- using R version 4.4.1 (2024-06-14)
- using platform: x86_64-apple-darwin20
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.3.1
- using session charset: UTF-8
- checking for file ‘DSMolgenisArmadillo/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘DSMolgenisArmadillo’ version ‘3.0.0’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... NOTE
Package suggested but not available for checking: ‘dsBaseClient’
- 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 ‘DSMolgenisArmadillo’ can be installed ... [4s/5s] 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 ... [1s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the package can be unloaded cleanly ... [1s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
- checking loading without being on the library search path ... [1s/1s] 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/0s] OK
- checking Rd metadata ... 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 ... [1s/1s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [40s/56s] ERROR
Running ‘testthat.R’ [40s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(DSMolgenisArmadillo)
Loading required package: DSI
Loading required package: progress
Loading required package: R6
Loading required package: MolgenisAuth
> library(tibble)
>
> test_check("DSMolgenisArmadillo")
An object of class "ArmadilloCredentials"
Slot "access_token":
[1] "access456"
Slot "expires_in":
[1] 300
Slot "expires_at":
[1] "2025-08-09 19:35:01 EDT"
Slot "id_token":
[1] "id123"
Slot "refresh_token":
[1] "refresh123"
Slot "token_type":
[1] "Bearer"
Slot "auth_type":
[1] "keycloak"
[ FAIL 2 | WARN 2 | SKIP 1 | PASS 396 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• I still don't get the .deparse arguments (1): 'test-utils.R:91:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-ArmadilloOAuth.R:86:3'): .refresh_token returns success message if new credentials are not null and option fusionauth ──
DSMolgenisArmadillo:::.refresh_token(server, credentials_in) not equal to `credentials_out`.
Attributes: < Component "expires_in": Mean relative difference: 0.31444 >
── Failure ('test-ArmadilloOAuth.R:143:3'): .refresh_token returns success message if new credentials are not null and option keycloak ──
DSMolgenisArmadillo:::.refresh_token(server, credentials_in) not equal to `credentials_out`.
Attributes: < Component "expires_at": Mean absolute difference: 1.007468 >
[ FAIL 2 | WARN 2 | SKIP 1 | PASS 396 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [14s/19s] OK
- checking PDF version of manual ... [6s/7s] OK
- DONE
Status: 1 ERROR, 1 NOTE
- using check arguments '--no-clean-on-error '