Last updated on 2024-06-16 05:53:18 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| CodelistGenerator | 13 | ||
| CohortConstructor | 1 | 12 | |
| CohortSurvival | 13 | ||
| IncidencePrevalence | 2 | 1 | 10 |
Current CRAN status: OK: 13
Current CRAN status: ERROR: 1, OK: 12
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a00_introduction.Rmd’ using rmarkdown
--- finished re-building ‘a00_introduction.Rmd’
--- re-building ‘a01_building_base_cohorts.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 49-56 [unnamed-chunk-3] (a01_building_base_cohorts.Rmd)
Error: processing vignette 'a01_building_base_cohorts.Rmd' failed with diagnostics:
rapi_prepare: Failed to prepare query CREATE TABLE main.my_study_tmp_001_og_002_1718195530 AS SELECT
LHS.*,
requirements,
age_range,
sex_req,
min_prior_observation,
min_future_observation,
cohort_definition_id,
cohort_name,
min_age,
max_age
FROM (
SELECT
cohort_definition_id AS target_cohort_rand01,
subject_id,
cohort_start_date,
cohort_end_date,
date_of_birth,
CAST((date_0 + 18*INTERVAL'1 year') AS DATE) AS date_18,
CAST((date_0 + 66*INTERVAL'1 year') AS DATE) AS date_66
FROM main.my_study_date_0
) LHS
LEFT JOIN (
SELECT
requirements,
CASE WHEN ((target_cohort_rand01 IS NULL)) THEN cohort_definition_id WHEN NOT ((target_cohort_rand01 IS NULL)) THEN target_cohort_rand01 END AS target_cohort_rand01,
age_range,
sex AS sex_req,
min_prior_observation,
min_future_observation,
cohort_definition_id,
cohort_name,
min_age,
max_age
FROM main.my_study_tmp_001_og_001_1718195530
) RHS
ON (LHS.target_cohort_rand01 = RHS.target_cohort_rand01)
Error: Binder Error: Referenced column "date_0" not found in FROM clause!
Candidate bindings: "my_study_date_0.date_of_birth"
LINE 19: CAST((date_0 + 18*INTERVAL'1 year') AS DATE) AS date_18,
CAST((date_0 + 66*INTERVAL'1 year') AS DATE) AS date_66
FROM main.my_study_date_0
) LHS
LEFT JOIN (
SELECT
requirements,
CASE WHEN ((target_cohort_rand01 IS NULL)) THEN cohort_definition_id WHEN NOT ((target_cohort_rand01 IS NULL)) THEN target_cohort_rand01 END AS target_cohort_rand01,
age_range,
sex AS sex_req,
min_prior_observation,
min_future_observation,
cohort_definition_id,
cohort_name,
min_age,
max_age
FROM main.my_study_tmp_001_og_001_1718195530
) RHS
ON (LHS.target_cohort_rand01 = RHS.target_cohort_rand01)...
^
--- failed re-building ‘a01_building_base_cohorts.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a02_applying_cohort_restrictions.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 ‘a02_applying_cohort_restrictions.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a03_age_sex_matching.Rmd’ using rmarkdown
--- finished re-building ‘a03_age_sex_matching.Rmd’
--- re-building ‘a04_cohort_manipulations.Rmd’ using rmarkdown
--- finished re-building ‘a04_cohort_manipulations.Rmd’
SUMMARY: processing the following file failed:
‘a01_building_base_cohorts.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Current CRAN status: OK: 13
Current CRAN status: ERROR: 2, NOTE: 1, OK: 10
Version: 0.7.3
Check: package dependencies
Result: NOTE
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.7.3
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘a02_Creating_denominator_populations.Rmd’
...
> library(knitr)
> library(here)
here() starts at /private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/RtmpznQNvL/file15ec8360a31a6/vignettes
> knitr::include_graphics(here("vignettes/dpop1.png"))
When sourcing ‘a02_Creating_denominator_populations.R’:
Error: Cannot find the file(s): "/private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/RtmpznQNvL/file15ec8360a31a6/vignettes/vignettes/dpop1.png"
Execution halted
when running code in ‘a04_Calculating_prevalence.Rmd’
...
> library(knitr)
> library(IncidencePrevalence)
> knitr::include_graphics(here("vignettes/point_prev.png"))
When sourcing ‘a04_Calculating_prevalence.R’:
Error: Cannot find the file(s): "/private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/RtmpEmLnBG/file160656f4123b6/vignettes/vignettes/point_prev.png"
Execution halted
when running code in ‘a05_Calculating_incidence.Rmd’
...
> library(knitr)
> library(IncidencePrevalence)
> knitr::include_graphics(here("vignettes/inc_no_rep_no_washout.png"))
When sourcing ‘a05_Calculating_incidence.R’:
Error: Cannot find the file(s): "/private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/Rtmpv0UZlr/file160847db15be0/vignettes/vignettes/inc_no_rep_no_washout.png"
Execution halted
‘a01_Introduction_to_IncidencePrevalence.Rmd’ using ‘UTF-8’... [12s/13s] OK
‘a02_Creating_denominator_populations.Rmd’ using ‘UTF-8’... failed
‘a03_Creating_target_denominator_populations.Rmd’ using ‘UTF-8’... [11s/12s] OK
‘a04_Calculating_prevalence.Rmd’ using ‘UTF-8’... failed
‘a05_Calculating_incidence.Rmd’ using ‘UTF-8’... failed
‘a06_Plotting_options.Rmd’ using ‘UTF-8’... [10s/10s] OK
Flavor: r-oldrel-macos-arm64
Version: 0.7.3
Check: running R code from vignettes
Result: ERROR
Errors in running code in vignettes:
when running code in ‘a02_Creating_denominator_populations.Rmd’
...
> library(knitr)
> library(here)
here() starts at /private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/RtmpTA2wwO/file59a16e1560ab/vignettes
> knitr::include_graphics(here("vignettes/dpop1.png"))
When sourcing ‘a02_Creating_denominator_populations.R’:
Error: Cannot find the file(s): "/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/RtmpTA2wwO/file59a16e1560ab/vignettes/vignettes/dpop1.png"
Execution halted
when running code in ‘a04_Calculating_prevalence.Rmd’
...
> library(knitr)
> library(IncidencePrevalence)
> knitr::include_graphics(here("vignettes/point_prev.png"))
When sourcing ‘a04_Calculating_prevalence.R’:
Error: Cannot find the file(s): "/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/RtmprMr75N/file71f65a0e60bb/vignettes/vignettes/point_prev.png"
Execution halted
when running code in ‘a05_Calculating_incidence.Rmd’
...
> library(knitr)
> library(IncidencePrevalence)
> knitr::include_graphics(here("vignettes/inc_no_rep_no_washout.png"))
When sourcing ‘a05_Calculating_incidence.R’:
Error: Cannot find the file(s): "/private/var/folders/2b/t0kwbtmn3p7brv2mvx39c9cr0000gn/T/Rtmp2DhT4w/file736a13c0aa71/vignettes/vignettes/inc_no_rep_no_washout.png"
Execution halted
‘a01_Introduction_to_IncidencePrevalence.Rmd’ using ‘UTF-8’... [21s/28s] OK
‘a02_Creating_denominator_populations.Rmd’ using ‘UTF-8’... failed
‘a03_Creating_target_denominator_populations.Rmd’ using ‘UTF-8’... [21s/27s] OK
‘a04_Calculating_prevalence.Rmd’ using ‘UTF-8’... failed
‘a05_Calculating_incidence.Rmd’ using ‘UTF-8’... failed
‘a06_Plotting_options.Rmd’ using ‘UTF-8’... [17s/23s] OK
Flavor: r-oldrel-macos-x86_64