• using R Under development (unstable) (2025-07-30 r88476)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (3+b1)     Debian flang-new version 19.1.7 (3+b1)
• running under: Debian GNU/Linux 13 (trixie)
• using session charset: UTF-8
• checking for file ‘warbleR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘warbleR’ version ‘1.1.36’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] 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 ‘warbleR’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘Debian clang version 19.1.7 (3+b1)’
• 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 ... [1s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
• checking loading without being on the library search path ... [1s/2s] OK
• checking whether startup messages can be suppressed ... [1s/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 ... [54s/65s] OK
• checking Rd files ... [1s/2s] 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 ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [32s/44s] OK Examples with CPU (user + system) or elapsed time > 5s                    user system elapsed test_coordination 6.573 0.028 8.847 wpd_features 4.553 0.084 6.980
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [23s/35s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘a_warbleR.Rmd’ using rmarkdown --- finished re-building ‘a_warbleR.Rmd’ --- re-building ‘b_annotation_data_format.Rmd’ using rmarkdown Quitting from b_annotation_data_format.Rmd:536-550 [unnamed-chunk-12] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `names(results)[match(c("id", "gen", "sp", "ssp", "en", "rec", "cnt", "loc", "lat", "lng", "alt",     "type", "file", "lic", "url", "q", "length", "time", "date", "uploaded", "rmk", "bird.seen",     "playback.used"), names(results))] <- c("Recording_ID", "Genus", "Specific_epithet", "Subspecies",     "English_name", "Recordist", "Country", "Locality", "Latitude", "Longitude", "Altitude",     "Vocalization_type", "Audio_file", "License", "Url", "Quality", "Length", "Time", "Date",     "Uploaded", "Remarks", "Bird_seen", "Playback_used")[which(c("id", "gen", "sp", "ssp", "en",     "rec", "cnt", "loc", "lat", "lng", "alt", "type", "file", "lic", "url", "q", "length", "time",     "date", "uploaded", "rmk", "bird.seen", "playback.used") %in% names(results))]`: ! NAs are not allowed in subscripted assignments --- Backtrace:     ▆  1. └─warbleR::query_xc(qword = "nr:15607", download = TRUE, path = tempdir()) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'b_annotation_data_format.Rmd' failed with diagnostics: NAs are not allowed in subscripted assignments --- failed re-building ‘b_annotation_data_format.Rmd’ --- re-building ‘c_warbleR_workflow_02.Rmd’ using rmarkdown --- finished re-building ‘c_warbleR_workflow_02.Rmd’ SUMMARY: processing the following file failed:   ‘b_annotation_data_format.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [10s/14s] OK
• checking HTML version of manual ... [6s/12s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR