• 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 ‘scopr/DESCRIPTION’ ... OK
• this is package ‘scopr’ version ‘0.3.5’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [0s/1s] 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 ‘scopr’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [0s/1s] 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 ... [5s/7s] 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 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 examples ... [1s/2s] ERROR Running examples in ‘scopr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: link_ethoscope_metadata_remote > ### Title: Link ethoscope metadata to the matching result files > ### Aliases: link_ethoscope_metadata_remote link_ethoscope_metadata > > ### ** Examples > > # Metadata with no region_id -> all regions will be loaded with the same metadata > dir <- paste0(scopr_example_dir(), "/ethoscope_results/") > data(no_region_id_metadata) > metadata <- link_ethoscope_metadata(no_region_id_metadata, dir) Error in `[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", :   attempt access index 6/6 in VECTOR_ELT Calls: link_ethoscope_metadata -> build_query -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [5s/8s] ERROR   Running ‘testthat.R’ [5s/7s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(scopr)   Loading required package: behavr   Loading required package: data.table      Attaching package: 'data.table'      The following object is masked from 'package:base':          %notin%      >   > test_check("scopr")   Saving _problems/test-build_query-12.R   Saving _problems/test-build_query-40.R   Saving _problems/test-build_query-53.R   Saving _problems/test-build_query-68.R   Saving _problems/test-build_query-83.R     machine_name date time test   1 E_014 2016-01-25 21:36:04 1   2 E_014 2016-02-17 <NA> 2   3 E_029 2016-01-25 <NA> 3   Saving _problems/test-build_query-110.R   Saving _problems/test-link_ethocope_metadata-6.R   Saving _problems/test-link_ethocope_metadata-24.R   Saving _problems/test-link_ethocope_metadata-39.R   Saving _problems/test-link_ethocope_metadata-60.R   Saving _problems/test-link_ethocope_metadata-73.R   Saving _problems/test-link_ethocope_metadata-94.R   Saving _problems/test-link_ethoscope_metadata_remote-18.R   Saving _problems/test-link_ethoscope_metadata_remote-55.R   Saving _problems/test-load_ethoscope-11.R   Saving _problems/test-load_ethoscope-23.R   Saving _problems/test-load_ethoscope-36.R   [ FAIL 17 | WARN 0 | SKIP 0 | PASS 17 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test-build_query.R:12:3'): build query works when time is supplied ──   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr:::build_query(dir, query) at test-build_query.R:12:3    2. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    3. └─data.table:::`[.data.table`(...)   ── Error ('test-build_query.R:40:3'): build_query with date, machine name, and ROIs, and two experiments on the same date, but different times! ──   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr:::build_query(dir, query) at test-build_query.R:40:3    2. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    3. └─data.table:::`[.data.table`(...)   ── Error ('test-build_query.R:53:3'): build query works when only date supplied ──   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. ├─testthat::expect_warning(...) at test-build_query.R:53:3    2. │ └─testthat:::quasi_capture(...)    3. │ ├─testthat (local) .capture(...)    4. │ │ └─base::withCallingHandlers(...)    5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))    6. └─scopr:::build_query(dir, query)    7. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    8. └─data.table:::`[.data.table`(...)   ── Error ('test-build_query.R:68:3'): build query works when only date supplied and ROIs ──   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. ├─testthat::expect_warning(...) at test-build_query.R:68:3    2. │ └─testthat:::quasi_capture(...)    3. │ ├─testthat (local) .capture(...)    4. │ │ └─base::withCallingHandlers(...)    5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))    6. └─scopr:::build_query(dir, query)    7. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    8. └─data.table:::`[.data.table`(...)   ── Error ('test-build_query.R:83:3'): missing results! ─────────────────────────   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. ├─testthat::expect_warning(...) at test-build_query.R:83:3    2. │ └─testthat:::quasi_capture(...)    3. │ ├─testthat (local) .capture(...)    4. │ │ └─base::withCallingHandlers(...)    5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))    6. └─scopr:::build_query(dir, query)    7. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    8. └─data.table:::`[.data.table`(...)   ── Error ('test-build_query.R:110:3'): build query works datetime is a datetime, not a string (https://github.com/rethomics/scopr/issues/16) ──   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr:::build_query(dir, query) at test-build_query.R:110:3    2. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    3. └─data.table:::`[.data.table`(...)   ── Error ('test-link_ethocope_metadata.R:6:3'): link_ethoscope_metadata with single file ──   Error in ``[.data.table`(out, , `:=`(n, .N), keyby = key(out))`: attempt access index 3/3 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr::link_ethoscope_metadata(test_file) at test-link_ethocope_metadata.R:6:3    2. ├─out[, `:=`(n, .N), keyby = key(out)]    3. └─data.table:::`[.data.table`(out, , `:=`(n, .N), keyby = key(out))   ── Error ('test-link_ethocope_metadata.R:24:3'): link_ethoscope_metadata with date and machine name ──   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr::link_ethoscope_metadata(query, dir) at test-link_ethocope_metadata.R:24:3    2. └─scopr:::build_query(result_dir, query, index_file)    3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    4. └─data.table:::`[.data.table`(...)   ── Error ('test-link_ethocope_metadata.R:39:3'): link_ethoscope_metadata with name of a text csv ──   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr::link_ethoscope_metadata(file, dir) at test-link_ethocope_metadata.R:39:3    2. └─scopr:::build_query(result_dir, query, index_file)    3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    4. └─data.table:::`[.data.table`(...)   ── Error ('test-link_ethocope_metadata.R:60:3'): link_ethoscope_metadata with date, machine name, and ROIs ──   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr::link_ethoscope_metadata(query, dir) at test-link_ethocope_metadata.R:60:3    2. └─scopr:::build_query(result_dir, query, index_file)    3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    4. └─data.table:::`[.data.table`(...)   ── Error ('test-link_ethocope_metadata.R:73:3'): link_ethoscope_metadata with path ──   Error in ``[.data.table`(out, , `:=`(n, .N), keyby = key(out))`: attempt access index 4/4 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr::link_ethoscope_metadata(query, dir) at test-link_ethocope_metadata.R:73:3    2. ├─out[, `:=`(n, .N), keyby = key(out)]    3. └─data.table:::`[.data.table`(out, , `:=`(n, .N), keyby = key(out))   ── Error ('test-link_ethocope_metadata.R:94:3'): link_ethoscope_metadata detect duplicated rows ──   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. ├─testthat::expect_warning(...) at test-link_ethocope_metadata.R:94:3    2. │ └─testthat:::quasi_capture(...)    3. │ ├─testthat (local) .capture(...)    4. │ │ └─base::withCallingHandlers(...)    5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))    6. └─scopr:::link_ethoscope_metadata(query, dir)    7. └─scopr:::build_query(result_dir, query, index_file)    8. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    9. └─data.table:::`[.data.table`(...)   ── Error ('test-link_ethoscope_metadata_remote.R:14:3'): link_ethoscope_metadata_remote with date and machine name ──   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr:::link_ethoscope_metadata_remote(...) at test-link_ethoscope_metadata_remote.R:14:3    2. └─scopr:::build_query(result_dir = remote_dir, query = query, index_file = index_file)    3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    4. └─data.table:::`[.data.table`(...)   ── Error ('test-link_ethoscope_metadata_remote.R:51:3'): parse_query with date, machine name, and ROIs ──   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr:::link_ethoscope_metadata_remote(...) at test-link_ethoscope_metadata_remote.R:51:3    2. └─scopr:::build_query(result_dir = remote_dir, query = query, index_file = index_file)    3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    4. └─data.table:::`[.data.table`(...)   ── Error ('test-load_ethoscope.R:11:3'): query ethoscopes functions ────────────   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr::link_ethoscope_metadata(metadata, dir) at test-load_ethoscope.R:11:3    2. └─scopr:::build_query(result_dir, query, index_file)    3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    4. └─data.table:::`[.data.table`(...)   ── Error ('test-load_ethoscope.R:23:3'): query ethoscopes works ────────────────   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr::link_ethoscope_metadata(metadata, dir) at test-load_ethoscope.R:23:3    2. └─scopr:::build_query(result_dir, query, index_file)    3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    4. └─data.table:::`[.data.table`(...)   ── Error ('test-load_ethoscope.R:36:3'): query ethoscopes works with multiple cores ──   Error in ``[.data.table`(unique_fi_last_of_day, , `:=`(n, .N), by = c("date", "machine_name"))`: attempt access index 6/6 in VECTOR_ELT   Backtrace:       ▆    1. └─scopr::link_ethoscope_metadata(query, dir) at test-load_ethoscope.R:36:3    2. └─scopr:::build_query(result_dir, query, index_file)    3. ├─unique_fi_last_of_day[, `:=`(n, .N), by = c("date", "machine_name")]    4. └─data.table:::`[.data.table`(...)      [ FAIL 17 | WARN 0 | SKIP 0 | PASS 17 ]   Error:   ! Test failures.   Execution halted
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs