• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.7 (1)     Debian flang version 21.1.7 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘rTwig/DESCRIPTION’ ... OK
• this is package ‘rTwig’ version ‘1.4.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/2s] 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 ‘rTwig’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 21.1.7 (1)’
• 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/5s] OK
• checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the package can be unloaded cleanly ... [3s/5s] OK
• checking whether the namespace can be loaded with stated dependencies ... [3s/4s] OK
• checking whether the namespace can be unloaded cleanly ... [3s/5s] OK
• checking loading without being on the library search path ... [4s/4s] OK
• checking whether startup messages can be suppressed ... [3s/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 ... [28s/38s] OK
• checking Rd files ... [4s/6s] 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 line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... NOTE File ‘rTwig/libs/rTwig.so’:   Found non-API call to R: ‘ATTRIB’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points.
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [6s/6s] ERROR Running examples in ‘rTwig-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: cluster_cloud > ### Title: Cluster Cloud > ### Aliases: cluster_cloud > > ### ** Examples > > > ## Load Data > file <- system.file("extdata/QSM.mat", package = "rTwig") > file2 <- system.file("extdata/cloud.txt", package = "rTwig") > > qsm <- run_rtwig(file, twig_radius = 4.23, metrics = FALSE) Importing TreeQSM Updating Cylinder Ordering Calculating Total Children Building Cylinder Network Caching Network Verifying Topology Calculating Growth Length Calculating Reverse Branch Order Error in `[.data.table`(~.df, , `:=`(c("depth", "reverseBranchOrder"), :   attempt access index 4/4 in VECTOR_ELT Calls: run_rtwig ... mutate -> mutate.tidytable -> eval_tidy -> [ -> [.data.table Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [66s/85s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘Box-Dimension.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Box-Dimension.Rmd’ --- re-building ‘Dictionary.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Dictionary.Rmd’ --- re-building ‘Metrics.Rmd’ using rmarkdown Quitting from Metrics.Rmd:41-50 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 4/4 in VECTOR_ELT --- Backtrace:      ▆   1. ├─rTwig::run_rtwig(file, twig_radius = 4.23, metrics = FALSE)   2. │ └─rTwig::update_cylinders(cylinder)   3. │ └─rTwig:::reverse_branch_order(...)   4. │ └─... %>% rename({{ id }} := "id")   5. ├─tidytable::rename(...)   6. ├─tidytable::summarise(...)   7. ├─tidytable::group_by(., "id")   8. ├─tidytable::mutate(...)   9. ├─tidytable:::mutate.grouped_tt(...)  10. │ ├─tidytable::mutate(...)  11. │ └─tidytable:::mutate.tidytable(...)  12. │ └─rlang::eval_tidy(dt_expr, .df, dt_env)  13. ├─...[]  14. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Metrics.Rmd' failed with diagnostics: attempt access index 4/4 in VECTOR_ELT --- failed re-building ‘Metrics.Rmd’ --- re-building ‘Overview.Rmd’ using rmarkdown Quitting from Overview.Rmd:141-147 [unnamed-chunk-12] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 4/4 in VECTOR_ELT --- Backtrace:      ▆   1. ├─rTwig::update_cylinders(cylinder)   2. │ └─rTwig:::reverse_branch_order(...)   3. │ └─... %>% rename({{ id }} := "id")   4. ├─tidytable::rename(...)   5. ├─tidytable::summarise(...)   6. ├─tidytable::group_by(., "id")   7. ├─tidytable::mutate(...)   8. ├─tidytable:::mutate.grouped_tt(...)   9. │ ├─tidytable::mutate(...)  10. │ └─tidytable:::mutate.tidytable(...)  11. │ └─rlang::eval_tidy(dt_expr, .df, dt_env)  12. ├─...[]  13. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Overview.Rmd' failed with diagnostics: attempt access index 4/4 in VECTOR_ELT --- failed re-building ‘Overview.Rmd’ --- re-building ‘Twigs.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Twigs.Rmd’ --- re-building ‘Validation.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘Validation.Rmd’ SUMMARY: processing the following files failed:   ‘Metrics.Rmd’ ‘Overview.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [5s/6s] OK
• checking HTML version of manual ... [2s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs, 1 NOTE