Last updated on 2025-05-08 04:52:37 CEST.
| Package | ERROR | OK |
|---|---|---|
| Characterization | 2 | 11 |
| OhdsiReportGenerator | 6 | 7 |
| OhdsiShinyAppBuilder | 13 |
Current CRAN status: ERROR: 2, OK: 11
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [81s/130s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> test_check("Characterization")
Loading required package: Characterization
Removing values less than 5 from val
Removing values less than 50 from val
Removing values less than 5 from val
Removing values less than 5 from val and val2
Removing values less than 5 from val and val2
Removing values less than 5 from val3
Constructing features on server
Fetching data from server
Fetching data took 2.63 secs
Constructing features on server
Fetching data from server
Fetching data took 1.08 secs
Constructing during cohort covariates
|
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|================== | 25%
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|=================================== | 50%
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|==================================================== | 75%
|
|======================================================================| 100%
Censoring num_exposure_eras counts less than 9999
Censoring num_persons_exposed counts less than 9999
Censoring num_cases counts less than 9999
Censoring/removing dechallenge_attempt counts less than 9999
Censoring/removing DECHALLENGE FAIL or SUCCESS counts less than 9999
Censoring/removing rechallenge_attempt counts less than 9999
Censoring/removing rechallenge_fail or rechallenge_success counts less than 9999
Constructing features on server
Fetching data from server
Fetching data took 1.42 secs
<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.04 secs
Constructing during cohort covariates
|
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|
|================== | 25%
|
|=================================== | 50%
|
|==================================================== | 75%
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|======================================================================| 100%
<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.15 secs
<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.63 secs
Constructing during cohort covariates
|
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<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.05 secs
<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.13 secs
Constructing during cohort covariates
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<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Removing num_events less than 1e+06
Censoring num_exposure_eras counts less than 1e+06
Censoring num_persons_exposed counts less than 1e+06
Censoring num_cases counts less than 1e+06
Censoring/removing dechallenge_attempt counts less than 1e+06
Censoring/removing DECHALLENGE FAIL or SUCCESS counts less than 1e+06
Censoring/removing rechallenge_attempt counts less than 1e+06
Censoring/removing rechallenge_fail or rechallenge_success counts less than 1e+06
Constructing features on server
Fetching data from server
Fetching data took 1.09 secs
<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.04 secs
Constructing during cohort covariates
|
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<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Removing num_events less than 9999
Constructing features on server
Fetching data from server
Fetching data took 1.32 secs
<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.4 secs
Constructing during cohort covariates
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<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Creating characterization results tables
Migrating data set
Migrator using SQL files in Characterization
Creating migrations table
Migrations table created
Executing migration: Migration_1-v0_3_0_store_version.sql
Saving migration: Migration_1-v0_3_0_store_version.sql
Migration complete Migration_1-v0_3_0_store_version.sql
Executing migration: Migration_2-v2_1_1_mean_exposure_time_type.sql
Saving migration: Migration_2-v2_1_1_mean_exposure_time_type.sql
Migration complete Migration_2-v2_1_1_mean_exposure_time_type.sql
Closing database connection
Updating version number
- Preparing to upload rows 1 through 102
Uploading data took 4.4 secs
[ FAIL 12 | WARN 29 | SKIP 7 | PASS 180 ]
══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• not run locally (7): 'test-dbs.R:163:5', 'test-dbs.R:163:5',
'test-dbs.R:163:5', 'test-dbs.R:163:5', 'test-dbs.R:163:5',
'test-dbs.R:163:5', 'test-dbs.R:163:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-aggregateCovariate.R:391:3'): computeTargetAggregateCovariateAnalyses ──
Error in `connection_valid(dbObj@ptr)`: no slot of name "ptr" for this object of class "CovariateData"
Backtrace:
▆
1. └─Characterization:::computeTargetAggregateCovariateAnalyses(...) at test-aggregateCovariate.R:391:3
2. └─Characterization:::exportAndromedaToCsv(...)
3. ├─andromeda$analysisRef
4. └─andromeda$analysisRef
5. ├─x[[name]]
6. └─x[[name]]
7. └─Andromeda (local) .local(x, i, ...)
8. └─Andromeda:::checkIfValid(x)
9. └─Andromeda::isValidAndromeda(x)
10. ├─duckdb::dbIsValid(x)
11. └─duckdb::dbIsValid(x)
12. └─RSQLite:::connection_valid(dbObj@ptr)
── Error ('test-aggregateCovariate.R:473:3'): computeCaseAggregateCovariateAnalyses ──
Error in `connection_valid(dbObj@ptr)`: no slot of name "ptr" for this object of class "CovariateData"
Backtrace:
▆
1. └─Characterization:::computeCaseAggregateCovariateAnalyses(...) at test-aggregateCovariate.R:473:3
2. └─Characterization:::exportAndromedaToCsv(...)
3. ├─andromeda$analysisRef
4. └─andromeda$analysisRef
5. ├─x[[name]]
6. └─x[[name]]
7. └─Andromeda (local) .local(x, i, ...)
8. └─Andromeda:::checkIfValid(x)
9. └─Andromeda::isValidAndromeda(x)
10. ├─duckdb::dbIsValid(x)
11. └─duckdb::dbIsValid(x)
12. └─RSQLite:::connection_valid(dbObj@ptr)
── Error ('test-manualData.R:234:3'): manual data runCharacterizationAnalyses ──
Error in `file(file, "rt")`: cannot open the connection
Backtrace:
▆
1. └─utils::read.csv(file.path(tempdir(), "result", "c_cohort_counts.csv")) at test-manualData.R:234:3
2. └─utils::read.table(...)
3. └─base::file(file, "rt")
── Error ('test-manualData.R:496:3'): manual data checking exclude count works ──
Error in `file(file, "rt")`: cannot open the connection
Backtrace:
▆
1. └─utils::read.csv(file.path(tempdir(), "result2", "c_cohort_counts.csv")) at test-manualData.R:496:3
2. └─utils::read.table(...)
3. └─base::file(file, "rt")
── Failure ('test-runCharacterization.R:141:3'): runCharacterizationAnalyses ───
file.exists(file.path(tempFolder, "result", "c_cohort_details.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-runCharacterization.R:144:3'): runCharacterizationAnalyses ───
file.exists(file.path(tempFolder, "result", "c_settings.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-runCharacterization.R:147:3'): runCharacterizationAnalyses ───
file.exists(file.path(tempFolder, "result", "c_analysis_ref.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-runCharacterization.R:150:3'): runCharacterizationAnalyses ───
file.exists(file.path(tempFolder, "result", "c_covariate_ref.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-runCharacterization.R:153:3'): runCharacterizationAnalyses ───
file.exists(file.path(tempFolder, "result", "c_covariates.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-runCharacterization.R:156:3'): runCharacterizationAnalyses ───
file.exists(file.path(tempFolder, "result", "c_covariates_continuous.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-runCharacterization.R:403:3'): min cell count works ──────────
file.exists(file.path(tempFolder, "result_mincell", "c_cohort_counts.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Error ('test-runCharacterization.R:406:3'): min cell count works ────────────
Error: '/tmp/RtmpGWAneY/working_dir/RtmpNUifKL/CharacterizationMin5855d761c12d4/result_mincell/c_cohort_counts.csv' does not exist.
Backtrace:
▆
1. ├─readr::read_csv(file.path(tempFolder, "result_mincell", "c_cohort_counts.csv")) at test-runCharacterization.R:406:3
2. │ └─vroom::vroom(...)
3. │ └─vroom:::vroom_(...)
4. └─vroom (local) `<fn>`("/tmp/RtmpGWAneY/working_dir/RtmpNUifKL/CharacterizationMin5855d761c12d4/result_mincell/c_cohort_counts.csv")
5. └─vroom:::check_path(path)
[ FAIL 12 | WARN 29 | SKIP 7 | PASS 180 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.1.3
Check: tests
Result: ERROR
Running ‘testthat.R’ [81s/117s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> test_check("Characterization")
Loading required package: Characterization
Removing values less than 5 from val
Removing values less than 50 from val
Removing values less than 5 from val
Removing values less than 5 from val and val2
Removing values less than 5 from val and val2
Removing values less than 5 from val3
Constructing features on server
Fetching data from server
Fetching data took 1.56 secs
Constructing features on server
Fetching data from server
Fetching data took 1.19 secs
Constructing during cohort covariates
|
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|================== | 25%
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|=================================== | 50%
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|==================================================== | 75%
|
|======================================================================| 100%
Censoring num_exposure_eras counts less than 9999
Censoring num_persons_exposed counts less than 9999
Censoring num_cases counts less than 9999
Censoring/removing dechallenge_attempt counts less than 9999
Censoring/removing DECHALLENGE FAIL or SUCCESS counts less than 9999
Censoring/removing rechallenge_attempt counts less than 9999
Censoring/removing rechallenge_fail or rechallenge_success counts less than 9999
Constructing features on server
Fetching data from server
Fetching data took 1.09 secs
<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.05 secs
Constructing during cohort covariates
|
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|======================================================================| 100%
<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.34 secs
<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.15 secs
Constructing during cohort covariates
|
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<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.07 secs
<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.22 secs
Constructing during cohort covariates
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<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Removing num_events less than 1e+06
Censoring num_exposure_eras counts less than 1e+06
Censoring num_persons_exposed counts less than 1e+06
Censoring num_cases counts less than 1e+06
Censoring/removing dechallenge_attempt counts less than 1e+06
Censoring/removing DECHALLENGE FAIL or SUCCESS counts less than 1e+06
Censoring/removing rechallenge_attempt counts less than 1e+06
Censoring/removing rechallenge_fail or rechallenge_success counts less than 1e+06
Constructing features on server
Fetching data from server
Fetching data took 1.5 secs
<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.06 secs
Constructing during cohort covariates
|
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<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Removing num_events less than 9999
Constructing features on server
Fetching data from server
Fetching data took 1.13 secs
<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Constructing features on server
Fetching data from server
Fetching data took 1.52 secs
Constructing during cohort covariates
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<simpleError in connection_valid(dbObj@ptr): no slot of name "ptr" for this object of class "CovariateData">
Creating characterization results tables
Migrating data set
Migrator using SQL files in Characterization
Creating migrations table
Migrations table created
Executing migration: Migration_1-v0_3_0_store_version.sql
Saving migration: Migration_1-v0_3_0_store_version.sql
Migration complete Migration_1-v0_3_0_store_version.sql
Executing migration: Migration_2-v2_1_1_mean_exposure_time_type.sql
Saving migration: Migration_2-v2_1_1_mean_exposure_time_type.sql
Migration complete Migration_2-v2_1_1_mean_exposure_time_type.sql
Closing database connection
Updating version number
- Preparing to upload rows 1 through 102
Uploading data took 3.79 secs
[ FAIL 12 | WARN 29 | SKIP 7 | PASS 180 ]
══ Skipped tests (7) ═══════════════════════════════════════════════════════════
• not run locally (7): 'test-dbs.R:163:5', 'test-dbs.R:163:5',
'test-dbs.R:163:5', 'test-dbs.R:163:5', 'test-dbs.R:163:5',
'test-dbs.R:163:5', 'test-dbs.R:163:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-aggregateCovariate.R:391:3'): computeTargetAggregateCovariateAnalyses ──
Error in `connection_valid(dbObj@ptr)`: no slot of name "ptr" for this object of class "CovariateData"
Backtrace:
▆
1. └─Characterization:::computeTargetAggregateCovariateAnalyses(...) at test-aggregateCovariate.R:391:3
2. └─Characterization:::exportAndromedaToCsv(...)
3. ├─andromeda$analysisRef
4. └─andromeda$analysisRef
5. ├─x[[name]]
6. └─x[[name]]
7. └─Andromeda (local) .local(x, i, ...)
8. └─Andromeda:::checkIfValid(x)
9. └─Andromeda::isValidAndromeda(x)
10. ├─duckdb::dbIsValid(x)
11. └─duckdb::dbIsValid(x)
12. └─RSQLite:::connection_valid(dbObj@ptr)
── Error ('test-aggregateCovariate.R:473:3'): computeCaseAggregateCovariateAnalyses ──
Error in `connection_valid(dbObj@ptr)`: no slot of name "ptr" for this object of class "CovariateData"
Backtrace:
▆
1. └─Characterization:::computeCaseAggregateCovariateAnalyses(...) at test-aggregateCovariate.R:473:3
2. └─Characterization:::exportAndromedaToCsv(...)
3. ├─andromeda$analysisRef
4. └─andromeda$analysisRef
5. ├─x[[name]]
6. └─x[[name]]
7. └─Andromeda (local) .local(x, i, ...)
8. └─Andromeda:::checkIfValid(x)
9. └─Andromeda::isValidAndromeda(x)
10. ├─duckdb::dbIsValid(x)
11. └─duckdb::dbIsValid(x)
12. └─RSQLite:::connection_valid(dbObj@ptr)
── Error ('test-manualData.R:234:3'): manual data runCharacterizationAnalyses ──
Error in `file(file, "rt")`: cannot open the connection
Backtrace:
▆
1. └─utils::read.csv(file.path(tempdir(), "result", "c_cohort_counts.csv")) at test-manualData.R:234:3
2. └─utils::read.table(...)
3. └─base::file(file, "rt")
── Error ('test-manualData.R:496:3'): manual data checking exclude count works ──
Error in `file(file, "rt")`: cannot open the connection
Backtrace:
▆
1. └─utils::read.csv(file.path(tempdir(), "result2", "c_cohort_counts.csv")) at test-manualData.R:496:3
2. └─utils::read.table(...)
3. └─base::file(file, "rt")
── Failure ('test-runCharacterization.R:141:3'): runCharacterizationAnalyses ───
file.exists(file.path(tempFolder, "result", "c_cohort_details.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-runCharacterization.R:144:3'): runCharacterizationAnalyses ───
file.exists(file.path(tempFolder, "result", "c_settings.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-runCharacterization.R:147:3'): runCharacterizationAnalyses ───
file.exists(file.path(tempFolder, "result", "c_analysis_ref.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-runCharacterization.R:150:3'): runCharacterizationAnalyses ───
file.exists(file.path(tempFolder, "result", "c_covariate_ref.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-runCharacterization.R:153:3'): runCharacterizationAnalyses ───
file.exists(file.path(tempFolder, "result", "c_covariates.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-runCharacterization.R:156:3'): runCharacterizationAnalyses ───
file.exists(file.path(tempFolder, "result", "c_covariates_continuous.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test-runCharacterization.R:403:3'): min cell count works ──────────
file.exists(file.path(tempFolder, "result_mincell", "c_cohort_counts.csv")) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Error ('test-runCharacterization.R:406:3'): min cell count works ────────────
Error: '/tmp/RtmppJHewR/working_dir/RtmpkH79Di/CharacterizationMin1969082448b732/result_mincell/c_cohort_counts.csv' does not exist.
Backtrace:
▆
1. ├─readr::read_csv(file.path(tempFolder, "result_mincell", "c_cohort_counts.csv")) at test-runCharacterization.R:406:3
2. │ └─vroom::vroom(...)
3. │ └─vroom:::vroom_(...)
4. └─vroom (local) `<fn>`("/tmp/RtmppJHewR/working_dir/RtmpkH79Di/CharacterizationMin1969082448b732/result_mincell/c_cohort_counts.csv")
5. └─vroom:::check_path(path)
[ FAIL 12 | WARN 29 | SKIP 7 | PASS 180 ]
Error: Test failures
In addition: Warning message:
call dbDisconnect() when finished working with a connection
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: ERROR: 6, OK: 7
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [20s/19s]
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-devel-linux-x86_64-debian-gcc
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [28s/31s]
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-patched-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
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [8s/6s]
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-x86_64
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [9s/7s]
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-x86_64
Current CRAN status: OK: 13
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