Last updated on 2024-09-13 00:50:08 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.1 | 6.02 | 639.30 | 645.32 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.0 | 4.76 | 446.01 | 450.77 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.0 | 1141.89 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.2.0 | 1076.43 | OK | |||
| r-devel-windows-x86_64 | 1.2.0 | 13.00 | 447.00 | 460.00 | OK | |
| r-patched-linux-x86_64 | 1.1.1 | 7.32 | 603.09 | 610.41 | OK | |
| r-release-linux-x86_64 | 1.1.1 | 6.75 | 601.94 | 608.69 | OK | |
| r-release-macos-arm64 | 1.2.0 | 200.00 | OK | |||
| r-release-macos-x86_64 | 1.2.0 | 423.00 | OK | |||
| r-release-windows-x86_64 | 1.1.1 | 9.00 | 425.00 | 434.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.0 | 87.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 1.2.0 | 150.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 1.1.1 | 11.00 | 590.00 | 601.00 | OK |
Version: 1.2.0
Check: dependencies in R code
Result: WARN
Missing or unexported objects:
‘omopgenerics::assertCharacter’ ‘omopgenerics::assertChoice’
‘omopgenerics::assertClass’ ‘omopgenerics::assertList’
‘omopgenerics::assertNumeric’ ‘omopgenerics::assertTable’
‘omopgenerics::assertTrue’ ‘omopgenerics::uniqueId’
‘omopgenerics::validateCdmArgument’
‘omopgenerics::validateNameArgument’
‘omopgenerics::validateWindowArgument’
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [11s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Expected `... <- NULL` to run without any errors.
i Actually got a <simpleError> with text:
'assertList' is not an exported object from 'namespace:omopgenerics'
── Error ('test-summariseResult.R:623:3'): density works correctly ─────────────
Error in `eval(code, test_env)`: object 's' not found
Backtrace:
▆
1. ├─testthat::expect_false(...) at test-summariseResult.R:623:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─"density_x" %in% s$estimate_name[s$variable_name == "group"]
[ FAIL 22 | WARN 0 | SKIP 106 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 1.2.0
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘cohort-intersect.Rmd’
...
> library(ggplot2)
> cdm <- mockPatientProfiles(numberIndividuals = 1000)
When sourcing ‘cohort-intersect.R’:
Error: 'assertList' is not an exported object from 'namespace:omopgenerics'
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
when running code in ‘concept-intersect.Rmd’
...
- acetaminophen (7 codes)
> cdm$ankle_sprain %>% addConceptIntersectFlag(conceptSet = acetaminophen_cs,
+ indexDate = "cohort_start_date", window = c(0, 30)) %>% dplyr::gl .... [TRUNCATED]
When sourcing ‘concept-intersect.R’:
Error: 'assertChoice' is not an exported object from 'namespace:omopgenerics'
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
when running code in ‘demographics.rmd’
...
intersect, setdiff, setequal, union
> cdm <- mockPatientProfiles(numberIndividuals = 10000)
When sourcing ‘demographics.R’:
Error: 'assertList' is not an exported object from 'namespace:omopgenerics'
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
when running code in ‘summarise.Rmd’
...
> cdm <- generateConceptCohortSet(cdm = cdm, conceptSet = getDrugIngredientCodes(cdm = cdm,
+ name = c("morphine", "aspirin", "oxycodone")), name .... [TRUNCATED]
> x <- addTableIntersectDays(addTableIntersectDate(addConceptIntersectFlag(addCohortIntersectCount(addDemographics(cdm$my_cohort),
+ targetCohort .... [TRUNCATED]
When sourcing ‘summarise.R’:
Error: 'assertChoice' is not an exported object from 'namespace:omopgenerics'
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
when running code in ‘table-intersect.Rmd’
...
10 1 3076 1993-05-23 1993-06-27
# ℹ more rows
> tally(cdm$ankle_sprain %>% addTableIntersectFlag(tableName = "condition_occurrence",
+ window = c(-30, -1)))
When sourcing ‘table-intersect.R’:
Error: 'assertCharacter' is not an exported object from 'namespace:omopgenerics'
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
‘cohort-intersect.Rmd’ using ‘UTF-8’... failed
‘concept-intersect.Rmd’ using ‘UTF-8’... failed
‘demographics.rmd’ using ‘UTF-8’... failed
‘summarise.Rmd’ using ‘UTF-8’... failed
‘table-intersect.Rmd’ using ‘UTF-8’... failed
Flavor: r-oldrel-macos-arm64
Version: 1.2.0
Check: re-building of vignette outputs
Result: NOTE
Error(s) in re-building vignettes:
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown
Quitting from lines 23-38 [unnamed-chunk-1] (cohort-intersect.Rmd)
Error: processing vignette 'cohort-intersect.Rmd' failed with diagnostics:
'assertList' is not an exported object from 'namespace:omopgenerics'
--- failed re-building ‘cohort-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘concept-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 85-92 [unnamed-chunk-5] (concept-intersect.Rmd)
Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics:
'assertChoice' is not an exported object from 'namespace:omopgenerics'
--- failed re-building ‘concept-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘demographics.rmd’ using rmarkdown
Quitting from lines 20-28 [unnamed-chunk-1] (demographics.rmd)
Error: processing vignette 'demographics.rmd' failed with diagnostics:
'assertList' is not an exported object from 'namespace:omopgenerics'
--- failed re-building ‘demographics.rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘summarise.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 85-138 [unnamed-chunk-4] (summarise.Rmd)
Error: processing vignette 'summarise.Rmd' failed with diagnostics:
'assertChoice' is not an exported object from 'namespace:omopgenerics'
--- failed re-building ‘summarise.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘table-intersect.Rmd’ using rmarkdown
trying URL 'https://example-data.ohdsi.dev/GiBleed.zip'
Content type 'application/zip' length 6754786 bytes (6.4 MB)
==================================================
downloaded 6.4 MB
Quitting from lines 42-73 [unnamed-chunk-4] (table-intersect.Rmd)
Error: processing vignette 'table-intersect.Rmd' failed with diagnostics:
'assertCharacter' is not an exported object from 'namespace:omopgenerics'
--- failed re-building ‘table-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following files failed:
‘cohort-intersect.Rmd’ ‘concept-intersect.Rmd’ ‘demographics.rmd’
‘summarise.Rmd’ ‘table-intersect.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [16s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Expected `... <- NULL` to run without any errors.
i Actually got a <simpleError> with text:
'assertList' is not an exported object from 'namespace:omopgenerics'
── Error ('test-summariseResult.R:623:3'): density works correctly ─────────────
Error in `eval(code, test_env)`: object 's' not found
Backtrace:
▆
1. ├─testthat::expect_false(...) at test-summariseResult.R:623:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─"density_x" %in% s$estimate_name[s$variable_name == "group"]
[ FAIL 22 | WARN 0 | SKIP 106 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 1.2.0
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘cohort-intersect.Rmd’
...
> library(ggplot2)
> cdm <- mockPatientProfiles(numberIndividuals = 1000)
When sourcing ‘cohort-intersect.R’:
Error: 'assertList' is not an exported object from 'namespace:omopgenerics'
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
when running code in ‘concept-intersect.Rmd’
...
- acetaminophen (7 codes)
> cdm$ankle_sprain %>% addConceptIntersectFlag(conceptSet = acetaminophen_cs,
+ indexDate = "cohort_start_date", window = c(0, 30)) %>% dplyr::gl .... [TRUNCATED]
When sourcing ‘concept-intersect.R’:
Error: 'assertChoice' is not an exported object from 'namespace:omopgenerics'
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
when running code in ‘demographics.rmd’
...
intersect, setdiff, setequal, union
> cdm <- mockPatientProfiles(numberIndividuals = 10000)
When sourcing ‘demographics.R’:
Error: 'assertList' is not an exported object from 'namespace:omopgenerics'
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
when running code in ‘summarise.Rmd’
...
> cdm <- generateConceptCohortSet(cdm = cdm, conceptSet = getDrugIngredientCodes(cdm = cdm,
+ name = c("morphine", "aspirin", "oxycodone")), name .... [TRUNCATED]
> x <- addTableIntersectDays(addTableIntersectDate(addConceptIntersectFlag(addCohortIntersectCount(addDemographics(cdm$my_cohort),
+ targetCohort .... [TRUNCATED]
When sourcing ‘summarise.R’:
Error: 'assertChoice' is not an exported object from 'namespace:omopgenerics'
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
when running code in ‘table-intersect.Rmd’
...
10 1 4586 2003-08-14 2003-09-04
# ℹ more rows
> tally(cdm$ankle_sprain %>% addTableIntersectFlag(tableName = "condition_occurrence",
+ window = c(-30, -1)))
When sourcing ‘table-intersect.R’:
Error: 'assertCharacter' is not an exported object from 'namespace:omopgenerics'
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
‘cohort-intersect.Rmd’ using ‘UTF-8’... failed
‘concept-intersect.Rmd’ using ‘UTF-8’... failed
‘demographics.rmd’ using ‘UTF-8’... failed
‘summarise.Rmd’ using ‘UTF-8’... failed
‘table-intersect.Rmd’ using ‘UTF-8’... failed
Flavor: r-oldrel-macos-x86_64