- using R Under development (unstable) (2025-11-13 r89017)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 21.1.5
flang version 21.1.5
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘MolgenisArmadillo/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘MolgenisArmadillo’ version ‘2.9.1’
- package encoding: UTF-8
- 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 ‘MolgenisArmadillo’ can be installed ... [14s/39s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... 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 ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... [4s/11s] OK
- checking loading without being on the library search path ... [3s/10s] 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 ... [19s/54s] OK
- checking Rd files ... 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 ... OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [15s/42s] ERROR
Running ‘testthat.R’ [14s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tibble)
> library(MolgenisArmadillo)
> library(webmockr)
>
> test_check("MolgenisArmadillo")
crul not installed, skipping enable
HttrAdapter enabled!
Httr2Adapter enabled!
Saving _problems/test-object-46.R
Saving _problems/test-object-86.R
Attempting to install package [ 'C:/test/test.tar.gz' ]
Attempting to install package [ 'C:/test/test.tar.gz' ]
Package [ 'C:/test/test.tar.gz' ] installed
Deleted 'project/folder2'
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Renaming .csv column name `folder` to `source_folder`: please update your .csv file to silence this message.
Renaming .csv column name `table` to `source_table`: please update your .csv file to silence this message.
'target_folder' not specified in .csv file: defaulting to source folder name
'target_table' not specified in .csv file: defaulting to source table name
'target_folder' not specified in .csv file: defaulting to source folder name
'target_table' not specified in .csv file: defaulting to source table name
Argument `new project` has now been deprecated: please use `target_project` instead
x View 'target_folder/target_table' failed with status '409': 'Project 'link-test222' already has an object 'core-variables/nonrep.alf'
v View 'target_folder/target_table' successfully created
Renaming .csv column name `folder` to `source_folder`: please update your .csv file to silence this message.
Renaming .csv column name `table` to `source_table`: please update your .csv file to silence this message.
'target_folder' not specified in .csv file: defaulting to source folder name
'target_table' not specified in .csv file: defaulting to source table name
[1] "project/folder1/obj1" "project/folder1/obj2" "project/folder2/obj3"
[4] "project/folder2/obj4"
[1] "project/folder1/obj1" "project/folder1/obj2" "project/folder2/obj3"
[4] "project/folder2/obj4"
Saving _problems/test-utils-17.R
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 237 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-object.R:30:3'): .upload_object handles errors ─────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `with_mock()` was deprecated in testthat 3.2.0 and is now defunct.
i Please use `with_mocked_bindings()` instead.
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-object.R:30:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─testthat::with_mock(...)
8. └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
── Error ('test-object.R:70:3'): .upload_object uploads object ─────────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `with_mock()` was deprecated in testthat 3.2.0 and is now defunct.
i Please use `with_mocked_bindings()` instead.
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-object.R:70:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─testthat::with_mock(...)
8. └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
9. └─lifecycle:::deprecate_stop0(msg)
10. └─rlang::cnd_signal(...)
── Error ('test-object.R:310:3'): .load_object loads the object from file ──────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `with_mock()` was deprecated in testthat 3.2.0 and is now defunct.
i Please use `with_mocked_bindings()` instead.
Backtrace:
▆
1. ├─testthat::expect_silent(...) at test-object.R:310:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. └─testthat::with_mock(...)
10. └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
11. └─lifecycle:::deprecate_stop0(msg)
12. └─rlang::cnd_signal(...)
── Error ('test-utils.R:11:3'): .handle_request_error handles 500 ──────────────
<lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
Error: `with_mock()` was deprecated in testthat 3.2.0 and is now defunct.
i Please use `with_mocked_bindings()` instead.
Backtrace:
▆
1. └─testthat::with_mock(...) at test-utils.R:11:3
2. └─lifecycle::deprecate_stop("3.2.0", "with_mock()", "with_mocked_bindings()")
3. └─lifecycle:::deprecate_stop0(msg)
4. └─rlang::cnd_signal(...)
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 237 ]
Error:
! Test failures.
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [10s/25s] OK
- checking PDF version of manual ... [10s/32s] OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR