• using R Under development (unstable) (2025-12-23 r89222)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-11) 15.2.0     GNU Fortran (Debian 15.2.0-11) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘rangeMapper/DESCRIPTION’ ... OK
• this is package ‘rangeMapper’ version ‘2.0.3’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] NOTE Maintainer: ‘Mihai Valcu <valcu@orn.mpg.de>’ Package CITATION file contains call(s) to old-style personList() or as.personList(). Please use c() on person objects instead. Package CITATION file contains call(s) to old-style citEntry(). Please use bibentry() instead.
• 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 ‘rangeMapper’ 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 ... [7s/9s] OK
• checking whether the package can be loaded with stated dependencies ... [8s/10s] OK
• checking whether the package can be unloaded cleanly ... [7s/10s] OK
• checking whether the namespace can be loaded with stated dependencies ... [7s/10s] OK
• checking whether the namespace can be unloaded cleanly ... [7s/9s] OK
• checking loading without being on the library search path ... [7s/9s] OK
• checking whether startup messages can be suppressed ... [7s/7s] 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 ... [32s/37s] 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [6s/8s] 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 ... [8s/10s] ERROR Running examples in ‘rangeMapper-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: rmap_save_map > ### Title: Save maps > ### Aliases: rmap_save_map > ### rmap_save_map,rmapConnection,missing,missing,missing,missing,missing-method > ### rmap_save_map,rmapConnection,missing,missing,missing,character,character-method > ### rmap_save_map,rmapConnection,character,character,character,missing,character-method > ### rmap_save_map,rmapConnection,character,character,character,character,character-method > ### rmap_save_map,rmapConnection,function,character,character,missing,character-method > ### rmap_save_map,rmapConnection,function,character,character,character,character-method > ### rmap_save_map,rmapConnection,function,character,ANY,missing,character-method > ### rmap_save_map,rmapConnection,function,character,ANY,character,character-method > ### rmap_save_map,rmapConnection,character,Raster,missing,missing,character-method > > ### ** Examples > > require(rangeMapper) > require(data.table) Loading required package: data.table Attaching package: ‘data.table’ The following object is masked from ‘package:base’:     %notin% > con = rmap_connect() > wrens = read_wrens() > rmap_add_ranges(con, x = wrens, ID = 'sci_name') > rmap_prepare(con, 'hex', cellsize=500)  --> Making hex canvas ...done.     (i) The canvas has 576 cells.  --> Processing 84 ranges ... --> Updating rmap_nfo & rmap_master tables ...done.     (i) Finished in 0.219s elapsed (0.212s cpu) > rmap_save_map(con) # default is a species_richness map. > > rmap_add_bio(con, wrens, 'sci_name') > rmap_save_map(con, fun='avg', src='wrens',v='body_mass', dst='avg_bodymass') > > rmap_save_subset(con,dst ='ss1', species_richness = 'species_richness > 10') Error in `[.data.table`(W, type == "map", `:=`(joinCall, paste("JOIN", :   attempt access index 5/5 in VECTOR_ELT Calls: rmap_save_subset -> rmap_save_subset -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [12s/14s] ERROR   Running ‘testthat.R’ [12s/14s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(rangeMapper)   rangeMapper 2.0.3   >   > test_check("rangeMapper")   Saving _problems/test-3_subsets-28.R   Saving _problems/test-3_subsets-65.R   Saving _problems/test-3_subsets-75.R   Saving _problems/test-4_maps-7.R   Saving _problems/test-5_get-6.R   [ FAIL 5 | WARN 0 | SKIP 0 | PASS 35 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-3_subsets.R:26:5'): rmap_save_subset returns TRUE ──────────────   Error in ``[.data.table`(W, type == "map", `:=`(joinCall, paste("JOIN", name, "ON", "c.cell_id = ", name, ".cell_id", collapse = "")), by = pk)`: attempt access index 5/5 in VECTOR_ELT   Backtrace:       ▆    1. ├─testthat::expect_true(rmap_save_subset(con, "s1", species_richness = "species_richness > 10")) at test-3_subsets.R:26:5    2. │ └─testthat::quasi_label(enquo(object), label)    3. │ └─rlang::eval_bare(expr, quo_get_env(quo))    4. ├─rangeMapper::rmap_save_subset(con, "s1", species_richness = "species_richness > 10")    5. └─rangeMapper::rmap_save_subset(con, "s1", species_richness = "species_richness > 10")    6. ├─...[]    7. └─data.table:::`[.data.table`(...)   ── Error ('test-3_subsets.R:61:5'): rmap_save_subset works with LIKE ───────────   Error in ``[.data.table`(W, type == "map", `:=`(joinCall, paste("JOIN", name, "ON", "c.cell_id = ", name, ".cell_id", collapse = "")), by = pk)`: attempt access index 5/5 in VECTOR_ELT   Backtrace:       ▆    1. ├─testthat::expect_true(rmap_save_subset(con, "s1", wrens = "female_tarsus BETWEEN 20 and 30 AND subspecies > 1 AND com_name LIKE \"%-wren%\" ")) at test-3_subsets.R:61:5    2. │ └─testthat::quasi_label(enquo(object), label)    3. │ └─rlang::eval_bare(expr, quo_get_env(quo))    4. ├─rangeMapper::rmap_save_subset(con, "s1", wrens = "female_tarsus BETWEEN 20 and 30 AND subspecies > 1 AND com_name LIKE \"%-wren%\" ")    5. └─rangeMapper::rmap_save_subset(con, "s1", wrens = "female_tarsus BETWEEN 20 and 30 AND subspecies > 1 AND com_name LIKE \"%-wren%\" ")    6. ├─...[]    7. └─data.table:::`[.data.table`(...)   ── Error ('test-3_subsets.R:71:5'): rmap_save_subset works with where > (select .... ) ──   Error in ``[.data.table`(W, type == "map", `:=`(joinCall, paste("JOIN", name, "ON", "c.cell_id = ", name, ".cell_id", collapse = "")), by = pk)`: attempt access index 5/5 in VECTOR_ELT   Backtrace:       ▆    1. ├─testthat::expect_true(rmap_save_subset(con, "s1", wrens = "clutch_size > (SELECT avg(clutch_size) from wrens)")) at test-3_subsets.R:71:5    2. │ └─testthat::quasi_label(enquo(object), label)    3. │ └─rlang::eval_bare(expr, quo_get_env(quo))    4. ├─rangeMapper::rmap_save_subset(con, "s1", wrens = "clutch_size > (SELECT avg(clutch_size) from wrens)")    5. └─rangeMapper::rmap_save_subset(con, "s1", wrens = "clutch_size > (SELECT avg(clutch_size) from wrens)")    6. ├─...[]    7. └─data.table:::`[.data.table`(...)   ── Error ('test-4_maps.R:7:1'): (code run outside of `test_that()`) ────────────   Error in ``[.data.table`(W, type == "map", `:=`(joinCall, paste("JOIN", name, "ON", "c.cell_id = ", name, ".cell_id", collapse = "")), by = pk)`: attempt access index 5/5 in VECTOR_ELT   Backtrace:       ▆    1. ├─rangeMapper::rmap_save_subset(con, "s1", wrens = "clutch_size > 2") at test-4_maps.R:7:1    2. └─rangeMapper::rmap_save_subset(con, "s1", wrens = "clutch_size > 2")    3. ├─...[]    4. └─data.table:::`[.data.table`(...)   ── Error ('test-5_get.R:6:1'): (code run outside of `test_that()`) ─────────────   Error in ``[.data.table`(W, type == "map", `:=`(joinCall, paste("JOIN", name, "ON", "c.cell_id = ", name, ".cell_id", collapse = "")), by = pk)`: attempt access index 5/5 in VECTOR_ELT   Backtrace:       ▆    1. ├─rangeMapper::rmap_save_subset(con, dst = "ss1", species_richness = "species_richness > 10") at test-5_get.R:6:1    2. └─rangeMapper::rmap_save_subset(con, dst = "ss1", species_richness = "species_richness > 10")    3. ├─...[]    4. └─data.table:::`[.data.table`(...)      [ FAIL 5 | WARN 0 | SKIP 0 | PASS 35 ]   Error:   ! Test failures.   Warning message:   call dbDisconnect() when finished working with a connection   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [19s/23s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘Case_studies_Valcu_et_al_2012.Rmd’ using rmarkdown Quitting from Case_studies_Valcu_et_al_2012.Rmd:115-125 [unnamed-chunk-6] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 5/5 in VECTOR_ELT --- Backtrace:     ▆  1. ├─rangeMapper::rmap_save_subset(...)  2. └─rangeMapper::rmap_save_subset(...)  3. ├─...[]  4. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Case_studies_Valcu_et_al_2012.Rmd' failed with diagnostics: attempt access index 5/5 in VECTOR_ELT --- failed re-building ‘Case_studies_Valcu_et_al_2012.Rmd’ --- re-building ‘rangeMapper.Rmd’ using rmarkdown Quitting from rangeMapper.Rmd:71-73 [unnamed-chunk-6] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 5/5 in VECTOR_ELT --- Backtrace:     ▆  1. ├─rangeMapper::rmap_save_subset(con, "sset1", species_richness = "species_richness > 10")  2. └─rangeMapper::rmap_save_subset(con, "sset1", species_richness = "species_richness > 10")  3. ├─...[]  4. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'rangeMapper.Rmd' failed with diagnostics: attempt access index 5/5 in VECTOR_ELT --- failed re-building ‘rangeMapper.Rmd’ SUMMARY: processing the following files failed:   ‘Case_studies_Valcu_et_al_2012.Rmd’ ‘rangeMapper.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/5s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs, 1 NOTE