Last updated on 2025-03-01 06:51:02 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.4.0 | 6.98 | 704.96 | 711.94 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.4.0 | 4.12 | 483.64 | 487.76 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.4.0 | 1158.22 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.4.0 | 1206.51 | ERROR | |||
| r-devel-macos-arm64 | 0.4.0 | 268.00 | OK | |||
| r-devel-macos-x86_64 | 0.4.0 | 488.00 | NOTE | |||
| r-devel-windows-x86_64 | 0.4.0 | 8.00 | 460.00 | 468.00 | NOTE | |
| r-patched-linux-x86_64 | 0.4.0 | 7.42 | 366.35 | 373.77 | ERROR | |
| r-release-linux-x86_64 | 0.4.0 | 6.31 | 365.25 | 371.56 | ERROR | |
| r-release-macos-arm64 | 0.4.0 | 219.00 | NOTE | |||
| r-release-macos-x86_64 | 0.4.0 | 324.00 | NOTE | |||
| r-release-windows-x86_64 | 0.4.0 | 9.00 | 270.00 | 279.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.4.0 | NOTE | ||||
| r-oldrel-macos-x86_64 | 0.4.0 | 377.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.4.0 | 11.00 | 607.00 | 618.00 | ERROR |
Version: 0.4.0
Check: DESCRIPTION meta-information
Result: NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘benchmarkCohortCharacteristics.R’ ‘checks.R’ ‘plot.R’
‘plotCharacteristics.Rd’ ‘plotCohortAttrition.R’
‘plotCohortAttrition.Rd’ ‘plotCohortCount.Rd’ ‘plotCohortTiming.R’
‘plotComparedLargeScaleCharacteristics.R’
‘plotLargeScaleCharacteristics.R’ ‘summariseCharacteristics.R’
‘summariseCharacteristics.Rd’ ‘summariseCohortAttrition.R’
‘summariseCohortAttrition.Rd’ ‘summariseCohortCount.R’
‘summariseCohortCount.Rd’ ‘summariseCohortOverlap.R’
‘summariseCohortOverlap.Rd’ ‘summariseCohortTiming.R’
‘summariseCohortTiming.Rd’ ‘summariseLargeScaleCharacteristics.R’
‘table.R’ ‘tableCharacteristics.R’ ‘tableCohortAttrition.R’
‘tableCohortCount.R’ ‘tableCohortOverlap.R’ ‘tableCohortTiming.R’
‘tableLargeScaleCharacteristics.R’ ‘utilities.R’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [454s/271s]
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(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 2 | WARN 4 | SKIP 17 | PASS 208 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-benchmarkCohortCharacteristics.R:2:3',
'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:136:3',
'test-plotCohortOverlap.R:2:3', 'test-plotCohortTiming.R:2:3',
'test-plotCohortTiming.R:94:3', 'test-plotLargeScaleCharacteristics.R:3:3',
'test-summariseCohortCount.R:2:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:120:3',
'test-tableCohortOverlap.R:2:3', 'test-tableCohortTiming.R:2:3',
'test-tableLargeScaleCharacteristics.R:2:3',
'test-summariseCharacteristics.R:1159:3',
'test-summariseCharacteristics.R:1389:3',
'test-summariseCharacteristics.R:1505:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-summariseCharacteristics.R:337:3'): test summariseCharacteristics ──
Expected `... <- NULL` to run without any errors.
i Actually got a <rlang_error> with text:
Failed to collect lazy table.
Caused by error in `dbSendQuery()`:
! rapi_prepare: Failed to prepare query SELECT
strata_id,
SUM(variable_00047 * ".data".id_hmd) AS counts_variable_00047,
SUM(variable_00048 * ".data".id_hmd) AS counts_variable_00048,
SUM(variable_00049 * ".data".id_hmd) AS counts_variable_00049
FROM (
SELECT q01.*, 1.0 AS id_hmd
FROM (
SELECT strata_id, subject_id, variable_00047, variable_00048, variable_00049
FROM og_066_1740668225
LEFT JOIN test_dus_cohort_set
ON (og_066_1740668225.cohort_definition_id = test_dus_cohort_set.cohort_definition_id)
INNER JOIN og_076_1740668230
ON (test_dus_cohort_set.cohort_name = og_076_1740668230.cohort_name)
) q01
) q01
GROUP BY strata_id
Error: Binder Error: Referenced table ".data" not found!
Candidate tables: "q01"
LINE 3: SUM(variable_00047 * ".data".id_hmd) AS counts_variable_00047,
^
── Failure ('test-summariseCharacteristics.R:346:3'): test summariseCharacteristics ──
any(...) is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 2 | WARN 4 | SKIP 17 | PASS 208 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [302s/177s]
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(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 2 | WARN 4 | SKIP 17 | PASS 208 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-benchmarkCohortCharacteristics.R:2:3',
'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:136:3',
'test-plotCohortOverlap.R:2:3', 'test-plotCohortTiming.R:2:3',
'test-plotCohortTiming.R:94:3', 'test-plotLargeScaleCharacteristics.R:3:3',
'test-summariseCohortCount.R:2:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:120:3',
'test-tableCohortOverlap.R:2:3', 'test-tableCohortTiming.R:2:3',
'test-tableLargeScaleCharacteristics.R:2:3',
'test-summariseCharacteristics.R:1159:3',
'test-summariseCharacteristics.R:1389:3',
'test-summariseCharacteristics.R:1505:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-summariseCharacteristics.R:337:3'): test summariseCharacteristics ──
Expected `... <- NULL` to run without any errors.
i Actually got a <rlang_error> with text:
Failed to collect lazy table.
Caused by error in `dbSendQuery()`:
! rapi_prepare: Failed to prepare query SELECT
strata_id,
SUM(variable_00047 * ".data".id_mwb) AS counts_variable_00047,
SUM(variable_00048 * ".data".id_mwb) AS counts_variable_00048,
SUM(variable_00049 * ".data".id_mwb) AS counts_variable_00049
FROM (
SELECT q01.*, 1.0 AS id_mwb
FROM (
SELECT strata_id, subject_id, variable_00047, variable_00048, variable_00049
FROM og_066_1740743641
LEFT JOIN test_dus_cohort_set
ON (og_066_1740743641.cohort_definition_id = test_dus_cohort_set.cohort_definition_id)
INNER JOIN og_076_1740743644
ON (test_dus_cohort_set.cohort_name = og_076_1740743644.cohort_name)
) q01
) q01
GROUP BY strata_id
Error: Binder Error: Referenced table ".data" not found!
Candidate tables: "q01"
LINE 3: SUM(variable_00047 * ".data".id_mwb) AS counts_variable_00047,
^
── Failure ('test-summariseCharacteristics.R:346:3'): test summariseCharacteristics ──
any(...) is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 2 | WARN 4 | SKIP 17 | PASS 208 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [13m/10m]
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(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 2 | WARN 4 | SKIP 17 | PASS 208 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-benchmarkCohortCharacteristics.R:2:3',
'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:136:3',
'test-plotCohortOverlap.R:2:3', 'test-plotCohortTiming.R:2:3',
'test-plotCohortTiming.R:94:3', 'test-plotLargeScaleCharacteristics.R:3:3',
'test-summariseCohortCount.R:2:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:120:3',
'test-tableCohortOverlap.R:2:3', 'test-tableCohortTiming.R:2:3',
'test-tableLargeScaleCharacteristics.R:2:3',
'test-summariseCharacteristics.R:1159:3',
'test-summariseCharacteristics.R:1389:3',
'test-summariseCharacteristics.R:1505:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-summariseCharacteristics.R:337:3'): test summariseCharacteristics ──
Expected `... <- NULL` to run without any errors.
i Actually got a <rlang_error> with text:
Failed to collect lazy table.
Caused by error in `dbSendQuery()`:
! rapi_prepare: Failed to prepare query SELECT
strata_id,
SUM(variable_00047 * ".data".id_xgv) AS counts_variable_00047,
SUM(variable_00048 * ".data".id_xgv) AS counts_variable_00048,
SUM(variable_00049 * ".data".id_xgv) AS counts_variable_00049
FROM (
SELECT q01.*, 1.0 AS id_xgv
FROM (
SELECT strata_id, subject_id, variable_00047, variable_00048, variable_00049
FROM og_066_1740783373
LEFT JOIN test_dus_cohort_set
ON (og_066_1740783373.cohort_definition_id = test_dus_cohort_set.cohort_definition_id)
INNER JOIN og_076_1740783383
ON (test_dus_cohort_set.cohort_name = og_076_1740783383.cohort_name)
) q01
) q01
GROUP BY strata_id
Error: Binder Error: Referenced table ".data" not found!
Candidate tables: "q01"
LINE 3: SUM(variable_00047 * ".data".id_xgv) AS counts_variable_00047,
^
── Failure ('test-summariseCharacteristics.R:346:3'): test summariseCharacteristics ──
any(...) is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 2 | WARN 4 | SKIP 17 | PASS 208 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [13m/20m]
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(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 2 | WARN 4 | SKIP 17 | PASS 208 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-benchmarkCohortCharacteristics.R:2:3',
'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:136:3',
'test-plotCohortOverlap.R:2:3', 'test-plotCohortTiming.R:2:3',
'test-plotCohortTiming.R:94:3', 'test-plotLargeScaleCharacteristics.R:3:3',
'test-summariseCohortCount.R:2:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:120:3',
'test-tableCohortOverlap.R:2:3', 'test-tableCohortTiming.R:2:3',
'test-tableLargeScaleCharacteristics.R:2:3',
'test-summariseCharacteristics.R:1159:3',
'test-summariseCharacteristics.R:1389:3',
'test-summariseCharacteristics.R:1505:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-summariseCharacteristics.R:337:3'): test summariseCharacteristics ──
Expected `... <- NULL` to run without any errors.
i Actually got a <rlang_error> with text:
Failed to collect lazy table.
Caused by error in `dbSendQuery()`:
! rapi_prepare: Failed to prepare query SELECT
strata_id,
SUM(variable_00047 * ".data".id_cbx) AS counts_variable_00047,
SUM(variable_00048 * ".data".id_cbx) AS counts_variable_00048,
SUM(variable_00049 * ".data".id_cbx) AS counts_variable_00049
FROM (
SELECT q01.*, 1.0 AS id_cbx
FROM (
SELECT strata_id, subject_id, variable_00047, variable_00048, variable_00049
FROM og_066_1740776562
LEFT JOIN test_dus_cohort_set
ON (og_066_1740776562.cohort_definition_id = test_dus_cohort_set.cohort_definition_id)
INNER JOIN og_076_1740776586
ON (test_dus_cohort_set.cohort_name = og_076_1740776586.cohort_name)
) q01
) q01
GROUP BY strata_id
Error: Binder Error: Referenced table ".data" not found!
Candidate tables: "q01"
LINE 3: SUM(variable_00047 * ".data".id_cbx) AS counts_variable_00047,
^
── Failure ('test-summariseCharacteristics.R:346:3'): test summariseCharacteristics ──
any(...) is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 2 | WARN 4 | SKIP 17 | PASS 208 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.4.0
Check: DESCRIPTION meta-information
Result: NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘benchmarkCohortCharacteristics.R’ ‘checks.R’ ‘plot.R’
‘plotCohortAttrition.R’ ‘plotCohortTiming.R’
‘plotComparedLargeScaleCharacteristics.R’
‘plotLargeScaleCharacteristics.R’ ‘summariseCharacteristics.R’
‘summariseCohortAttrition.R’ ‘summariseCohortCount.R’
‘summariseCohortOverlap.R’ ‘summariseCohortTiming.R’
‘summariseLargeScaleCharacteristics.R’ ‘table.R’
‘tableCharacteristics.R’ ‘tableCohortAttrition.R’
‘tableCohortCount.R’ ‘tableCohortOverlap.R’ ‘tableCohortTiming.R’
‘tableLargeScaleCharacteristics.R’ ‘utilities.R’
Flavors: r-devel-macos-x86_64, r-devel-windows-x86_64
Version: 0.4.0
Check: dependencies in R code
Result: WARN
Missing or unexported object: ‘CDMConnector::cdm_from_con’
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-x86_64
Version: 0.4.0
Check: examples
Result: ERROR
Running examples in ‘CohortCharacteristics-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: availablePlotColumns
> ### Title: Available columns to use in 'facet' and 'colour' arguments in
> ### plot functions.
> ### Aliases: availablePlotColumns
>
> ### ** Examples
>
> {
+ cdm <- mockCohortCharacteristics()
+
+ result <- summariseCharacteristics(cdm$cohort1)
+
+ availablePlotColumns(result)
+
+ mockDisconnect(cdm)
+ }
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [139s/83s]
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(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 12 | WARN 4 | SKIP 17 | PASS 16 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-benchmarkCohortCharacteristics.R:2:3',
'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:136:3',
'test-plotCohortOverlap.R:2:3', 'test-plotCohortTiming.R:2:3',
'test-plotCohortTiming.R:94:3', 'test-summariseCharacteristics.R:1159:3',
'test-summariseCharacteristics.R:1389:3',
'test-summariseCharacteristics.R:1505:3', 'test-summariseCohortCount.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:120:3',
'test-tableCohortOverlap.R:2:3', 'test-tableCohortTiming.R:2:3',
'test-tableLargeScaleCharacteristics.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plotCohortAttrition.R:2:3'): plot cohort attrition ─────────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(numberIndividuals = 1000) at test-plotCohortAttrition.R:2:3
── Error ('test-summariseCharacteristics.R:55:3'): test summariseCharacteristics ──
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:55:3
── Error ('test-summariseCharacteristics.R:407:3'): test empty cohort ──────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:407:3
── Error ('test-summariseCharacteristics.R:517:3'): test cohort id ─────────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:517:3
── Error ('test-summariseCharacteristics.R:654:3'): arguments tableIntersect ───
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:654:3
── Error ('test-summariseCharacteristics.R:987:3'): arguments cohortIntersect ──
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:987:3
── Error ('test-summariseCharacteristics.R:1360:3'): empty input cohort contains name issue #170 ──
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:1360:3
── Error ('test-summariseCharacteristics.R:1452:3'): arrange ageGroup ──────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:1452:3
── Error ('test-summariseCohortAttrition.R:2:3'): check summariseCohortAttrition is deterministic ──
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(numberIndividuals = 1000) at test-summariseCohortAttrition.R:2:3
── Error ('test-summariseCohortOverlap.R:41:3'): summariseCohortOverlap ────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortOverlap.R:41:3
── Error ('test-summariseCohortOverlap.R:246:3'): test countBy ─────────────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortOverlap.R:246:3
── Error ('test-summariseCohortTiming.R:35:3'): summariseCohortTiming ──────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortTiming.R:35:3
[ FAIL 12 | WARN 4 | SKIP 17 | PASS 16 ]
Error: Test failures
Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.4.0
Check: installed package size
Result: NOTE
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 3.5Mb
help 1.9Mb
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.4.0
Check: examples
Result: ERROR
Running examples in 'CohortCharacteristics-Ex.R' failed
The error most likely occurred in:
> ### Name: availablePlotColumns
> ### Title: Available columns to use in 'facet' and 'colour' arguments in
> ### plot functions.
> ### Aliases: availablePlotColumns
>
> ### ** Examples
>
> {
+ cdm <- mockCohortCharacteristics()
+
+ result <- summariseCharacteristics(cdm$cohort1)
+
+ availablePlotColumns(result)
+
+ mockDisconnect(cdm)
+ }
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [66s]
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(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 12 | WARN 4 | SKIP 17 | PASS 16 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-benchmarkCohortCharacteristics.R:2:3',
'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:136:3',
'test-plotCohortOverlap.R:2:3', 'test-plotCohortTiming.R:2:3',
'test-plotCohortTiming.R:94:3', 'test-summariseCharacteristics.R:1159:3',
'test-summariseCharacteristics.R:1389:3',
'test-summariseCharacteristics.R:1505:3', 'test-summariseCohortCount.R:2:3',
'test-plotLargeScaleCharacteristics.R:3:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:120:3',
'test-tableCohortOverlap.R:2:3', 'test-tableCohortTiming.R:2:3',
'test-tableLargeScaleCharacteristics.R:2:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-plotCohortAttrition.R:2:3'): plot cohort attrition ─────────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(numberIndividuals = 1000) at test-plotCohortAttrition.R:2:3
── Error ('test-summariseCharacteristics.R:55:3'): test summariseCharacteristics ──
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:55:3
── Error ('test-summariseCharacteristics.R:407:3'): test empty cohort ──────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:407:3
── Error ('test-summariseCharacteristics.R:517:3'): test cohort id ─────────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:517:3
── Error ('test-summariseCharacteristics.R:654:3'): arguments tableIntersect ───
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:654:3
── Error ('test-summariseCharacteristics.R:987:3'): arguments cohortIntersect ──
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:987:3
── Error ('test-summariseCharacteristics.R:1360:3'): empty input cohort contains name issue #170 ──
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:1360:3
── Error ('test-summariseCharacteristics.R:1452:3'): arrange ageGroup ──────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCharacteristics.R:1452:3
── Error ('test-summariseCohortAttrition.R:2:3'): check summariseCohortAttrition is deterministic ──
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(numberIndividuals = 1000) at test-summariseCohortAttrition.R:2:3
── Error ('test-summariseCohortOverlap.R:41:3'): summariseCohortOverlap ────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortOverlap.R:41:3
── Error ('test-summariseCohortOverlap.R:246:3'): test countBy ─────────────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortOverlap.R:246:3
── Error ('test-summariseCohortTiming.R:35:3'): summariseCohortTiming ──────────
Error: 'cdm_from_con' is not an exported object from 'namespace:CDMConnector'
Backtrace:
▆
1. └─PatientProfiles (local) mockCohortCharacteristics(...) at test-summariseCohortTiming.R:35:3
[ FAIL 12 | WARN 4 | SKIP 17 | PASS 16 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [312s]
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(CohortCharacteristics)
>
> test_check("CohortCharacteristics")
Starting 2 test processes
[ FAIL 2 | WARN 4 | SKIP 17 | PASS 208 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (17): 'test-benchmarkCohortCharacteristics.R:2:3',
'test-plotCharacteristics.R:2:3', 'test-plotCharacteristics.R:136:3',
'test-plotCohortOverlap.R:2:3', 'test-plotCohortTiming.R:2:3',
'test-plotCohortTiming.R:94:3', 'test-plotLargeScaleCharacteristics.R:3:3',
'test-summariseCohortCount.R:2:3',
'test-summariseLargeScaleCharacteristics.R:2:3',
'test-tableCharacteristics.R:2:3', 'test-tableCharacteristics.R:120:3',
'test-tableCohortOverlap.R:2:3', 'test-tableCohortTiming.R:2:3',
'test-tableLargeScaleCharacteristics.R:2:3',
'test-summariseCharacteristics.R:1159:3',
'test-summariseCharacteristics.R:1389:3',
'test-summariseCharacteristics.R:1505:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-summariseCharacteristics.R:337:3'): test summariseCharacteristics ──
Expected `... <- NULL` to run without any errors.
i Actually got a <rlang_error> with text:
Failed to collect lazy table.
Caused by error in `dbSendQuery()`:
! rapi_prepare: Failed to prepare query SELECT
strata_id,
SUM(variable_00047 * ".data".id_laj) AS counts_variable_00047,
SUM(variable_00048 * ".data".id_laj) AS counts_variable_00048,
SUM(variable_00049 * ".data".id_laj) AS counts_variable_00049
FROM (
SELECT q01.*, 1.0 AS id_laj
FROM (
SELECT strata_id, subject_id, variable_00047, variable_00048, variable_00049
FROM og_066_1740721255
LEFT JOIN test_dus_cohort_set
ON (og_066_1740721255.cohort_definition_id = test_dus_cohort_set.cohort_definition_id)
INNER JOIN og_076_1740721261
ON (test_dus_cohort_set.cohort_name = og_076_1740721261.cohort_name)
) q01
) q01
GROUP BY strata_id
Error: Binder Error: Referenced table ".data" not found!
Candidate tables: "q01"
LINE 3: SUM(variable_00047 * ".data".id_laj) AS counts_variable_00047,
^
── Failure ('test-summariseCharacteristics.R:346:3'): test summariseCharacteristics ──
any(...) is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 2 | WARN 4 | SKIP 17 | PASS 208 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64