• using R Under development (unstable) (2025-06-27 r88363)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-19) 14.2.0     GNU Fortran (Debian 14.2.0-19) 14.2.0
• running under: Debian GNU/Linux 13 (trixie)
• using session charset: UTF-8
• checking for file ‘ridigbio/DESCRIPTION’ ... OK
• this is package ‘ridigbio’ version ‘0.4.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/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 serialization versions ... OK
• checking whether package ‘ridigbio’ 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/0s] 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 whether startup messages can be suppressed ... [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 ... [3s/4s] OK
• checking Rd files ... [0s/1s] 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 ... [0s/0s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [2s/2s] OK   Running ‘testthat.R’ [2s/2s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [92s/442s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘BadCoordinateID.Rmd’ using rmarkdown --- finished re-building ‘BadCoordinateID.Rmd’ --- re-building ‘BasicUsage.Rmd’ using rmarkdown --- finished re-building ‘BasicUsage.Rmd’ --- re-building ‘Fields.Rmd’ using rmarkdown --- finished re-building ‘Fields.Rmd’ --- re-building ‘FindTissue.Rmd’ using rmarkdown [WARNING] Div at FindTissue.knit.md line 173 column 1 unclosed at FindTissue.knit.md line 8381 column 1, closing implicitly. --- finished re-building ‘FindTissue.Rmd’ --- re-building ‘IDDataFlags.Rmd’ using rmarkdown Quitting from IDDataFlags.Rmd:57-90 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `as.environment()`: ! using 'as.environment(NULL)' is defunct --- Backtrace:     ▆  1. ├─... %>% ...  2. ├─dplyr::select(...)  3. ├─dplyr::rename(...)  4. └─ridigbio::idig_search_records(...)  5. └─ridigbio::idig_search(...)  6. ├─plyr::rbind.fill(dat, fmt_search_txt_to_df(search_results, fields))  7. └─ridigbio:::fmt_search_txt_to_df(search_results, fields)  8. └─base::exists("items", httr::content(txt)) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'IDDataFlags.Rmd' failed with diagnostics: using 'as.environment(NULL)' is defunct --- failed re-building ‘IDDataFlags.Rmd’ --- re-building ‘MediaAPIDemo.Rmd’ using rmarkdown --- finished re-building ‘MediaAPIDemo.Rmd’ --- re-building ‘ModifiedDataID.Rmd’ using rmarkdown --- finished re-building ‘ModifiedDataID.Rmd’ --- re-building ‘RecordAPIDemo.Rmd’ using rmarkdown [WARNING] Div at RecordAPIDemo.knit.md line 200 column 1 unclosed at RecordAPIDemo.knit.md line 12004 column 1, closing implicitly. --- finished re-building ‘RecordAPIDemo.Rmd’ --- re-building ‘ridigbio.Rmd’ using rmarkdown --- finished re-building ‘ridigbio.Rmd’ SUMMARY: processing the following file failed:   ‘IDDataFlags.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [0s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR