* using log directory ‘/srv/hornik/tmp/CRAN_pretest/iRfcb.Rcheck’ * using R Under development (unstable) (2025-03-05 r87881) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (1+b1) Debian flang-new version 19.1.7 (1+b1) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘iRfcb/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘iRfcb’ version ‘0.4.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [4s/8s] NOTE Maintainer: ‘Anders Torstensson ’ New submission Possibly misspelled words in DESCRIPTION: FlowCytobot (3:35, 24:109) IFCB (3:48, 24:99, 24:197) Sosik (24:464) geospatial (24:157) * 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 ‘iRfcb’ can be installed ... [8s/8s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Author field differs from that derived from Authors@R Author: ‘Anders Torstensson [aut, cre] (Swedish Meteorological and Hydrological Institute, ), Kendra Hayashi [ctb] (), Jamie Enslein [ctb], Raphael Kudela [ctb] (), Alle Lie [ctb] (), Jayme Smith [ctb] (), DTO-BioFlow [fnd] (Horizon Europe, HORIZON-MISS-2022-OCEAN-01-07)’ Authors@R: ‘Anders Torstensson [aut, cre] (affiliation: Swedish Meteorological and Hydrological Institute, ORCID: ), Kendra Hayashi [ctb] (ORCID: ), Jamie Enslein [ctb], Raphael Kudela [ctb] (ORCID: ), Alle Lie [ctb] (ORCID: ), Jayme Smith [ctb] (ORCID: ), DTO-BioFlow [fnd] (funder: Horizon Europe, project_id: HORIZON-MISS-2022-OCEAN-01-07)’ * 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/2s] OK * checking loading without being on the library search path ... [2s/2s] OK * checking whether startup messages can be suppressed ... [2s/2s] 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 ... [11s/11s] 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [11s/11s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [16s/18s] OK Running ‘testthat.R’ [15s/18s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [84s/99s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘a-general-tutorial.Rmd’ using rmarkdown --- finished re-building ‘a-general-tutorial.Rmd’ --- re-building ‘ecotaxa-tutorial.Rmd’ using rmarkdown --- finished re-building ‘ecotaxa-tutorial.Rmd’ --- re-building ‘image-export-tutorial.Rmd’ using rmarkdown --- finished re-building ‘image-export-tutorial.Rmd’ --- re-building ‘matlab-tutorial.Rmd’ using rmarkdown The virtual environment was not created successfully because ensurepip is not available. On Debian/Ubuntu systems, you need to install the python3-venv package using the following command. apt install python3.13-venv You may need to use sudo with that command. After installing the python3-venv package, recreate your virtual environment. Failing command: /tmp/RtmpOkeSnX/working_dir/RtmpbzJFHM/iRfcb/bin/python3.13 Quitting from lines 212-230 [unnamed-chunk-14] (matlab-tutorial.Rmd) Error: processing vignette 'matlab-tutorial.Rmd' failed with diagnostics: Error creating virtual environment '/tmp/RtmpOkeSnX/working_dir/RtmpbzJFHM/iRfcb' [error code 1] --- failed re-building ‘matlab-tutorial.Rmd’ --- re-building ‘qc-tutorial.Rmd’ using rmarkdown The virtual environment was not created successfully because ensurepip is not available. On Debian/Ubuntu systems, you need to install the python3-venv package using the following command. apt install python3.13-venv You may need to use sudo with that command. After installing the python3-venv package, recreate your virtual environment. Failing command: /tmp/RtmpOkeSnX/working_dir/Rtmp2Dpgf4/iRfcb/bin/python3.13 Quitting from lines 103-125 [unnamed-chunk-7] (qc-tutorial.Rmd) Error: processing vignette 'qc-tutorial.Rmd' failed with diagnostics: Error creating virtual environment '/tmp/RtmpOkeSnX/working_dir/Rtmp2Dpgf4/iRfcb' [error code 1] --- failed re-building ‘qc-tutorial.Rmd’ SUMMARY: processing the following files failed: ‘matlab-tutorial.Rmd’ ‘qc-tutorial.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] 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