Last updated on 2024-09-26 21:49:24 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 3.1.0 | 6.82 | 477.47 | 484.29 | OK | |
| r-devel-linux-x86_64-debian-gcc | 3.2.0 | 4.92 | 251.97 | 256.89 | OK | |
| r-devel-linux-x86_64-fedora-clang | 3.2.0 | 581.49 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 3.2.0 | 579.40 | OK | |||
| r-devel-windows-x86_64 | 3.2.0 | 10.00 | 223.00 | 233.00 | OK | |
| r-patched-linux-x86_64 | 3.1.0 | 7.04 | 446.86 | 453.90 | ERROR | |
| r-release-linux-x86_64 | 3.2.0 | 6.32 | 342.34 | 348.66 | OK | |
| r-release-macos-arm64 | 3.2.0 | 88.00 | OK | |||
| r-release-macos-x86_64 | 3.2.0 | 127.00 | OK | |||
| r-release-windows-x86_64 | 3.2.0 | 8.00 | 229.00 | 237.00 | OK | |
| r-oldrel-macos-arm64 | 3.2.0 | 118.00 | OK | |||
| r-oldrel-macos-x86_64 | 3.2.0 | 157.00 | OK | |||
| r-oldrel-windows-x86_64 | 3.2.0 | 10.00 | 278.00 | 288.00 | OK |
Version: 3.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [375s/212s]
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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(CodelistGenerator)
>
> test_check("CodelistGenerator")
Starting 2 test processes
[ FAIL 15 | WARN 754 | SKIP 14 | PASS 399 ]
══ Skipped tests (14) ══════════════════════════════════════════════════════════
• On CRAN (6): 'test-drugCodes.R:123:3', 'test-drugCodes.R:435:3',
'test-getICD10StandardCodes.R:84:3', 'test-getCandidateCodes.R:310:3',
'test-summariseCodeUse.R:2:1', 'test-summariseCodeUse.R:295:3'
• Sys.getenv("CDM5_POSTGRESQL_DBNAME") == "" is TRUE (1): 'test-dbms.R:292:3'
• Sys.getenv("CDM5_REDSHIFT_DBNAME") == "" is TRUE (4):
'test-codesFrom.R:131:3', 'test-dbms.R:5:3', 'test-findUnmappedCodes.R:3:3',
'test-summariseCodeUse.R:492:3'
• Sys.getenv("CDM5_SQL_SERVER_SERVER") == "" is TRUE (1):
'test-codesInUse.R:36:3'
• Sys.getenv("SNOWFLAKE_SERVER") == "" is TRUE (1): 'test-dbms.R:154:3'
• Sys.getenv("darwinDbDatabaseServer") == "" is TRUE (1):
'test-synthea_sql_server.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-tableAchillesCodeUse.R:20:3'): table achilles code use expcted columns ──
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-tableAchillesCodeUse.R:66:3'): table achilles code use expcted columns ──
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-tableAchillesCodeUse.R:80:3'): table achilles code use expcted columns ──
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-tableCodeUse.R:39:3'): table code use expcted columns ────────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-tableCodeUse.R:55:3'): table code use expcted columns ────────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-tableCodeUse.R:71:3'): table code use expcted columns ────────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-tableCodeUse.R:87:3'): table code use expcted columns ────────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-tableCodeUse.R:118:3'): table code use expcted columns ───────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-tableCodeUse.R:136:3'): table code use expcted columns ───────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-tableCodeUse.R:141:3'): table code use expcted columns ───────
levels(tab6$body$dataset$group) == "Pharyngitis; Cs" is not TRUE
`actual`: FALSE
`expected`: TRUE
── Error ('test-tableCodeUse.R:144:3'): table code use expcted columns ─────────
Error in `checkColumnsFormat(x = x, "summarised_result")`: The following colum does not have a correct format
* NA: format=character (expected=NA)
Backtrace:
▆
1. └─CodelistGenerator::tableCohortCodeUse(...) at test-tableCodeUse.R:144:3
2. └─CodelistGenerator:::internalTableCodeUse(...)
3. └─visOmopResults::visOmopTable(...)
4. └─omopgenerics::validateResultArguemnt(result)
5. └─omopgenerics::validateResultArgument(...)
6. └─omopgenerics:::validateSummariseResult(result)
7. └─omopgenerics:::checkColumnsFormat(x = x, "summarised_result")
8. └─cli::cli_abort(...)
9. └─rlang::abort(...)
── Failure ('test-tableCodeUse.R:272:3'): table code use output formats ────────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-tableCodeUse.R:273:3'): table code use output formats ────────
as.character(tab1$body$dataset$`Codelist name`[1:3]) (`actual`) not equal to c("Acetiminophen", NA, NA) (`expected`).
`actual`: "acetiminophen" NA NA
`expected`: "Acetiminophen" NA NA
── Failure ('test-tableCodeUse.R:307:3'): table code use output formats ────────
all(...) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-tableCodeUse.R:342:3'): tableCodeUse expected behaviour ──────
`tableCodeUse(...)` did not throw the expected error.
[ FAIL 15 | WARN 754 | SKIP 14 | PASS 399 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64