-html/plot_trajectory-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 19472 bytes Input file size = 19574 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14652 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14652 Output IDAT size = 14652 bytes (4820 bytes decrease) Output file size = 14730 bytes (4844 bytes = 24.75% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/simulated-data_files/figure-html/visualise_tafs-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16253 bytes Input file size = 16343 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11827 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11827 Output IDAT size = 11827 bytes (4426 bytes decrease) Output file size = 11905 bytes (4438 bytes = 27.16% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SCORPIUS.Rcheck/vign_test/SCORPIUS/vignettes/simulated-data_files/figure-html/moduled_tafs-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 17734 bytes Input file size = 17836 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12733 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12733 Output IDAT size = 12733 bytes (5001 bytes decrease) Output file size = 12811 bytes (5025 bytes = 28.17% decrease) --- finished re-building ‘simulated-data.Rmd’ --- re-building ‘singlecellexperiment.Rmd’ using rmarkdown Quitting from lines at lines 26-40 [load_data] (singlecellexperiment.Rmd) Error: processing vignette 'singlecellexperiment.Rmd' failed with diagnostics: there is no package called 'SingleCellExperiment' --- failed re-building ‘singlecellexperiment.Rmd’ SUMMARY: processing the following file failed: ‘singlecellexperiment.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [6s/8s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR, 2 NOTEs