Last updated on 2026-01-18 19:50:39 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| PKbioanalysis | 2 | 3 | 8 |
Current CRAN status: ERROR: 2, NOTE: 3, OK: 8
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PKbioanalysis)
Attaching package: 'PKbioanalysis'
The following object is masked from 'package:stats':
integrate
>
> test_check("PKbioanalysis")
Error in `source_dir()`:
! Failed to evaluate './helper-global.R'.
Caused by error in `.local()`:
! {"exception_type":"IO","exception_message":"Could not set lock on file \"/data/gannet/ripley/.local/share/R/PKbioanalysis/samples.db\": Conflicting lock is held in /data/gannet/ripley/R/R-devel/bin/exec/R (PID 3797446) by user ripley. However, you would be able to open this database in read-only mode, e.g. by using the -readonly parameter in the CLI. See also https://duckdb.org/docs/stable/connect/concurrency","errno":"11"}
ℹ Context: rapi_startup
Backtrace:
▆
1. ├─testthat::test_check("PKbioanalysis")
2. │ └─testthat::test_dir(...)
3. │ └─testthat:::test_files(...)
4. │ └─testthat:::test_files_serial(...)
5. │ └─testthat:::test_files_setup_state(...)
6. │ └─testthat::source_test_helpers(".", env)
7. │ └─testthat::source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
8. │ └─base::lapply(...)
9. │ └─testthat (local) FUN(X[[i]], ...)
10. │ └─testthat::source_file(...)
11. │ ├─base::withCallingHandlers(...)
12. │ └─base::eval(exprs, env)
13. │ └─base::eval(exprs, env)
14. │ └─PKbioanalysis:::.save_cmpd_db(x) at ./helper-global.R:21:1
15. │ └─PKbioanalysis:::.connect_to_db()
16. │ ├─duckdb::dbConnect(duckdb::duckdb(), dbdir = db_path)
17. │ └─duckdb::dbConnect(duckdb::duckdb(), dbdir = db_path)
18. │ └─duckdb (local) .local(drv, ...)
19. │ └─duckdb::duckdb(dbdir, read_only, bigint, config)
20. │ ├─methods::new(...)
21. │ │ ├─methods::initialize(value, ...)
22. │ │ └─methods::initialize(value, ...)
23. │ └─duckdb:::rethrow_rapi_startup(dbdir, read_only, config, environment_scan)
24. │ ├─rlang::try_fetch(...)
25. │ │ ├─base::tryCatch(...)
26. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
27. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
28. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
29. │ │ └─base::withCallingHandlers(...)
30. │ └─duckdb:::rapi_startup(dbdir, readonly, configsexp, environment_scan)
31. ├─duckdb (local) `<fn>`("rapi_startup", "{\"exception_type\":\"IO\",\"exception_message\":\"Could not set lock on file \\\"/data/gannet/ripley/.local/share/R/PKbioanalysis/samples.db\\\": Conflicting lock is held in /data/gannet/ripley/R/R-devel/bin/exec/R (PID 3797446) by user ripley. However, you would be able to open this database in read-only mode, e.g. by using the -readonly parameter in the CLI. See also https://duckdb.org/docs/stable/connect/concurrency\",\"errno\":\"11\"}")
32. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
33. │ └─rlang:::signal_abort(cnd, .file)
34. │ └─base::signalCondition(cnd)
35. └─rlang (local) `<fn>`(`<dckdb_rr>`)
36. └─handlers[[1L]](cnd)
37. └─duckdb:::rethrow_error_from_rapi(e, call)
38. └─rlang::abort(msg, call = call)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [149s/534s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(PKbioanalysis)
Attaching package: 'PKbioanalysis'
The following object is masked from 'package:stats':
integrate
>
> test_check("PKbioanalysis")
Plate not registered. To register, use register_plate()
Plate not registered. To register, use register_plate()
Plate not registered. To register, use register_plate()
Plate not registered. To register, use register_plate()
Plate not registered. To register, use register_plate()
Plate not registered. To register, use register_plate()
Plate not registered. To register, use register_plate()
Plate not registered. To register, use register_plate()
"My Plate" |> generate_96() |> add_blank(group = "A") |> fill_scheme(fill = "h") |> add_suitability() |> fill_scheme(tbound = 1, fill = "v")i Created study with ID: aaf29b0b-bebb-45e4-b0c5-b7461bb37b1a
i Adding dosing and subjects information...
v Dosing information added.
i Adding subjects information...
v Subjects information added.
i Adding sample log information...
v Sample log information added.
i Created study with ID: 98755640-2ab4-445a-9071-315b6e62353a
v Dosing information added.
i Adding subjects information...
v Subjects information added.
i Adding sample log information...
v Sample log information added.
i Created study with ID: c7bd63b3-e6b2-4108-8e8b-2920626ea3cc
v Dosing information added.
i Adding subjects information...
v Subjects information added.
i Adding sample log information...
v Sample log information added.
`geom_smooth()` using formula = 'y ~ x'
Saving _problems/test_quant_object-12.R
[ FAIL 1 | WARN 0 | SKIP 16 | PASS 103 ]
══ Skipped tests (16) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-apps.R:1:1', 'test-injec_list.R:8:3',
'test-injec_list.R:51:3', 'test-injec_list.R:88:3',
'test-injec_list.R:118:3', 'test-injec_list.R:140:3',
'test-injec_list.R:178:3', 'test-plate.R:10:3', 'test-plate.R:22:3',
'test_methodsfile.R:1:1'
• empty test (5): 'test-estimresiduals.R:1:1', 'test-estimresiduals.R:18:1',
'test-plate.R:158:1', 'test-plate_expr.R:56:1', 'test-quant_parsers.R:9:1'
• scipy not available for testing (1): 'test-pydeps.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_quant_object.R:12:1'): (code run outside of `test_that()`) ─────
Error in `.get_method_cmpds(method_id)`: Method ID 1 not found in database.
Backtrace:
▆
1. └─PKbioanalysis:::create_quant_object(quantobj, 1) at test_quant_object.R:12:1
2. └─PKbioanalysis:::update_cmpd_info(res, method_id)
3. └─PKbioanalysis:::check_quant_method_quantres(quantres, method_id)
4. └─PKbioanalysis:::.get_method_cmpds(method_id)
[ FAIL 1 | WARN 0 | SKIP 16 | PASS 103 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.4.0
Check: installed package size
Result: NOTE
installed size is 7.9Mb
sub-directories of 1Mb or more:
R 3.1Mb
extdata 4.5Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64