Last updated on 2026-09-03 20:57:14 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-gcc | 0.6.1 | 5.28 | 232.27 | 237.55 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.6.1 | 6.00 | 41.04 | 47.04 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.6.1 | 216.30 | OK | |||
| r-devel-windows-x86_64 | 0.6.1 | 10.00 | 274.00 | 284.00 | OK | |
| r-patched-linux-x86_64 | 0.6.1 | 7.78 | 311.20 | 318.98 | OK | |
| r-release-macos-arm64 | 0.6.1 | 2.00 | 62.00 | 64.00 | OK | |
| r-release-macos-x86_64 | 0.6.1 | 5.00 | 295.00 | 300.00 | OK | |
| r-release-windows-x86_64 | 0.6.1 | 9.00 | 268.00 | 277.00 | OK | |
| r-oldrel-macos-arm64 | 0.6.1 | 2.00 | 68.00 | 70.00 | OK | |
| r-oldrel-macos-x86_64 | 0.6.1 | 5.00 | 276.00 | 281.00 | OK | |
| r-oldrel-windows-x86_64 | 0.6.1 | 12.00 | 372.00 | 384.00 | OK |
Version: 0.6.1
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(CohortUtilisation)
>
> test_check("CohortUtilisation")
Attaching package: 'omopgenerics'
The following object is masked from 'package:stats':
filter
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
Attaching package: 'dbplyr'
The following objects are masked from 'package:dplyr':
ident, sql, sql_escape_ident, sql_escape_string
Saving _problems/test-add-emergency-2.R
Saving _problems/test-add-emergency-12.R
Saving _problems/test-add-emergency-43.R
Saving _problems/test-add-emergency-73.R
Saving _problems/test-add-emergency-92.R
Saving _problems/test-add-inpatients-2.R
Saving _problems/test-add-inpatients-13.R
Saving _problems/test-add-inpatients-43.R
Saving _problems/test-add-inpatients-66.R
Saving _problems/test-add-inpatients-100.R
Saving _problems/test-add-inpatients-119.R
Saving _problems/test-add-outpatient-2.R
Saving _problems/test-add-outpatient-12.R
Saving _problems/test-add-outpatient-39.R
Saving _problems/test-add-outpatient-72.R
Saving _problems/test-add-prescriptions-2.R
Saving _problems/test-add-prescriptions-31.R
Saving _problems/test-add-procedures-2.R
Saving _problems/test-add-procedures-27.R
Saving _problems/test-add-visits-2.R
Saving _problems/test-add-visits-13.R
Saving _problems/test-add-visits-58.R
Saving _problems/test-add-visits-76.R
Saving _problems/test-add-visits-108.R
Saving _problems/test-compute-episodes-2.R
Saving _problems/test-compute-episodes-28.R
Saving _problems/test-hospitalizations-2.R
Saving _problems/test-summarise-utilization-2.R
Saving _problems/test-summarise-utilization-30.R
[ FAIL 29 | WARN 0 | SKIP 0 | PASS 0 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-add-emergency.R:2:3'): addEmergencyCare validates input arguments correctly ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-emergency.R:2:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x)
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-emergency.R:12:3'): addEmergencyCare detects emergency encounters via visit concept IDs and provider specialties ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-emergency.R:12:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-emergency.R:43:3'): addEmergencyCare stratifies by granular specialty ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-emergency.R:43:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-emergency.R:73:3'): addEmergency and addEmergencyVisits aliases work identically ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-emergency.R:73:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-emergency.R:92:3'): addEmergencyCare supports infinite and NA windows ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-emergency.R:92:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-inpatients.R:2:3'): addInpatients validates input arguments correctly ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-inpatients.R:2:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-inpatients.R:13:3'): addInpatients computes admissions, LOS, ICU stays, and readmissions ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-inpatients.R:13:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-inpatients.R:43:3'): addInpatients detects ICU stays via provider icuSpecialtyConceptIds ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-inpatients.R:43:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-inpatients.R:66:3'): addInpatients computes granular specialty breakdowns ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-inpatients.R:66:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-inpatients.R:100:3'): addHospitalizations and addInpatient backward-compatibility aliases work identically ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-inpatients.R:100:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-inpatients.R:119:3'): addInpatients supports infinite and NA window bounds without case mismatch ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-inpatients.R:119:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-outpatient.R:2:3'): addOutpatientVisits validates input arguments ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermes_test_cdm() at test-add-outpatient.R:2:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-outpatient.R:12:3'): addOutpatientVisits stratifies GP, Specialist, and Emergency visits ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermes_test_cdm() at test-add-outpatient.R:12:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-outpatient.R:39:3'): addOutpatientVisits computes granular specialty breakdowns ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermes_test_cdm() at test-add-outpatient.R:39:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-outpatient.R:72:3'): addOutpatientVisits supports infinite and NA window bounds ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-outpatient.R:72:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-prescriptions.R:2:3'): addPrescriptions extracts fills, days supply, PDC, and infusions ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermes_test_cdm() at test-add-prescriptions.R:2:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-prescriptions.R:31:3'): addPrescriptions supports infinite and NA window bounds ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-prescriptions.R:31:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-procedures.R:2:3'): addProcedures extracts labs, imaging, and procedure occurrences ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermes_test_cdm() at test-add-procedures.R:2:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-procedures.R:27:3'): addProcedures supports infinite and NA window bounds ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-procedures.R:27:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-visits.R:2:3'): addVisits validates input arguments correctly ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-visits.R:2:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-visits.R:13:3'): addVisits executes multi-setting visit enrichment (inpatient, outpatient, emergency) ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-visits.R:13:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-visits.R:58:3'): addVisits filters by specific settings ────
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-visits.R:58:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-visits.R:76:3'): addVisits unifies granular specialty stratification across settings ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-visits.R:76:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-add-visits.R:108:3'): addVisits supports infinite and NA window bounds with censorDate ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-add-visits.R:108:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-compute-episodes.R:2:3'): computeHospitalizationCohorts collapses stays and flags readmissions ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermes_test_cdm() at test-compute-episodes.R:2:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-compute-episodes.R:28:3'): computeInfusionCohorts creates infusion episodes ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermes_test_cdm() at test-compute-episodes.R:28:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-hospitalizations.R:2:3'): compute_hospitalization_cohorts collapses overlaps, contiguous visits, and finds readmissions ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─DBI::dbConnect(duckdb::duckdb(), ":memory:") at test-hospitalizations.R:2:3
2. ├─base::loadNamespace(x)
3. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
4. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
5. │ │ └─base (local) doWithOneRestart(return(expr), restart)
6. │ └─base::stop(cond)
7. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-summarise-utilization.R:2:3'): summariseUtilization returns a valid summarised_result object ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-summarise-utilization.R:2:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
── Error ('test-summarise-utilization.R:30:3'): tableUtilization and plotUtilization format and plot results ──
Error in `(function (cond) .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "there is no package called 'duckdb'", call = loadNamespace(x), package = "duckdb", lib.loc = NULL), class = c("packageNotFoundError", "error", "condition")))`: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': there is no package called 'duckdb'
Backtrace:
▆
1. ├─CohortUtilisation:::hermesTestCdm() at test-summarise-utilization.R:30:3
2. │ └─DBI::dbConnect(duckdb::duckdb(), ":memory:") at ./helper-eunomia.R:8:3
3. ├─base::loadNamespace(x) at ./helper-eunomia.R:8:3
4. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
5. │ │ └─base (local) withOneRestart(expr, restarts[[1L]])
6. │ │ └─base (local) doWithOneRestart(return(expr), restart)
7. │ └─base::stop(cond)
8. └─base (local) `<fn>`(`<pckgNtFE>`)
[ FAIL 29 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang