Last updated on 2025-05-11 07:50:51 CEST.
| Package | ERROR | OK |
|---|---|---|
| Characterization | 13 | |
| OhdsiReportGenerator | 5 | 8 |
| OhdsiShinyAppBuilder | 13 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 5, OK: 8
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [28s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> test_check("OhdsiReportGenerator")
Loading required package: OhdsiReportGenerator
Connecting using SQLite driver
<1b>[31m
processing file: assure_study_presentation_multiple.qmd
<1b>[39m<1b>[31moutput file: assure_study_presentation_multiple.knit.md
<1b>[39mClosing database connection
<1b>[1mpandoc <1b>[22m
to: revealjs
output-file: assure_study_presentation_multiple.html
standalone: true
self-contained: true
wrap: none
default-image-extension: png
html-math-method:
method: mathjax
url: >-
https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/MathJax.js?config=TeX-AMS_HTML-full
slide-level: 2
variables: {}
<1b>[1mmetadata<1b>[22m
link-citations: true
width: 1050
height: 700
margin: 0.1
center: false
navigationMode: linear
controlsLayout: edges
controlsTutorial: false
hash: true
history: true
hashOneBasedIndex: false
fragmentInURL: false
transition: none
backgroundTransition: none
pdfSeparateFragments: false
lang: en
auto-stretch: true
title: Signal Evaluation Report
scrollable: true
theme:
- default
- presentation_style.scss
logo: img/logo.png
title-slide-attributes:
data-background-color: '#EB1700'
footer: ASSURE Standardized report
slideNumber: true
showSlideNumber: all
menu:
side: left
numbers: true
Error running filter /opt/quarto/share/filters/main.lua:
/opt/quarto/share/filters/main.lua:21750: attempt to index a nil value (field 'tabs')
stack traceback:
/opt/quarto/share/filters/main.lua:935: in function </opt/quarto/share/filters/main.lua:934>
(...tail calls...)
/opt/quarto/share/filters/main.lua:1152: in function </opt/quarto/share/filters/main.lua:1147>
(...tail calls...)
/opt/quarto/share/filters/main.lua:2943: in function </opt/quarto/share/filters/main.lua:2937>
(...tail calls...)
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:34: in upvalue 'run_filter_function'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:223: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202>
(...tail calls...)
[C]: in function 'pandoc.List.map'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:125: in upvalue 'recurse'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in local 'jogger'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:98: in upvalue 'recurse'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202>
(...tail calls...)
... (skipping 2 levels)
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:98: in upvalue 'recurse'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202>
(...tail calls...)
[C]: in function 'pandoc.List.map'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:125: in upvalue 'recurse'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in local 'jogger'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:171: in upvalue 'recurse'
...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:222: in function <...uarto/share/pandoc/datadir/../../filters/modules/jog.lua:202>
(...tail calls...)
/opt/quarto/share/filters/main.lua:572: in function </opt/quarto/share/filters/main.lua:550>
(...tail calls...)
/opt/quarto/share/filters/main.lua:1318: in local 'callback'
/opt/quarto/share/filters/main.lua:1336: in upvalue 'run_emulated_filter_chain'
/opt/quarto/share/filters/main.lua:1372: in function </opt/quarto/share/filters/main.lua:1369>
[ FAIL 1 | WARN 1 | SKIP 2 | PASS 385 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-Helpers.R:89:1'
• skip prediction report due to odd linux error (1):
'test-PredictionReport.R:5:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Generate.R:10:3'): generatePresentationMultiple ────────────────
Error in `quarto::quarto_render(input = file.path(intermediateDir, "presentation",
"assure_study_presentation_multiple.qmd"), execute_params = list(server = server,
username = username, password = password, dbms = dbms, resultsSchema = resultsSchema,
targetId = targetId, targetName = targetName, cmSubsetId = cmSubsetId,
sccsSubsetId = sccsSubsetId, indicationName = indicationName,
outcomeIds = outcomeIds, outcomeNames = outcomeNames, comparatorIds = comparatorIds,
comparatorNames = comparatorNames, covariateIds = covariateIds,
title = title, lead = lead, date = date, details = details,
evaluationText = evaluationText))`: ✖ Error running quarto cli.
Caused by error:
! System command 'quarto' failed
Backtrace:
▆
1. └─OhdsiReportGenerator::generatePresentationMultiple(...) at test-Generate.R:10:3
2. └─quarto::quarto_render(...)
3. └─quarto:::quarto_run(args, echo = TRUE, quarto_bin = quarto_bin)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─value[[3L]](cond)
8. └─cli::cli_abort(msg, call = .call, parent = e)
9. └─rlang::abort(...)
[ FAIL 1 | WARN 1 | SKIP 2 | PASS 385 ]
Error: Test failures
Execution halted
Closing database connection
Flavor: r-release-linux-x86_64
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> test_check("OhdsiReportGenerator")
Loading required package: OhdsiReportGenerator
Connecting using SQLite driver
[ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-Helpers.R:89:1'
• skip prediction report due to odd linux error (1):
'test-PredictionReport.R:5:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Backwards.R:11:3'): generatePresentationMultiple old works ─────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-Backwards.R:11:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─OhdsiReportGenerator::generatePresentationMultiple(...)
7. └─OhdsiReportGenerator::generatePresentation(...)
8. └─quarto::quarto_render(...)
9. └─quarto:::find_quarto()
10. └─cli::cli_abort(quarto_not_found_msg)
11. └─rlang::abort(...)
── Error ('test-Generate.R:10:3'): generatePresentation ────────────────────────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. └─OhdsiReportGenerator::generatePresentation(...) at test-Generate.R:10:3
2. └─quarto::quarto_render(...)
3. └─quarto:::find_quarto()
4. └─cli::cli_abort(quarto_not_found_msg)
5. └─rlang::abort(...)
── Error ('test-Generate.R:61:3'): generateFullReport ──────────────────────────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. └─OhdsiReportGenerator::generateFullReport(...) at test-Generate.R:61:3
2. └─quarto::quarto_render(...)
3. └─quarto:::find_quarto()
4. └─cli::cli_abort(quarto_not_found_msg)
5. └─rlang::abort(...)
[ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ]
Error: Test failures
Execution halted
Closing database connection
Flavor: r-release-macos-arm64
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘OhdsiReportGenerator-Ex.R’ failed
The error most likely occurred in:
> ### Name: getBinaryCaseSeries
> ### Title: A function to extract case series characterization results
> ### Aliases: getBinaryCaseSeries
>
> ### ** Examples
>
> conDet <- getExampleConnectionDetails()
Warning in utils::unzip(zipfile = system.file("exampledata", "results.sqlite.zip", :
write error in extracting from zip file
>
> connectionHandler <- ResultModelManager::ConnectionHandler$new(conDet)
Connecting using SQLite driver
Warning: Couldn't set synchronous mode: database disk image is malformed
Use `synchronous` = NULL to turn off this warning.
>
> cs <- getBinaryCaseSeries(
+ connectionHandler = connectionHandler,
+ schema = 'main',
+ targetId = 1,
+ outcomeId = 3
+ )
Error in value[[3L]](cond) : SELECT
cov.database_id,
d.CDM_SOURCE_ABBREVIATION as database_name,
target.cohort_name as target_name,
cov.TARGET_COHORT_ID,
outcome.cohort_name as outcome_name,
cov.Outcome_COHORT_ID,
case
when cov.cohort_type = 'CasesBefore' then 'Before'
when cov.cohort_type = 'CasesBetween' then 'During'
when cov.cohort_type = 'CasesAfter' then 'After'
end as type,
cr.covariate_name,
cr.covariate_id,
s.min_prior_observation,
s.outcome_washout_days,
s.case_post_outcome_duration,
s.case_pre_target_duration,
s.risk_window_start,
s.start_anchor,
s.risk_window_end,
s.end_anchor,
cov.sum_value,
cov.average_value
from
main.c_covariates cov
inner join main.c_covariate_ref cr
on cov.setting_id = cr.setting_id and
cov.database_id = cr.database_id and
cov.covariate_id = cr.covariate_id
inner join main.c_settings s
on cov.setting_id = s.setting_id
and cov.database_i
Calls: getBinaryCaseSeries ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Closing database connection
Flavor: r-release-macos-x86_64
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> test_check("OhdsiReportGenerator")
Loading required package: OhdsiReportGenerator
Connecting using SQLite driver
<simpleError in value[[3L]](cond): select *
from main.cg_cohort_subset_definition
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
>
[ FAIL 41 | WARN 10 | SKIP 1 | PASS 56 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• skip prediction report due to odd linux error (1):
'test-PredictionReport.R:5:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Backwards.R:11:3'): generatePresentationMultiple old works ─────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-Backwards.R:11:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─OhdsiReportGenerator::generatePresentationMultiple(...)
7. └─OhdsiReportGenerator::generatePresentation(...)
8. └─quarto::quarto_render(...)
9. └─quarto:::find_quarto()
10. └─cli::cli_abort(quarto_not_found_msg)
11. └─rlang::abort(...)
── Error ('test-CharacterizationPlots.R:4:3'): plotAgeDistributions ────────────
Error in `value[[3L]](cond)`: select
d.CDM_SOURCE_ABBREVIATION as database_name,
target.cohort_name as target_name,
cd.TARGET_COHORT_ID,
outcome.cohort_name as outcome_name,
cd.Outcome_COHORT_ID,
s.min_prior_observation,
s.outcome_washout_days,
s.RISK_WINDOW_START,
s.RISK_WINDOW_END,
s.START_ANCHOR,
s.END_ANCHOR,
coi.covariate_id,
coi.covariate_name,
c.sum_value,
c.average_value
from main.c_COVARIATES c
inner join
(
select * from main.c_COVARIATE_REF
where analysis_id in (3)
) coi
on
c.database_id = coi.database_id and
c.setting_id = coi.setting_id and
c.covariate_id = coi.covariate_id
inner join
main.c_COHORT_DETAILS cd
on cd.TARGET_COHORT_ID = c.TARGET_COHORT_ID
and cd.OUTCOME_COHORT_ID = c.OUTCOME_COHORT_ID
and cd.COHORT_TYPE = c.COHORT_TYPE
and cd.database_id = c.database_id
and cd.setting_id = c.setting_id
inner join
main.database_meta_data d
on
c.database_id = d.database_id
inner join main.c_settings s
on s.setting_id = c.setting_id
and s.database_id = c.database_id
inner join
main.cg_cohort_definition target
on target.cohort_definition_id = cd.target_cohort_ID
inner join
main.cg_cohort_definition outcome
on outcome.cohort_definition_id = cd.outcome_cohort_ID
where
cd.COHORT_TYPE in ('Cases')
and c.TARGET_COHORT_ID in (1)
and c.OUTCOME_COHORT_ID in (3)
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getCharacterizationDemographics(...) at test-CharacterizationPlots.R:4:3
2. └─OhdsiReportGenerator::getCaseBinaryFeatures(...)
3. └─connectionHandler$queryDb(...)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─value[[3L]](cond)
── Error ('test-CharacterizationPlots.R:16:3'): plotSexDistributions ───────────
Error in `value[[3L]](cond)`: select
d.CDM_SOURCE_ABBREVIATION as database_name,
target.cohort_name as target_name,
cd.TARGET_COHORT_ID,
outcome.cohort_name as outcome_name,
cd.Outcome_COHORT_ID,
s.min_prior_observation,
s.outcome_washout_days,
s.RISK_WINDOW_START,
s.RISK_WINDOW_END,
s.START_ANCHOR,
s.END_ANCHOR,
coi.covariate_id,
coi.covariate_name,
c.sum_value,
c.average_value
from main.c_COVARIATES c
inner join
(
select * from main.c_COVARIATE_REF
where analysis_id in (1)
) coi
on
c.database_id = coi.database_id and
c.setting_id = coi.setting_id and
c.covariate_id = coi.covariate_id
inner join
main.c_COHORT_DETAILS cd
on cd.TARGET_COHORT_ID = c.TARGET_COHORT_ID
and cd.OUTCOME_COHORT_ID = c.OUTCOME_COHORT_ID
and cd.COHORT_TYPE = c.COHORT_TYPE
and cd.database_id = c.database_id
and cd.setting_id = c.setting_id
inner join
main.database_meta_data d
on
c.database_id = d.database_id
inner join main.c_settings s
on s.setting_id = c.setting_id
and s.database_id = c.database_id
inner join
main.cg_cohort_definition target
on target.cohort_definition_id = cd.target_cohort_ID
inner join
main.cg_cohort_definition outcome
on outcome.cohort_definition_id = cd.outcome_cohort_ID
where
cd.COHORT_TYPE in ('Cases')
and c.TARGET_COHORT_ID in (1)
and c.OUTCOME_COHORT_ID in (3)
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getCharacterizationDemographics(...) at test-CharacterizationPlots.R:16:3
2. └─OhdsiReportGenerator::getCaseBinaryFeatures(...)
3. └─connectionHandler$queryDb(...)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:5:3'): incidence rates ───────────────
Error in `value[[3L]](cond)`: select
d.cdm_source_abbreviation as database_name,
cg1.cohort_name as target_name,
i.target_cohort_definition_id as target_id,
cg2.cohort_name as outcome_name,
i.outcome_cohort_definition_id as outcome_id,
i.clean_window,
i.subgroup_name,
i.age_group_name,
i.gender_name,
i.start_year,
i.tar_start_with,
i.tar_start_offset,
i.tar_end_with,
i.tar_end_offset,
i.persons_at_risk_pe,
i.persons_at_risk,
i.person_days_pe,
i.person_days,
i.person_outcomes_pe,
i.person_outcomes,
i.outcomes_pe,
i.outcomes,
i.incidence_proportion_p100p,
i.incidence_rate_p100py
from
(select od.outcome_cohort_definition_id, od.clean_window, agd.age_group_name,
tad.tar_start_with, tad.tar_start_offset, tad.tar_end_with, tad.tar_end_offset,
sd.subgroup_name, i.*
from main.ci_INCIDENCE_SUMMARY i
join main.ci_OUTCOME_DEF
od on i.outcome_id = od.outcome_id
and i.ref_id = od.ref_id
join main.ci_TAR_DEF tad on i.tar_id = tad.tar_id
and i.ref_id = tad.ref_id
join main.ci_SUBGROUP_DEF sd on i.subgroup_id = sd.subgroup_id
and i.ref_id = sd.ref_id
left join main.ci_AGE_GROUP_DEF agd on i.age_group_id = agd.age_group_id
and i.ref_id = agd.ref_id
) i
inner join main.database_meta_data d
on d.database_id = i.database_id
inner join main.cg_cohort_definition cg1
on cg1.cohort_definition_id = i.target_cohort_definition_id
inner join main.cg_cohort_definition cg2
on cg2.cohort_definition_id = i.outcome_cohort_definition_id
where
1 = 1
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getIncidenceRates(...) at test-CharacterizationQueries.R:5:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:24:3'): getTimeToEvent ───────────────
Error in `value[[3L]](cond)`: SELECT
d.CDM_SOURCE_ABBREVIATION as database_name,
target_cohorts.cohort_name as target_name,
tte.target_cohort_definition_id as target_id,
outcome_cohorts.cohort_name as outcome_name,
tte.outcome_cohort_definition_id as outcome_id,
tte.outcome_type,
tte.target_outcome_type,
tte.time_to_event,
tte.num_events,
tte.time_scale
FROM main.c_TIME_TO_EVENT tte
inner join main.database_meta_data d
on tte.database_id = d.database_id
inner join main.cg_cohort_definition target_cohorts
on target_cohorts.cohort_definition_id = tte.TARGET_COHORT_DEFINITION_ID
inner join main.cg_cohort_definition outcome_cohorts
on outcome_cohorts.cohort_definition_id = tte.OUTCOME_COHORT_DEFINITION_ID
where 1 = 1
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getTimeToEvent(...) at test-CharacterizationQueries.R:24:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:53:3'): getDechallengeRechallenge ────
Error in `value[[3L]](cond)`: SELECT
d.CDM_SOURCE_ABBREVIATION as database_name,
target_cohorts.cohort_name as target_name,
dr.target_cohort_definition_id as target_id,
outcome_cohorts.cohort_name as outcome_name,
dr.outcome_cohort_definition_id as outcome_id,
dr.dechallenge_stop_interval,
dr.dechallenge_evaluation_window,
dr.num_exposure_eras,
dr.num_persons_exposed,
dr.num_cases,
dr.dechallenge_attempt,
dr.dechallenge_fail,
dr.dechallenge_success,
dr.rechallenge_attempt,
dr.rechallenge_fail,
dr.rechallenge_success,
dr.pct_dechallenge_attempt,
dr.pct_dechallenge_fail,
dr.pct_dechallenge_success,
dr.pct_rechallenge_attempt,
dr.pct_rechallenge_fail,
dr.pct_rechallenge_success
FROM main.c_DECHALLENGE_RECHALLENGE dr
inner join main.database_meta_data d
on dr.database_id = d.database_id
inner join main.cg_cohort_definition target_cohorts
on target_cohorts.cohort_definition_id = dr.TARGET_COHORT_DEFINITION_ID
inner join main.cg_cohort_definition outcome_cohorts
on outcome_cohorts.cohort_definition_id = dr.OUTCOME_COHORT_DEFINITION_ID
where 1 = 1
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getDechallengeRechallenge(...) at test-CharacterizationQueries.R:53:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:84:3'): target counts ────────────────
Error in `value[[3L]](cond)`: select distinct
targets.database_name,
target_cohorts.cohort_name as target_name,
targets.target_id,
outcome_cohorts.cohort_name as outcome_name,
targets.outcome_id,
case when excludes.row_count is NULL then targets.row_count else
targets.row_count - excludes.row_count end as row_count,
case when excludes.person_count is NULL then targets.person_count
else targets.person_count - excludes.person_count end as person_count,
targets.min_prior_observation,
targets.outcome_washout_days
from
(select
d.CDM_SOURCE_ABBREVIATION as database_name,
cc.target_cohort_ID as target_id,
s2.outcome_cohort_id as outcome_id,
cc.row_count,
cc.person_count,
cc.min_prior_observation,
s2.outcome_washout_days
from
main.c_cohort_counts cc
inner join
main.database_meta_data d
on cc.database_id = d.database_id
inner join
(
select distinct
tcd.target_cohort_id,
tcd.outcome_cohort_id,
ts.outcome_washout_days
from
main.c_settings ts
inner join
main.c_cohort_details tcd
on ts.setting_id = tcd.setting_id
and ts.database_id = tcd.database_id
where tcd.outcome_cohort_id != 0
) s2
on
cc.target_cohort_id = s2.target_cohort_id
where
cc.COHORT_TYPE in ('Target')
) targets
left join
(select
d.CDM_SOURCE_ABBREVIATION as database_name,
cc.target_cohort_ID as target_id,
cc.outcome_cohort_ID as outcome_id,
cc.row_count as row_count,
cc.person_count as person_count,
cc.min_prior_observation,
cc.outcome_washout_days
from
main.c_cohort_counts cc
inner join
main.database_meta_data d
on cc.database_id = d.database_id
where
cc.COHORT_TYPE in ('Exclude')
) excludes
on targets.database_name = excludes.database_name
and targets.target_id = excludes.target_id
and targets.min_prior_observation = excludes.min_prior_observation
inner join main.cg_cohort_definition target_cohorts
on target_cohorts.cohort_definition_id = targets.target_id
left join main.cg_cohort_definition outcome_cohorts
on outcome_cohorts.cohort_definition_id = targets.outcome_id
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getTargetCounts(...) at test-CharacterizationQueries.R:84:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:111:3'): getCaseCounts ───────────────
Error in `value[[3L]](cond)`: select
d.CDM_SOURCE_ABBREVIATION as database_name,
target_cohorts.cohort_name as target_name,
cc.target_cohort_ID as target_id,
outcome_cohorts.cohort_name as outcome_name,
cc.outcome_cohort_ID as outcome_id,
cc.ROW_COUNT,
cc.PERSON_COUNT,
cc.min_prior_observation,
cc.outcome_washout_days,
cc.RISK_WINDOW_START,
cc.RISK_WINDOW_END,
cc.START_ANCHOR,
cc.END_ANCHOR
from
main.c_cohort_counts cc
inner join
main.database_meta_data d
on cc.database_id = d.database_id
inner join
main.cg_cohort_definition target_cohorts
on target_cohorts.cohort_definition_id = cc.target_cohort_ID
inner join
main.cg_cohort_definition outcome_cohorts
on outcome_cohorts.cohort_definition_id = cc.outcome_cohort_ID
where
cc.COHORT_TYPE in ('Cases')
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getCaseCounts(...) at test-CharacterizationQueries.R:111:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:138:3'): getCaseBinaryFeatures ───────
Error in `value[[3L]](cond)`: select
d.CDM_SOURCE_ABBREVIATION as database_name,
target.cohort_name as target_name,
cd.TARGET_COHORT_ID,
outcome.cohort_name as outcome_name,
cd.Outcome_COHORT_ID,
s.min_prior_observation,
s.outcome_washout_days,
s.RISK_WINDOW_START,
s.RISK_WINDOW_END,
s.START_ANCHOR,
s.END_ANCHOR,
coi.covariate_id,
coi.covariate_name,
c.sum_value,
c.average_value
from main.c_COVARIATES c
inner join
(
select * from main.c_COVARIATE_REF
where analysis_id in (3)
) coi
on
c.database_id = coi.database_id and
c.setting_id = coi.setting_id and
c.covariate_id = coi.covariate_id
inner join
main.c_COHORT_DETAILS cd
on cd.TARGET_COHORT_ID = c.TARGET_COHORT_ID
and cd.OUTCOME_COHORT_ID = c.OUTCOME_COHORT_ID
and cd.COHORT_TYPE = c.COHORT_TYPE
and cd.database_id = c.database_id
and cd.setting_id = c.setting_id
inner join
main.database_meta_data d
on
c.database_id = d.database_id
inner join main.c_settings s
on s.setting_id = c.setting_id
and s.database_id = c.database_id
inner join
main.cg_cohort_definition target
on target.cohort_definition_id = cd.target_cohort_ID
inner join
main.cg_cohort_definition outcome
on outcome.cohort_definition_id = cd.outcome_cohort_ID
where
cd.COHORT_TYPE in ('Cases')
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getCaseBinaryFeatures(...) at test-CharacterizationQueries.R:138:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:164:3'): getTargetBinaryFeatures ─────
Error in `value[[3L]](cond)`: select
d.CDM_SOURCE_ABBREVIATION as database_name,
target.cohort_name as target_name,
t.TARGET_COHORT_ID,
outcome.cohort_name as outcome_name,
t.Outcome_COHORT_ID,
t.min_prior_observation,
t.outcome_washout_days,
t.covariate_id,
t.covariate_name,
case when e.sum_value is NULL then t.sum_value
else t.sum_value - e.sum_value end as sum_value,
t.sum_value as raw_sum,
t.average_value as raw_average
FROM
(select
c.database_id,
cd.TARGET_COHORT_ID,
s2.Outcome_COHORT_ID,
s.min_prior_observation,
s2.outcome_washout_days,
coi.covariate_id,
coi.covariate_name,
c.sum_value,
c.average_value
from main.c_COVARIATES c
inner join
(
select * from main.c_COVARIATE_REF
where analysis_id in (3)
) coi
on
c.database_id = coi.database_id and
c.setting_id = coi.setting_id and
c.covariate_id = coi.covariate_id
inner join
main.c_COHORT_DETAILS cd
on cd.TARGET_COHORT_ID = c.TARGET_COHORT_ID
and cd.OUTCOME_COHORT_ID = c.OUTCOME_COHORT_ID
and cd.COHORT_TYPE = c.COHORT_TYPE
and cd.database_id = c.database_id
and cd.setting_id = c.setting_id
inner join main.c_settings s
on s.setting_id = c.setting_id
and s.database_id = c.database_id
inner join
(
select distinct
tcd.target_cohort_id,
tcd.outcome_cohort_id,
ts.outcome_washout_days
from
main.c_settings ts
inner join
main.c_cohort_details tcd
on ts.setting_id = tcd.setting_id
and ts.database_id = tcd.database_id
where tcd.outcome_cohort_id != 0
) s2
on cd.target_cohort_id = s2.target_cohort_id
where
cd.COHORT_TYPE = 'Target'
) t
left join
( select
c.database_id,
cd.TARGET_COHORT_ID,
cd.Outcome_COHORT_ID,
s.min_prior_observation,
s.outcome_washout_days,
coi.covariate_id,
coi.covariate_name,
c.sum_value
from
main.c_COHORT_DETAILS cd
inner join
main.c_COVARIATES c
on
cd.TARGET_COHORT_ID = c.TARGET_COHORT_ID
and cd.OUTCOME_COHORT_ID = c.OUTCOME_COHORT_ID
and cd.COHORT_TYPE = c.COHORT_TYPE
and cd.database_id = c.database_id
and cd.setting_id = c.setting_id
inner join
(select * from main.c_COVARIATE_REF
where analysis_id in (3)
) coi
on
c.database_id = coi.database_id
and c.setting_id = coi.setting_id
and c.covariate_id = coi.covariate_id
inner join
main.c_settings s
on
s.setting_id = c.setting_id
and s.database_id = c.database_id
where
cd.COHORT_TYPE = 'Exclude'
) e
on
t.database_id = e.database_id
and t.TARGET_COHORT_ID = e.TARGET_COHORT_ID
and t.outcome_COHORT_ID = e.outcome_COHORT_ID
and t.min_prior_observation = e.min_prior_observation
and t.outcome_washout_days = e.outcome_washout_days
and t.covariate_name = e.covariate_name
and t.covariate_id = e.covariate_id
inner join
main.database_meta_data d
on
t.database_id = d.database_id
inner join
main.cg_cohort_definition target
on
target.cohort_definition_id = t.target_cohort_ID
inner join
main.cg_cohort_definition outcome
on
outcome.cohort_definition_id = t.outcome_cohort_ID
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getTargetBinaryFeatures(...) at test-CharacterizationQueries.R:164:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:190:3'): getCharacterizationDemographics ──
Error in `value[[3L]](cond)`: select
d.CDM_SOURCE_ABBREVIATION as database_name,
target.cohort_name as target_name,
cd.TARGET_COHORT_ID,
outcome.cohort_name as outcome_name,
cd.Outcome_COHORT_ID,
s.min_prior_observation,
s.outcome_washout_days,
s.RISK_WINDOW_START,
s.RISK_WINDOW_END,
s.START_ANCHOR,
s.END_ANCHOR,
coi.covariate_id,
coi.covariate_name,
c.sum_value,
c.average_value
from main.c_COVARIATES c
inner join
(
select * from main.c_COVARIATE_REF
where analysis_id in (3)
) coi
on
c.database_id = coi.database_id and
c.setting_id = coi.setting_id and
c.covariate_id = coi.covariate_id
inner join
main.c_COHORT_DETAILS cd
on cd.TARGET_COHORT_ID = c.TARGET_COHORT_ID
and cd.OUTCOME_COHORT_ID = c.OUTCOME_COHORT_ID
and cd.COHORT_TYPE = c.COHORT_TYPE
and cd.database_id = c.database_id
and cd.setting_id = c.setting_id
inner join
main.database_meta_data d
on
c.database_id = d.database_id
inner join main.c_settings s
on s.setting_id = c.setting_id
and s.database_id = c.database_id
inner join
main.cg_cohort_definition target
on target.cohort_definition_id = cd.target_cohort_ID
inner join
main.cg_cohort_definition outcome
on outcome.cohort_definition_id = cd.outcome_cohort_ID
where
cd.COHORT_TYPE in ('Cases')
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getCharacterizationDemographics(...) at test-CharacterizationQueries.R:190:3
2. └─OhdsiReportGenerator::getCaseBinaryFeatures(...)
3. └─connectionHandler$queryDb(...)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:239:3'): getTargetBinaryFeatures ─────
Error in `value[[3L]](cond)`: select
d.CDM_SOURCE_ABBREVIATION as database_name,
target.cohort_name as target_name,
t.TARGET_COHORT_ID,
outcome.cohort_name as outcome_name,
t.Outcome_COHORT_ID,
t.min_prior_observation,
t.outcome_washout_days,
t.covariate_id,
t.covariate_name,
case when e.sum_value is NULL then t.sum_value
else t.sum_value - e.sum_value end as sum_value,
t.sum_value as raw_sum,
t.average_value as raw_average
FROM
(select
c.database_id,
cd.TARGET_COHORT_ID,
s2.Outcome_COHORT_ID,
s.min_prior_observation,
s2.outcome_washout_days,
coi.covariate_id,
coi.covariate_name,
c.sum_value,
c.average_value
from main.c_COVARIATES c
inner join
(
select * from main.c_COVARIATE_REF
where analysis_id in (3)
) coi
on
c.database_id = coi.database_id and
c.setting_id = coi.setting_id and
c.covariate_id = coi.covariate_id
inner join
main.c_COHORT_DETAILS cd
on cd.TARGET_COHORT_ID = c.TARGET_COHORT_ID
and cd.OUTCOME_COHORT_ID = c.OUTCOME_COHORT_ID
and cd.COHORT_TYPE = c.COHORT_TYPE
and cd.database_id = c.database_id
and cd.setting_id = c.setting_id
inner join main.c_settings s
on s.setting_id = c.setting_id
and s.database_id = c.database_id
inner join
(
select distinct
tcd.target_cohort_id,
tcd.outcome_cohort_id,
ts.outcome_washout_days
from
main.c_settings ts
inner join
main.c_cohort_details tcd
on ts.setting_id = tcd.setting_id
and ts.database_id = tcd.database_id
where tcd.outcome_cohort_id != 0
) s2
on cd.target_cohort_id = s2.target_cohort_id
where
cd.COHORT_TYPE = 'Target'
) t
left join
( select
c.database_id,
cd.TARGET_COHORT_ID,
cd.Outcome_COHORT_ID,
s.min_prior_observation,
s.outcome_washout_days,
coi.covariate_id,
coi.covariate_name,
c.sum_value
from
main.c_COHORT_DETAILS cd
inner join
main.c_COVARIATES c
on
cd.TARGET_COHORT_ID = c.TARGET_COHORT_ID
and cd.OUTCOME_COHORT_ID = c.OUTCOME_COHORT_ID
and cd.COHORT_TYPE = c.COHORT_TYPE
and cd.database_id = c.database_id
and cd.setting_id = c.setting_id
inner join
(select * from main.c_COVARIATE_REF
where analysis_id in (3)
) coi
on
c.database_id = coi.database_id
and c.setting_id = coi.setting_id
and c.covariate_id = coi.covariate_id
inner join
main.c_settings s
on
s.setting_id = c.setting_id
and s.database_id = c.database_id
where
cd.COHORT_TYPE = 'Exclude'
) e
on
t.database_id = e.database_id
and t.TARGET_COHORT_ID = e.TARGET_COHORT_ID
and t.outcome_COHORT_ID = e.outcome_COHORT_ID
and t.min_prior_observation = e.min_prior_observation
and t.outcome_washout_days = e.outcome_washout_days
and t.covariate_name = e.covariate_name
and t.covariate_id = e.covariate_id
inner join
main.database_meta_data d
on
t.database_id = d.database_id
inner join
main.cg_cohort_definition target
on
target.cohort_definition_id = t.target_cohort_ID
inner join
main.cg_cohort_definition outcome
on
outcome.cohort_definition_id = t.outcome_cohort_ID
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getTargetBinaryFeatures(...) at test-CharacterizationQueries.R:239:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:265:3'): getBinaryRiskFactors ────────
Error in `value[[3L]](cond)`: select
d.CDM_SOURCE_ABBREVIATION as database_name,
target_cohorts.cohort_name as target_name,
cc.target_cohort_ID as target_id,
outcome_cohorts.cohort_name as outcome_name,
cc.outcome_cohort_ID as outcome_id,
cc.ROW_COUNT,
cc.PERSON_COUNT,
cc.min_prior_observation,
cc.outcome_washout_days,
cc.RISK_WINDOW_START,
cc.RISK_WINDOW_END,
cc.START_ANCHOR,
cc.END_ANCHOR
from
main.c_cohort_counts cc
inner join
main.database_meta_data d
on cc.database_id = d.database_id
inner join
main.cg_cohort_definition target_cohorts
on target_cohorts.cohort_definition_id = cc.target_cohort_ID
inner join
main.cg_cohort_definition outcome_cohorts
on outcome_cohorts.cohort_definition_id = cc.outcome_cohort_ID
where
cc.COHORT_TYPE in ('Cases')
and cc.TARGET_COHORT_ID in (1)
and cc.OUTCOME_COHORT_ID in (3)
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getBinaryRiskFactors(...) at test-CharacterizationQueries.R:265:3
2. └─OhdsiReportGenerator::getCaseCounts(...)
3. └─connectionHandler$queryDb(...)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:302:3'): getContinuousRiskFactors ────
Error in `value[[3L]](cond)`: select
d.CDM_SOURCE_ABBREVIATION as database_name,
target.cohort_name as target_name,
t.TARGET_COHORT_ID,
outcome.cohort_name as outcome_name,
t.Outcome_COHORT_ID,
t.min_prior_observation,
t.outcome_washout_days,
t.risk_window_start,
t.risk_window_end,
t.start_anchor,
t.end_anchor,
t.covariate_name,
t.covariate_id,
t.count_value,
t.min_value,
t.max_value,
t.average_value,
t.standard_deviation,
t.median_value,
t.p_10_value,
t.p_25_value,
t.p_75_value,
t.p_90_value
FROM
(select
c.database_id,
c.TARGET_COHORT_ID,
c.Outcome_COHORT_ID,
s.min_prior_observation,
s.outcome_washout_days,
s.risk_window_start,
s.risk_window_end,
s.start_anchor,
s.end_anchor,
coi.covariate_name,
coi.covariate_id,
c.count_value,
c.min_value,
c.max_value,
c.average_value,
c.standard_deviation,
c.median_value,
c.p_10_value,
c.p_25_value,
c.p_75_value,
c.p_90_value
from main.c_COVARIATES_CONTINUOUS c
inner join
(
select * from main.c_COVARIATE_REF
) coi
on
c.database_id = coi.database_id and
c.setting_id = coi.setting_id and
c.covariate_id = coi.covariate_id
inner join
main.c_COHORT_DETAILS cd
on cd.TARGET_COHORT_ID = c.TARGET_COHORT_ID
and cd.OUTCOME_COHORT_ID = c.OUTCOME_COHORT_ID
and cd.COHORT_TYPE = c.COHORT_TYPE
and cd.database_id = c.database_id
and cd.setting_id = c.setting_id
inner join main.c_settings s
on s.setting_id = c.setting_id
and s.database_id = c.database_id
where
cd.COHORT_TYPE = 'Cases'
and c.TARGET_COHORT_ID in (1)
and c.outcome_cohort_id in (3)
) t
inner join
main.database_meta_data d
on
t.database_id = d.database_id
inner join
main.cg_cohort_definition target
on
target.cohort_definition_id = t.target_cohort_ID
inner join
main.cg_cohort_definition outcome
on
outcome.cohort_definition_id = t.outcome_cohort_ID
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getContinuousRiskFactors(...) at test-CharacterizationQueries.R:302:3
2. └─OhdsiReportGenerator::getCaseContinuousFeatures(...)
3. └─connectionHandler$queryDb(...)
4. └─base::tryCatch(...)
5. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
6. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
7. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:325:3'): getBinaryCaseSeries ─────────
Error in `value[[3L]](cond)`: SELECT
cov.database_id,
d.CDM_SOURCE_ABBREVIATION as database_name,
target.cohort_name as target_name,
cov.TARGET_COHORT_ID,
outcome.cohort_name as outcome_name,
cov.Outcome_COHORT_ID,
case
when cov.cohort_type = 'CasesBefore' then 'Before'
when cov.cohort_type = 'CasesBetween' then 'During'
when cov.cohort_type = 'CasesAfter' then 'After'
end as type,
cr.covariate_name,
cr.covariate_id,
s.min_prior_observation,
s.outcome_washout_days,
s.case_post_outcome_duration,
s.case_pre_target_duration,
s.risk_window_start,
s.start_anchor,
s.risk_window_end,
s.end_anchor,
cov.sum_value,
cov.average_value
from
main.c_covariates cov
inner join main.c_covariate_ref cr
on cov.setting_id = cr.setting_id and
cov.database_id = cr.database_id and
cov.covariate_id = cr.covariate_id
inner join main.c_settings s
on cov.setting_id = s.setting_id
and cov.database_id = s.database_id
inner join
main.database_meta_data d
on
cov.database_id = d.database_id
inner join
main.cg_cohort_definition target
on
target.cohort_definition_id = cov.target_cohort_ID
inner join
main.cg_cohort_definition outcome
on
outcome.cohort_definition_id = cov.outcome_cohort_ID
where cov.target_cohort_id = 1
and cov.outcome_cohort_id = 3
and cov.cohort_type in ('CasesBetween','CasesAfter','CasesBefore')
and cr.analysis_id in (109, 110, 217, 218, 305, 417, 418, 505, 605, 713, 805, 926, 927)
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getBinaryCaseSeries(...) at test-CharacterizationQueries.R:325:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-CharacterizationQueries.R:354:3'): getContinuousCaseSeries ─────
Error in `value[[3L]](cond)`: SELECT
cov.database_id,
d.CDM_SOURCE_ABBREVIATION as database_name,
target.cohort_name as target_name,
cov.TARGET_COHORT_ID,
outcome.cohort_name as outcome_name,
cov.Outcome_COHORT_ID,
case
when cov.cohort_type = 'CasesBefore' then 'Before'
when cov.cohort_type = 'CasesBetween' then 'During'
when cov.cohort_type = 'CasesAfter' then 'After'
end as type,
cr.covariate_name,
cr.covariate_id,
s.min_prior_observation,
s.outcome_washout_days,
s.case_post_outcome_duration,
s.case_pre_target_duration,
s.risk_window_start,
s.start_anchor,
s.risk_window_end,
s.end_anchor,
cov.count_value,
cov.min_value,
cov.max_value,
cov.average_value,
cov.standard_deviation,
cov.median_value,
cov.p_10_value,
cov.p_25_value,
cov.p_75_value,
cov.p_90_value
from
main.c_covariates_continuous cov
inner join main.c_covariate_ref cr
on cov.setting_id = cr.setting_id and
cov.database_id = cr.database_id and
cov.covariate_id = cr.covariate_id
inner join main.c_settings s
on cov.setting_id = s.setting_id
and cov.database_id = s.database_id
inner join
main.database_meta_data d
on
cov.database_id = d.database_id
inner join
main.cg_cohort_definition target
on
target.cohort_definition_id = cov.target_cohort_ID
inner join
main.cg_cohort_definition outcome
on
outcome.cohort_definition_id = cov.outcome_cohort_ID
where cov.target_cohort_id = 1
and cov.outcome_cohort_id = 3
and cov.cohort_type in ('CasesBetween','CasesAfter','CasesBefore')
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getContinuousCaseSeries(...) at test-CharacterizationQueries.R:354:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-CohortQueries.R:5:3'): getCohortDefinitions ────────────────────
Error in `value[[3L]](cond)`: select *
from main.cg_cohort_definition
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getCohortDefinitions(...) at test-CohortQueries.R:5:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-CohortQueries.R:25:3'): processCohorts ─────────────────────────
Error in `value[[3L]](cond)`: select *
from main.cg_cohort_definition
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getCohortDefinitions(...) at test-CohortQueries.R:25:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Failure ('test-CohortQueries.R:49:3'): getCohortSubsetDefinitions ───────────
nrow(subsetDef) > 0 is not TRUE
`actual`:
`expected`: TRUE
── Error ('test-CohortQueries.R:51:3'): getCohortSubsetDefinitions ─────────────
Error: Argument 'txt' must be a JSON string, URL or file.
Backtrace:
▆
1. └─ParallelLogger::convertJsonToSettings(subsetDef$json[1]) at test-CohortQueries.R:51:3
2. └─jsonlite::fromJSON(json, simplifyVector = TRUE, simplifyDataFrame = FALSE)
3. └─jsonlite:::stop("Argument 'txt' must be a JSON string, URL or file.")
── Error ('test-EstimationPlots.R:5:3'): plotCmEstimates ───────────────────────
Error in `value[[3L]](cond)`: select
db.cdm_source_abbreviation as database_name,
r.analysis_id,
a.description,
c1.cohort_name as target_name,
r.target_id,
c2.cohort_name as comparator_name,
r.comparator_id,
c3.cohort_name as outcome_name,
r.outcome_id,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_rr end calibrated_rr,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_ci_95_lb end calibrated_ci_95_lb,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_ci_95_ub end calibrated_ci_95_ub,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_p end calibrated_p,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_one_sided_p end calibrated_one_sided_p,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_log_rr end calibrated_log_rr,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_se_log_rr end calibrated_se_log_rr,
r.target_subjects,
r.comparator_subjects,
r.target_days,
r.comparator_days,
r.target_outcomes,
r.comparator_outcomes,
r.target_estimator
from
main.cm_result as r
inner join
main.cm_target_comparator_outcome as tco
on
r.target_id = tco.target_id and
r.comparator_id = tco.comparator_id and
r.outcome_id = tco.outcome_id
inner join
main.cm_diagnostics_summary as unblind
on
r.analysis_id = unblind.analysis_id and
r.target_id = unblind.target_id and
r.comparator_id = unblind.comparator_id and
r.outcome_id = unblind.outcome_id and
r.database_id = unblind.database_id
inner join
main.database_meta_data as db
on db.database_id = r.database_id
inner join
main.cg_cohort_definition as c1
on c1.cohort_definition_id = r.target_id
inner join
main.cg_cohort_definition as c2
on c2.cohort_definition_id = r.comparator_id
inner join
main.cg_cohort_definition as c3
on c3.cohort_definition_id = r.outcome_id
inner join
main.cm_analysis as a
on a.analysis_id = r.analysis_id
where
tco.outcome_of_interest = 1
and r.target_id in (1002)
and r.outcome_id in (3)
and r.comparator_id in (2002)
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getCMEstimation(...) at test-EstimationPlots.R:5:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-EstimationPlots.R:28:3'): plotSccsEstimates ────────────────────
Error in `value[[3L]](cond)`: SELECT
ds.cdm_source_abbreviation as database_name,
sr.analysis_id,
a.description,
cg2.cohort_name as target_name,
sc.era_id as target_id,
cg1.cohort_name as outcome_name,
eos.outcome_id,
cg3.cohort_name as indication_name,
eos.nesting_cohort_id as indication_id,
sc.covariate_name,
sr.outcome_subjects,
sr.outcome_events,
sr.outcome_observation_periods,
sr.covariate_subjects,
sr.covariate_days,
sr.covariate_eras,
sr.covariate_outcomes,
sr.observed_days,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.rr end rr,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.ci_95_lb end ci_95_lb,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.ci_95_ub end ci_95_ub,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.p end p,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.log_rr end log_rr,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.se_log_rr end se_log_rr,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_rr end calibrated_rr,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_ci_95_lb end calibrated_ci_95_lb,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_ci_95_ub end calibrated_ci_95_ub,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_p end calibrated_p,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_one_sided_p end calibrated_one_sided_p,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_log_rr end calibrated_log_rr,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_se_log_rr end calibrated_se_log_rr,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.llr end llr,
sds.mdrr,
--sds.ease,
--sds.time_trend_p,
--sds.pre_exposure_p,
--sds.mdrr_diagnostic,
--sds.ease_diagnostic,
--sds.time_trend_diagnostic,
--sds.pre_exposure_diagnostic,
sds.unblind
FROM main.sccs_result sr
INNER JOIN
main.database_meta_data ds
ON sr.database_id = ds.database_id
INNER JOIN
main.sccs_diagnostics_summary sds ON (
sds.exposures_outcome_set_id = sr.exposures_outcome_set_id AND
sds.database_id = sr.database_id AND
sds.analysis_id = sr.analysis_id AND
sds.covariate_id = sr.covariate_id
)
INNER JOIN
main.sccs_covariate sc ON (
sc.exposures_outcome_set_id = sr.exposures_outcome_set_id AND
sc.database_id = sr.database_id AND
sc.analysis_id = sr.analysis_id AND
sc.covariate_id = sr.covariate_id
)
INNER JOIN main.sccs_exposures_outcome_set eos
ON
eos.exposures_outcome_set_id = sr.exposures_outcome_set_id
INNER JOIN
main.sccs_analysis a
on a.analysis_id = sr.analysis_id
inner join
main.cg_cohort_definition cg1
on cg1.cohort_definition_id = eos.outcome_id
inner join
main.cg_cohort_definition cg2
on cg2.cohort_definition_id = sc.era_id
left join
main.cg_cohort_definition as cg3
on eos.nesting_cohort_id = cg3.cohort_definition_id
WHERE
1 = 1
and eos.outcome_id IN (3)
and sc.era_id IN (1)
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getSccsEstimation(...) at test-EstimationPlots.R:28:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-EstimationQueries.R:5:3'): getCMEstimation ─────────────────────
Error in `value[[3L]](cond)`: select
db.cdm_source_abbreviation as database_name,
r.analysis_id,
a.description,
c1.cohort_name as target_name,
r.target_id,
c2.cohort_name as comparator_name,
r.comparator_id,
c3.cohort_name as outcome_name,
r.outcome_id,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_rr end calibrated_rr,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_ci_95_lb end calibrated_ci_95_lb,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_ci_95_ub end calibrated_ci_95_ub,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_p end calibrated_p,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_one_sided_p end calibrated_one_sided_p,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_log_rr end calibrated_log_rr,
case when COALESCE(unblind.unblind, 0) = 0 then NULL else r.calibrated_se_log_rr end calibrated_se_log_rr,
r.target_subjects,
r.comparator_subjects,
r.target_days,
r.comparator_days,
r.target_outcomes,
r.comparator_outcomes,
r.target_estimator
from
main.cm_result as r
inner join
main.cm_target_comparator_outcome as tco
on
r.target_id = tco.target_id and
r.comparator_id = tco.comparator_id and
r.outcome_id = tco.outcome_id
inner join
main.cm_diagnostics_summary as unblind
on
r.analysis_id = unblind.analysis_id and
r.target_id = unblind.target_id and
r.comparator_id = unblind.comparator_id and
r.outcome_id = unblind.outcome_id and
r.database_id = unblind.database_id
inner join
main.database_meta_data as db
on db.database_id = r.database_id
inner join
main.cg_cohort_definition as c1
on c1.cohort_definition_id = r.target_id
inner join
main.cg_cohort_definition as c2
on c2.cohort_definition_id = r.comparator_id
inner join
main.cg_cohort_definition as c3
on c3.cohort_definition_id = r.outcome_id
inner join
main.cm_analysis as a
on a.analysis_id = r.analysis_id
where
tco.outcome_of_interest = 1
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getCMEstimation(...) at test-EstimationQueries.R:5:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-EstimationQueries.R:33:3'): getCmDiagnosticsData ───────────────
Error in `value[[3L]](cond)`: SELECT DISTINCT
dmd.cdm_source_abbreviation database_name,
cma.analysis_id,
cma.description,
cgcd1.cohort_name target_name,
cmds.target_id,
cgcd2.cohort_name comparator_name,
cmds.comparator_id,
cgcd3.cohort_name outcome_name,
cmds.outcome_id,
cmds.max_sdm,
cmds.shared_max_sdm,
cmds.equipoise,
cmds.mdrr,
cmds.attrition_fraction,
cmds.ease,
cmds.balance_diagnostic,
cmds.shared_balance_diagnostic, -- added back
cmds.equipoise_diagnostic,
cmds.mdrr_diagnostic,
cmds.attrition_diagnostic,
cmds.ease_diagnostic,
cmds.unblind_for_evidence_synthesis,
cmds.unblind
FROM
main.cm_diagnostics_summary cmds
INNER JOIN main.cm_analysis cma ON cmds.analysis_id = cma.analysis_id
INNER JOIN main.database_meta_data dmd ON dmd.database_id = cmds.database_id
INNER JOIN main.cg_cohort_definition cgcd1 ON cmds.target_id = cgcd1.cohort_definition_id
INNER JOIN main.cg_cohort_definition cgcd2 ON cmds.comparator_id = cgcd2.cohort_definition_id
INNER JOIN main.cg_cohort_definition cgcd3 ON cmds.outcome_id = cgcd3.cohort_definition_id
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getCmDiagnosticsData(...) at test-EstimationQueries.R:33:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-EstimationQueries.R:68:3'): getCmMetaEstimation ────────────────
Error in `value[[3L]](cond)`: select
ev.evidence_synthesis_description as database_name,
r.analysis_id,
a.description,
c1.cohort_name as target_name,
r.target_id,
c2.cohort_name as comparator_name,
r.comparator_id,
c3.cohort_name as outcome_name,
r.outcome_id,
r.calibrated_rr, r.calibrated_ci_95_lb, r.calibrated_ci_95_ub,
r.calibrated_p, r.calibrated_one_sided_p,
r.calibrated_log_rr, r.calibrated_se_log_rr,
r. target_subjects, r.comparator_subjects, r.target_days,
r.comparator_days, r.target_outcomes, r.comparator_outcomes,
r.n_databases
from
main.es_cm_result as r
inner join
main.cm_target_comparator_outcome as tco
on
r.target_id = tco.target_id and
r.comparator_id = tco.comparator_id and
r.outcome_id = tco.outcome_id
inner join
main.es_cm_diagnostics_summary as unblind
on
r.analysis_id = unblind.analysis_id and
r.target_id = unblind.target_id and
r.comparator_id = unblind.comparator_id and
r.outcome_id = unblind.outcome_id
inner join
main.cg_cohort_definition as c1
on c1.cohort_definition_id = r.target_id
inner join
main.cg_cohort_definition as c2
on c2.cohort_definition_id = r.comparator_id
inner join
main.cg_cohort_definition as c3
on c3.cohort_definition_id = r.outcome_id
inner join
main.cm_analysis as a
on a.analysis_id = r.analysis_id
inner join
main.es_analysis as ev
on ev.evidence_synthesis_analysis_id = r.evidence_synthesis_analysis_id
where
r.calibrated_rr != 0 and
tco.outcome_of_interest = 1 and
unblind.unblind = 1
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getCmMetaEstimation(...) at test-EstimationQueries.R:68:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-EstimationQueries.R:99:3'): getSccsEstimation ──────────────────
Error in `value[[3L]](cond)`: SELECT
ds.cdm_source_abbreviation as database_name,
sr.analysis_id,
a.description,
cg2.cohort_name as target_name,
sc.era_id as target_id,
cg1.cohort_name as outcome_name,
eos.outcome_id,
cg3.cohort_name as indication_name,
eos.nesting_cohort_id as indication_id,
sc.covariate_name,
sr.outcome_subjects,
sr.outcome_events,
sr.outcome_observation_periods,
sr.covariate_subjects,
sr.covariate_days,
sr.covariate_eras,
sr.covariate_outcomes,
sr.observed_days,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.rr end rr,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.ci_95_lb end ci_95_lb,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.ci_95_ub end ci_95_ub,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.p end p,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.log_rr end log_rr,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.se_log_rr end se_log_rr,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_rr end calibrated_rr,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_ci_95_lb end calibrated_ci_95_lb,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_ci_95_ub end calibrated_ci_95_ub,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_p end calibrated_p,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_one_sided_p end calibrated_one_sided_p,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_log_rr end calibrated_log_rr,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.calibrated_se_log_rr end calibrated_se_log_rr,
case when COALESCE(sds.unblind, 0) = 0 then NULL else sr.llr end llr,
sds.mdrr,
--sds.ease,
--sds.time_trend_p,
--sds.pre_exposure_p,
--sds.mdrr_diagnostic,
--sds.ease_diagnostic,
--sds.time_trend_diagnostic,
--sds.pre_exposure_diagnostic,
sds.unblind
FROM main.sccs_result sr
INNER JOIN
main.database_meta_data ds
ON sr.database_id = ds.database_id
INNER JOIN
main.sccs_diagnostics_summary sds ON (
sds.exposures_outcome_set_id = sr.exposures_outcome_set_id AND
sds.database_id = sr.database_id AND
sds.analysis_id = sr.analysis_id AND
sds.covariate_id = sr.covariate_id
)
INNER JOIN
main.sccs_covariate sc ON (
sc.exposures_outcome_set_id = sr.exposures_outcome_set_id AND
sc.database_id = sr.database_id AND
sc.analysis_id = sr.analysis_id AND
sc.covariate_id = sr.covariate_id
)
INNER JOIN main.sccs_exposures_outcome_set eos
ON
eos.exposures_outcome_set_id = sr.exposures_outcome_set_id
INNER JOIN
main.sccs_analysis a
on a.analysis_id = sr.analysis_id
inner join
main.cg_cohort_definition cg1
on cg1.cohort_definition_id = eos.outcome_id
inner join
main.cg_cohort_definition cg2
on cg2.cohort_definition_id = sc.era_id
left join
main.cg_cohort_definition as cg3
on eos.nesting_cohort_id = cg3.cohort_definition_id
WHERE
1 = 1
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getSccsEstimation(...) at test-EstimationQueries.R:99:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-EstimationQueries.R:128:3'): getSccsDiagnosticsData ────────────
Error in `value[[3L]](cond)`: SELECT
d.cdm_source_abbreviation as database_name,
a.analysis_id,
a.description,
c2.cohort_name as target_name,
cov.era_id as target_id,
c.cohort_name as outcome_name,
eos.outcome_id,
cg3.cohort_name as indication_name,
eos.nesting_cohort_id as indication_id,
cov.covariate_name,
ds.mdrr,
ds.ease,
ds.time_trend_p,
ds.pre_exposure_p,
ds.mdrr_diagnostic,
ds.ease_diagnostic,
ds.time_trend_diagnostic,
ds.pre_exposure_diagnostic,
ds.unblind,
ds.unblind_for_evidence_synthesis
FROM main.sccs_diagnostics_summary ds
inner join
main.sccs_exposures_outcome_set eos
on ds.exposures_outcome_set_id = eos.exposures_outcome_set_id
inner join
main.cg_cohort_definition as c
on c.cohort_definition_id = eos.outcome_id
INNER JOIN
main.database_meta_data d
on d.database_id = ds.database_id
INNER JOIN
main.sccs_analysis a
on a.analysis_id = ds.analysis_id
INNER JOIN
main.sccs_covariate cov
on cov.covariate_id = ds.covariate_id and
cov.exposures_outcome_set_id = ds.exposures_outcome_set_id and
cov.analysis_id = ds.analysis_id and
cov.database_id = ds.database_id
inner join
main.cg_cohort_definition as c2
on cov.era_id = c2.cohort_definition_id
left join
main.cg_cohort_definition as cg3
on eos.nesting_cohort_id = cg3.cohort_definition_id
where
1 = 1
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getSccsDiagnosticsData(...) at test-EstimationQueries.R:128:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-EstimationQueries.R:158:3'): getSccsMetaEstimation ─────────────
Error in `value[[3L]](cond)`: select distinct
ev.evidence_synthesis_description as database_name,
r.analysis_id,
a.description,
c1.cohort_name as target_name,
cov.era_id as target_id,
c3.cohort_name as outcome_name,
eos.outcome_id,
cg3.cohort_name as indication_name,
eos.nesting_cohort_id as indication_id,
cov.covariate_name,
r.outcome_subjects,
r.outcome_events,
r.outcome_observation_periods,
r.covariate_subjects,
r.covariate_days,
r.covariate_eras,
r.covariate_outcomes,
r.observed_days,
r.calibrated_rr,
r.calibrated_ci_95_lb,
r.calibrated_ci_95_ub,
r.calibrated_p,
r.calibrated_one_sided_p,
r.calibrated_log_rr,
r.calibrated_se_log_rr,
r.n_databases
from
main.es_sccs_result as r
inner join
main.sccs_exposures_outcome_set as eos
on
r.exposures_outcome_set_id = eos.exposures_outcome_set_id
inner join
main.sccs_covariate as cov
on
r.covariate_id = cov.covariate_id and
r.analysis_id = cov.analysis_id and
r.exposures_outcome_set_id = cov.exposures_outcome_set_id
inner join
main.sccs_exposure as ex
on
ex.era_id = cov.era_id and
ex.exposures_outcome_set_id = cov.exposures_outcome_set_id
inner join
main.es_sccs_diagnostics_summary as unblind
on
r.analysis_id = unblind.analysis_id and
r.exposures_outcome_set_id = unblind.exposures_outcome_set_id and
r.covariate_id = unblind.covariate_id and
r.evidence_synthesis_analysis_id = unblind.evidence_synthesis_analysis_id
inner join
main.cg_cohort_definition as c1
on c1.cohort_definition_id = cov.era_id
inner join
main.cg_cohort_definition as c3
on c3.cohort_definition_id = eos.outcome_id
inner join
main.sccs_analysis as a
on a.analysis_id = r.analysis_id
inner join
main.es_analysis as ev
on ev.evidence_synthesis_analysis_id = r.evidence_synthesis_analysis_id
left join
main.cg_cohort_definition as cg3
on eos.nesting_cohort_id = cg3.cohort_definition_id
where
r.calibrated_rr != 0 and
--ex.true_effect_size != 1 and
cov.covariate_name in ('Main', 'Second dose') and
unblind.unblind = 1
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getSccsMetaEstimation(...) at test-EstimationQueries.R:158:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-Generate.R:10:3'): generatePresentation ────────────────────────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. └─OhdsiReportGenerator::generatePresentation(...) at test-Generate.R:10:3
2. └─quarto::quarto_render(...)
3. └─quarto:::find_quarto()
4. └─cli::cli_abort(quarto_not_found_msg)
5. └─rlang::abort(...)
── Error ('test-Generate.R:61:3'): generateFullReport ──────────────────────────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. └─OhdsiReportGenerator::generateFullReport(...) at test-Generate.R:61:3
2. └─quarto::quarto_render(...)
3. └─quarto:::find_quarto()
4. └─cli::cli_abort(quarto_not_found_msg)
5. └─rlang::abort(...)
── Error ('test-Helpers.R:75:3'): getAnalyses ──────────────────────────────────
Error: database disk image is malformed
Backtrace:
▆
1. └─OhdsiReportGenerator:::getAnalyses(...) at test-Helpers.R:75:3
2. └─DatabaseConnector::getTableNames(connection = connection, databaseSchema = schema)
3. ├─DBI::dbListTables(conn = connection, databaseSchema = databaseSchema)
4. └─DBI::dbListTables(conn = connection, databaseSchema = databaseSchema)
5. └─DatabaseConnector (local) .local(conn, ...)
6. ├─DBI::dbListTables(conn@dbiConnection, schema = databaseSchema)
7. └─DBI::dbListTables(conn@dbiConnection, schema = databaseSchema)
8. └─RSQLite:::sqliteListTables(conn)
9. ├─DBI::dbSendQuery(conn, sql)
10. └─RSQLite::dbSendQuery(conn, sql)
11. └─RSQLite (local) .local(conn, statement, ...)
12. ├─methods::new(...)
13. │ ├─methods::initialize(value, ...)
14. │ └─methods::initialize(value, ...)
15. └─RSQLite:::result_create(conn@ptr, statement)
── Error ('test-Helpers.R:91:3'): getDbs ───────────────────────────────────────
Error in `value[[3L]](cond)`: select CDM_SOURCE_ABBREVIATION from main.database_meta_data;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator:::getDbs(...) at test-Helpers.R:91:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-PredictionQueries.R:5:3'): getPredictionTopPredictors ──────────
Error in `value[[3L]](cond)`: select * from
(select d.cdm_source_abbreviation as database_name,
tars.tar_start_day, tars.tar_start_anchor,
tars.tar_end_day, tars.tar_end_anchor,
cov.*,
ROW_NUMBER() OVER(
PARTITION BY p.performance_id, d.cdm_source_abbreviation,
tars.tar_start_day, tars.tar_start_anchor,
tars.tar_end_day, tars.tar_end_anchor
ORDER BY ABS(cov.covariate_value) DESC
) AS rn
from main.plp_model_designs md
inner join main.plp_performances p
on md.model_design_id = p.model_design_id
inner join main.plp_covariate_summary cov
on p.performance_id = cov.performance_id
inner join main.plp_database_details dd
on dd.database_id = p.development_database_id
inner join main.database_meta_data d
on d.database_id = dd.database_meta_data_id
inner join main.plp_tars tars
on tars.tar_id = p.tar_id
inner join main.plp_cohorts t
on t.cohort_id = md.target_id
-- join to CG table to get target name
inner join main.plp_cohorts o
on o.cohort_id = md.outcome_id
-- join to CG table to get outcome name
) temp
where rn <= 100;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getPredictionTopPredictors(...) at test-PredictionQueries.R:5:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-PredictionQueries.R:33:3'): getPredictionCohorts ───────────────
Error in `value[[3L]](cond)`: SELECT distinct
cohorts.cohort_id,
cohorts.cohort_name,
'target' as type
FROM
main.plp_model_designs as model_designs
inner join
(SELECT c.cohort_id, cd.cohort_name FROM main.plp_cohorts c
inner join main.cg_cohort_definition cd
on c.cohort_definition_id = cd.cohort_definition_id
) AS cohorts
ON model_designs.target_id = cohorts.cohort_id
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getPredictionCohorts(...) at test-PredictionQueries.R:33:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-PredictionQueries.R:49:3'): getPredictionModelDesigns ──────────
Error in `value[[3L]](cond)`: SELECT
model_designs.model_design_id,
model_settings.model_type model_type,
targets.cohort_definition_id AS development_target_id,
targets.cohort_name AS development_target_name,
targets.json AS development_target_json,
outcomes.cohort_definition_id AS development_outcome_id,
outcomes.cohort_name AS development_outcome_name,
outcomes.json AS development_outcome_json,
tars.tar_start_day,
tars.tar_start_anchor,
tars.tar_end_day,
tars.tar_end_anchor,
covariate_settings.covariate_settings_json,
population_settings.population_settings_json,
tidy_covariates_settings.tidy_covariates_settings_json,
plp_data_settings.plp_data_settings_json,
feature_engineering_settings.feature_engineering_settings_json,
split_settings.split_settings_json,
sample_settings.sample_settings_json,
MIN(p.value) AS min_auroc,
AVG(p.value) AS mean_auroc,
MAX(p.value) AS max_auroc,
COUNT(distinct diag.database_id) AS no_diagnostic_databases,
COUNT(distinct d.database_id) AS no_development_databases,
COUNT(distinct v.database_id) AS no_validation_databases
FROM
main.plp_model_designs as model_designs
inner join
main.plp_model_settings as model_settings
on model_designs.model_setting_id = model_settings.model_setting_id
inner join
main.plp_covariate_settings as covariate_settings
on model_designs.covariate_setting_id = covariate_settings.covariate_setting_id
inner join
main.plp_population_settings as population_settings
on model_designs.population_setting_id = population_settings.population_setting_id
inner join
main.plp_tidy_covariates_settings as tidy_covariates_settings
on model_designs.tidy_covariates_setting_id = tidy_covariates_settings.tidy_covariates_setting_id
inner join
main.plp_sample_settings as sample_settings
on model_designs.sample_setting_id = sample_settings.sample_setting_id
inner join
main.plp_feature_engineering_settings as feature_engineering_settings
on model_designs.feature_engineering_setting_id = feature_engineering_settings.feature_engineering_setting_id
inner join
main.plp_split_settings as split_settings
on model_designs.split_setting_id = split_settings.split_setting_id
inner join
main.plp_plp_data_settings as plp_data_settings
on model_designs.plp_data_setting_id = plp_data_settings.plp_data_setting_id
LEFT JOIN
main.plp_performances AS results
on model_designs.model_design_id = results.model_design_id
LEFT JOIN
(select * from main.plp_EVALUATION_STATISTICS
where EVALUATION = 'Test' and METRIC = 'AUROC') p
on p.performance_id = results.performance_id
LEFT JOIN
(SELECT c.cohort_id, cd.cohort_name, cd.json, cd.cohort_definition_id
FROM main.plp_cohorts c
inner join main.cg_cohort_definition cd
on c.cohort_definition_id = cd.cohort_definition_id
) AS targets
ON model_designs.target_id = targets.cohort_id
LEFT JOIN
(SELECT c.cohort_id, cd.cohort_name, cd.json, cd.cohort_definition_id
FROM main.plp_cohorts c
inner join main.cg_cohort_definition cd
on c.cohort_definition_id = cd.cohort_definition_id
) AS outcomes
ON model_designs.outcome_id = outcomes.cohort_id
LEFT JOIN main.plp_tars AS tars
ON model_designs.tar_id = tars.tar_id
LEFT JOIN main.plp_database_details AS d
ON results.development_database_id = d.database_id
LEFT JOIN main.plp_database_details AS v
ON results.validation_database_id = v.database_id
LEFT JOIN main.plp_diagnostics AS diag
ON results.development_database_id = diag.database_id
where 1 == 1
GROUP BY
model_designs.model_design_id,
model_settings.model_type,
targets.cohort_definition_id,
targets.cohort_name,
targets.json,
outcomes.cohort_definition_id,
outcomes.cohort_name,
outcomes.json,
tars.tar_start_day,
tars.tar_start_anchor,
tars.tar_end_day,
tars.tar_end_anchor,
covariate_settings.covariate_settings_json,
population_settings.population_settings_json,
tidy_covariates_settings.tidy_covariates_settings_json,
feature_engineering_settings.feature_engineering_settings_json,
split_settings.split_settings_json,
plp_data_settings.plp_data_settings_json,
sample_settings.sample_settings_json;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getPredictionModelDesigns(...) at test-PredictionQueries.R:49:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-PredictionQueries.R:84:3'): getPredictionPerformances ──────────
Error in `value[[3L]](cond)`: SELECT distinct
results.performance_id,
results.model_design_id,
results.development_database_id,
results.validation_database_id,
devtargets.cohort_definition_id AS development_target_id,
devtargets.cohort_name AS development_target_name,
devoutcomes.cohort_definition_id AS development_outcome_id,
devoutcomes.cohort_name AS development_outcome_name,
d.database_acronym AS development_database,
v.database_acronym AS validation_database,
targets.cohort_name AS validation_target_name,
outcomes.cohort_name AS validation_outcome_name,
results.execution_date_time AS time_stamp,
tars.tar_start_day,
tars.tar_start_anchor,
tars.tar_end_day,
tars.tar_end_anchor,
aucResult.auc AS auroc,
auclbResult.auclb AS auroc_95lb,
aucubResult.aucub AS auroc_95ub,
calibration_in_large_result.calibration_in_large AS calibration_in_large,
estat.value as e_statistic,
brier.value as brier_score,
auprcResult.auprc AS auprc,
nResult.population_size,
oResult.outcome_count,
nTest.test_size*100.0/nResult.population_size AS eval_percent,
oResult.outcome_count*100.0/nResult.population_size AS outcome_percent,
results.model_development AS model_development_flag
FROM
(select * from main.plp_performances
)
AS results
inner join main.plp_model_designs as model_designs
on model_designs.model_design_id = results.model_design_id
LEFT JOIN
(SELECT c.cohort_id, c.cohort_definition_id, cd.cohort_name FROM main.plp_cohorts c
inner join main.cg_cohort_definition cd
on c.cohort_definition_id = cd.cohort_definition_id
) AS devtargets ON model_designs.target_id = devtargets.cohort_id
LEFT JOIN
(SELECT c.cohort_id, c.cohort_definition_id, cd.cohort_name FROM main.plp_cohorts c
inner join main.cg_cohort_definition cd
on c.cohort_definition_id = cd.cohort_definition_id
) AS targets ON results.target_id = targets.cohort_id
LEFT JOIN
(SELECT c.cohort_id, c.cohort_definition_id, cd.cohort_name FROM main.plp_cohorts c
inner join main.cg_cohort_definition cd
on c.cohort_definition_id = cd.cohort_definition_id
) AS outcomes ON results.outcome_id = outcomes.cohort_id
LEFT JOIN
(SELECT c.cohort_id, c.cohort_definition_id, cd.cohort_name FROM main.plp_cohorts c
inner join main.cg_cohort_definition cd
on c.cohort_definition_id = cd.cohort_definition_id
) AS devoutcomes ON model_designs.target_id = devoutcomes.cohort_id
LEFT JOIN
(select dd.database_id, md.cdm_source_abbreviation database_acronym
from main.database_meta_data md inner join
main.plp_database_details dd
on md.database_id = dd.database_meta_data_id
) AS d ON results.development_database_id = d.database_id
LEFT JOIN
(select dd.database_id, md.cdm_source_abbreviation database_acronym
from main.database_meta_data md inner join
main.plp_database_details dd
on md.database_id = dd.database_meta_data_id
) AS v ON results.validation_database_id = v.database_id
LEFT JOIN main.plp_tars AS tars ON results.tar_id = tars.tar_id
LEFT JOIN (SELECT performance_id, value AS auc FROM main.plp_evaluation_statistics where metric = 'AUROC' and evaluation in ('Test','Validation') ) AS aucResult ON results.performance_id = aucResult.performance_id
LEFT JOIN (SELECT performance_id, value AS auprc FROM main.plp_evaluation_statistics where metric = 'AUPRC' and evaluation in ('Test','Validation') ) AS auprcResult ON results.performance_id = auprcResult.performance_id
LEFT JOIN (SELECT performance_id, sum(value) AS population_size FROM main.plp_evaluation_statistics where metric = 'populationSize' and evaluation in ('Train','Test','Validation') group by performance_id) AS nResult ON results.performance_id = nResult.performance_id
LEFT JOIN (SELECT performance_id, sum(value) AS outcome_count FROM main.plp_evaluation_statistics where metric = 'outcomeCount' and evaluation in ('Train','Test','Validation') group by performance_id) AS oResult ON results.performance_id = oResult.performance_id
LEFT JOIN (select performance_id, value from main.plp_EVALUATION_STATISTICS where EVALUATION in ('Test','Validation') and METRIC = 'brier score scaled') AS brier
on brier.performance_id = results.performance_id
LEFT JOIN (select performance_id, value from main.plp_EVALUATION_STATISTICS where EVALUATION in ('Test','Validation') and METRIC = 'Eavg') AS estat
on estat.performance_id = results.performance_id
LEFT JOIN (SELECT performance_id, value AS test_size FROM main.plp_evaluation_statistics where metric = 'populationSize' and evaluation in ('Test', 'Validation') ) AS nTest ON results.performance_id = nTest.performance_id
LEFT JOIN (SELECT performance_id, value AS auclb FROM main.plp_evaluation_statistics where metric = '95% lower AUROC' and evaluation in ('Test','Validation') ) AS auclbResult ON results.performance_id = auclbResult.performance_id
LEFT JOIN (SELECT performance_id, value AS aucub FROM main.plp_evaluation_statistics where metric = '95% upper AUROC' and evaluation in ('Test','Validation') ) AS aucubResult ON results.performance_id = aucubResult.performance_id
LEFT JOIN (SELECT performance_id, value AS calibration_in_large FROM main.plp_evaluation_statistics where metric = 'calibrationInLarge intercept' and evaluation in ('Test','Validation') ) AS calibration_in_large_result ON results.performance_id = calibration_in_large_result.performance_id
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getPredictionPerformances(...) at test-PredictionQueries.R:84:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-PredictionQueries.R:124:3'): getPredictionPerformances ─────────
Error in `value[[3L]](cond)`: SELECT distinct
design.MODEL_DESIGN_ID,
diagnostics.diagnostic_id,
database.DATABASE_NAME as development_DATABASE_NAME,
cohortT.COHORT_NAME development_target_name,
cohortO.COHORT_NAME development_outcome_name,
summary.PROBAST_ID,
summary.RESULT_VALUE
from
(select * from main.plp_DIAGNOSTICS
) as diagnostics
inner join
main.plp_MODEL_DESIGNS design
on diagnostics.MODEL_DESIGN_ID = design.MODEL_DESIGN_ID
inner join
main.plp_DIAGNOSTIC_SUMMARY summary
on diagnostics.DIAGNOSTIC_ID = summary.DIAGNOSTIC_ID
inner join
(select dd.database_id, md.cdm_source_abbreviation as database_name
from main.database_meta_data md inner join
main.plp_database_details dd
on md.database_id = dd.database_meta_data_id) as database
on database.database_id = diagnostics.database_id
inner join
main.plp_COHORTS cohortT
on cohortT.cohort_id = design.target_id
inner join
main.plp_COHORTS cohortO
on cohortO.cohort_id = design.outcome_id;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getPredictionDiagnostics(...) at test-PredictionQueries.R:124:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-PredictionQueries.R:159:3'): getPredictionPerformances ─────────
Error in `value[[3L]](cond)`: SELECT * FROM main.plp_evaluation_statistics
WHERE performance_id = 1;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getPredictionPerformanceTable(...) at test-PredictionQueries.R:159:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-PredictionQueries.R:178:3'): getPredictionDiagnosticTable ──────
Error in `value[[3L]](cond)`: SELECT * FROM main.plp_diagnostic_participants
WHERE diagnostic_id = 1;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getPredictionDiagnosticTable(...) at test-PredictionQueries.R:178:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-PredictionQueries.R:200:3'): getPredictionHyperParamSearch ─────
Error in `value[[3L]](cond)`: SELECT train_details
FROM main.plp_models
WHERE database_id = 1
and model_design_id = 1;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getPredictionHyperParamSearch(...) at test-PredictionQueries.R:200:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
── Error ('test-PredictionQueries.R:219:3'): getPredictionHyperParamSearch ─────
Error in `value[[3L]](cond)`: SELECT intercept
FROM main.plp_models
WHERE database_id = 1
and model_design_id = 1
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/tests/testthat/errorReportSql.txt
Backtrace:
▆
1. └─OhdsiReportGenerator::getPredictionIntercept(...) at test-PredictionQueries.R:219:3
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
[ FAIL 41 | WARN 10 | SKIP 1 | PASS 56 ]
Error: Test failures
In addition: Warning messages:
1: In utils::unzip(zipfile = system.file("exampledata", "results.sqlite.zip", :
write error in extracting from zip file
2: Couldn't set synchronous mode: database disk image is malformed
Use `synchronous` = NULL to turn off this warning.
Execution halted
Closing database connection
Flavor: r-release-macos-x86_64
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘ExampleCode.Rmd’ using knitr
Quitting from ExampleCode.Rmd:42-57 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `value[[3L]]()`:
! select *
from main.cg_cohort_definition
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/vign_test/OhdsiReportGenerator/vignettes/errorReportSql.txt
---
Backtrace:
▆
1. └─OhdsiReportGenerator::getCohortDefinitions(...)
2. └─connectionHandler$queryDb(...)
3. └─base::tryCatch(...)
4. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
5. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
6. └─value[[3L]](cond)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'ExampleCode.Rmd' failed with diagnostics:
select *
from main.cg_cohort_definition
;
Error in `.createErrorReport()`:
! Error executing SQL:
database disk image is malformed
An error report has been created at /Volumes/Builds/packages/big-sur-x86_64/results/4.5/OhdsiReportGenerator.Rcheck/vign_test/OhdsiReportGenerator/vignettes/errorReportSql.txt
--- failed re-building ‘ExampleCode.Rmd’
SUMMARY: processing the following file failed:
‘ExampleCode.Rmd’
Error: Vignette re-building failed.
Execution halted
Closing database connection
Flavor: r-release-macos-x86_64
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> test_check("OhdsiReportGenerator")
Loading required package: OhdsiReportGenerator
Connecting using SQLite driver
[ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-Helpers.R:89:1'
• skip prediction report due to odd linux error (1):
'test-PredictionReport.R:5:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Backwards.R:11:3'): generatePresentationMultiple old works ─────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-Backwards.R:11:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─OhdsiReportGenerator::generatePresentationMultiple(...)
7. └─OhdsiReportGenerator::generatePresentation(...)
8. └─quarto::quarto_render(...)
9. └─quarto:::find_quarto()
10. └─cli::cli_abort(quarto_not_found_msg)
11. └─rlang::abort(...)
── Error ('test-Generate.R:10:3'): generatePresentation ────────────────────────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. └─OhdsiReportGenerator::generatePresentation(...) at test-Generate.R:10:3
2. └─quarto::quarto_render(...)
3. └─quarto:::find_quarto()
4. └─cli::cli_abort(quarto_not_found_msg)
5. └─rlang::abort(...)
── Error ('test-Generate.R:61:3'): generateFullReport ──────────────────────────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. └─OhdsiReportGenerator::generateFullReport(...) at test-Generate.R:61:3
2. └─quarto::quarto_render(...)
3. └─quarto:::find_quarto()
4. └─cli::cli_abort(quarto_not_found_msg)
5. └─rlang::abort(...)
[ FAIL 3 | WARN 2 | SKIP 2 | PASS 417 ]
Error: Test failures
Execution halted
Closing database connection
Flavor: r-oldrel-macos-arm64
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [11s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> test_check("OhdsiReportGenerator")
Loading required package: OhdsiReportGenerator
Connecting using SQLite driver
[ FAIL 3 | WARN 4 | SKIP 2 | PASS 417 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-Helpers.R:89:1'
• skip prediction report due to odd linux error (1):
'test-PredictionReport.R:5:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Backwards.R:11:3'): generatePresentationMultiple old works ─────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-Backwards.R:11:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─OhdsiReportGenerator::generatePresentationMultiple(...)
7. └─OhdsiReportGenerator::generatePresentation(...)
8. └─quarto::quarto_render(...)
9. └─quarto:::find_quarto()
10. └─cli::cli_abort(quarto_not_found_msg)
11. └─rlang::abort(...)
── Error ('test-Generate.R:10:3'): generatePresentation ────────────────────────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. └─OhdsiReportGenerator::generatePresentation(...) at test-Generate.R:10:3
2. └─quarto::quarto_render(...)
3. └─quarto:::find_quarto()
4. └─cli::cli_abort(quarto_not_found_msg)
5. └─rlang::abort(...)
── Error ('test-Generate.R:61:3'): generateFullReport ──────────────────────────
Error in `find_quarto()`: Quarto command-line tools path not found!
Please make sure you have installed and added Quarto to your PATH or set the
QUARTO_PATH environment variable.
Backtrace:
▆
1. └─OhdsiReportGenerator::generateFullReport(...) at test-Generate.R:61:3
2. └─quarto::quarto_render(...)
3. └─quarto:::find_quarto()
4. └─cli::cli_abort(quarto_not_found_msg)
5. └─rlang::abort(...)
[ FAIL 3 | WARN 4 | SKIP 2 | PASS 417 ]
Error: Test failures
Execution halted
Closing database connection
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 13