Last updated on 2024-08-25 03:49:16 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.1.1 | 7.30 | 637.60 | 644.90 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.1.1 | 5.27 | 429.80 | 435.07 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.1.1 | 1075.52 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.1.1 | 1016.54 | OK | |||
| r-devel-windows-x86_64 | 1.1.1 | 9.00 | 418.00 | 427.00 | OK | |
| r-patched-linux-x86_64 | 1.1.1 | 7.57 | 595.07 | 602.64 | OK | |
| r-release-linux-x86_64 | 1.1.1 | 6.52 | 595.02 | 601.54 | OK | |
| r-release-macos-arm64 | 1.1.1 | 227.00 | OK | |||
| r-release-macos-x86_64 | 1.1.1 | 526.00 | OK | |||
| r-release-windows-x86_64 | 1.1.1 | 9.00 | 424.00 | 433.00 | OK | |
| r-oldrel-macos-arm64 | 1.1.1 | 461.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 1.1.1 | 349.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 1.1.1 | 12.00 | 594.00 | 606.00 | OK |
Version: 1.1.1
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘concept-intersect.Rmd’
...
> ggplot(dplyr::bind_rows(dplyr::mutate(dplyr::arrange(dplyr::collect(dplyr::tally(dplyr::group_by(addCohortIntersectCount(cdm$ankle_sprain,
+ ta .... [TRUNCATED]
When sourcing ‘concept-intersect.R’:
Error: ℹ In argument: `161_acetaminophen_minf_to_inf`
Caused by error:
! Object `161_acetaminophen_minf_to_inf` not found.
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
‘cohort-intersect.Rmd’ using ‘UTF-8’... [21s/25s] OK
‘concept-intersect.Rmd’ using ‘UTF-8’... failed
‘demographics.rmd’ using ‘UTF-8’... [18s/22s] OK
‘summarise.Rmd’ using ‘UTF-8’... [25s/45s] OK
‘table-intersect.Rmd’ using ‘UTF-8’... [17s/26s] OK
Flavor: r-oldrel-macos-arm64
Version: 1.1.1
Check: re-building of vignette outputs
Result: NOTE
Error(s) in re-building vignettes:
--- re-building ‘cohort-intersect.Rmd’ using rmarkdown
--- finished re-building ‘cohort-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
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 185-229 [unnamed-chunk-11] (concept-intersect.Rmd)
Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics:
ℹ In argument: `161_acetaminophen_minf_to_inf`
Caused by error:
! Object `161_acetaminophen_minf_to_inf` not found.
--- failed re-building ‘concept-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘demographics.rmd’ using rmarkdown
--- finished 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
--- finished 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
--- finished re-building ‘table-intersect.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following file failed:
‘concept-intersect.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 1.1.1
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘concept-intersect.Rmd’
...
> library(ggplot2)
> con <- DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir())
Creating CDM database /var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T//RtmpIShcA2/GiBleed_5.3.zip
When sourcing ‘concept-intersect.R’:
Error: rapi_execute: Failed to run query
Error: FATAL Error: Failed to create checkpoint because of error: Could not write file "/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/RtmpIShcA2/GiBleed_5.3_1.0.duckdb": No space left on device
Execution halted
Warning: Database is garbage-collected, use dbConnect(duckdb()) with dbDisconnect(), or duckdb::duckdb_shutdown(drv) to avoid this.
when running code in ‘summarise.Rmd’
...
> cdm <- cdmFromCon(con = dbConnect(duckdb(), eunomia_dir()),
+ cdmSchema = "main", writeSchema = "main")
Creating CDM database /var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T//RtmpmGM4m8/GiBleed_5.3.zip
Warning in utils::unzip(zipfile = archiveLocation, exdir = tempFileLocation) :
write error in extracting from zip file
When sourcing ‘summarise.R’:
Error: error in evaluating the argument 'dbObj' in selecting a method for function 'dbIsValid': error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': rapi_startup: Failed to open database: {"exception_type":"IO","exception_message":"Could not write file \"/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/RtmpmGM4m8/GiBleed_5.3_1.0.duckdb\": No space left on device","errno":"28"}
Execution halted
Warning: Database is garbage-collected, use dbConnect(duckdb()) with dbDisconnect(), or duckdb::duckdb_shutdown(drv) to avoid this.
when running code in ‘table-intersect.Rmd’
...
> con <- DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir())
Creating CDM database /var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T//RtmpIaAKUG/GiBleed_5.3.zip
Warning in utils::unzip(zipfile = archiveLocation, exdir = tempFileLocation) :
write error in extracting from zip file
When sourcing ‘table-intersect.R’:
Error: error in evaluating the argument 'drv' in selecting a method for function 'dbConnect': rapi_startup: Failed to open database: {"exception_type":"IO","exception_message":"Could not write file \"/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/RtmpIaAKUG/GiBleed_5.3_1.0.duckdb\": No space left on device","errno":"28"}
Execution halted
Warning: Database is garbage-collected, use dbConnect(duckdb()) with dbDisconnect(), or duckdb::duckdb_shutdown(drv) to avoid this.
‘cohort-intersect.Rmd’ using ‘UTF-8’... [35s/70s] OK
‘concept-intersect.Rmd’ using ‘UTF-8’... failed
‘demographics.rmd’ using ‘UTF-8’... [32s/49s] OK
‘summarise.Rmd’ using ‘UTF-8’... failed
‘table-intersect.Rmd’ using ‘UTF-8’... failed
Flavor: r-oldrel-macos-x86_64
Version: 1.1.1
Check: re-building of vignette outputs
Result: NOTE
Error(s) in re-building vignettes:
...
Flavor: r-oldrel-macos-x86_64
Version: 1.1.1
Check: PDF version of manual
Result: ERROR
Rd conversion errors:
Flavor: r-oldrel-macos-x86_64