* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘OmopSketch/DESCRIPTION’ ... OK
* this is package ‘OmopSketch’ version ‘0.2.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmopSketch’ can be installed ... [11s/35s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/OmopSketch-00install.html' for details.
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [16s/48s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [17s/34s] OK
Running ‘testthat.R’ [17s/32s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [8m/21m] ERROR
Error(s) in re-building vignettes:
--- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown
Quitting from lines 108-120 [unnamed-chunk-7] (A-summarise_clinical_tables_records.Rmd)
Error: processing vignette 'A-summarise_clinical_tables_records.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `purrr::map()`:
ℹ In index: 1.
Caused by error in `dplyr::collect()`:
! Failed to collect lazy table.
Caused by error in `dbSendQuery()`:
! rapi_prepare: Failed to prepare query SELECT
strata_id,
SUM(number_subjects * ".data".id_hnv) AS counts_number_subjects
FROM (
SELECT q01.*, 1.0 AS id_hnv
FROM (
SELECT 1 AS strata_id, q01.*
FROM (
SELECT
CASE WHEN (n = 0.0) THEN 0 WHEN NOT (n = 0.0) THEN 1 END AS number_subjects,
n
FROM tmp_020_og_030_1740777062
) q01
) q01
) q01
GROUP BY strata_id
Error: Binder Error: Referenced table ".data" not found!
Candidate tables: "q01"
LINE 3: SUM(number_subjects * ".data".id_hnv) AS counts_number_subjects
^
--- failed re-building ‘A-summarise_clinical_tables_records.Rmd’
--- re-building ‘B-summarise_concept_set_counts.Rmd’ using rmarkdown
Quitting from lines 17-26 [unnamed-chunk-1] (B-summarise_concept_set_counts.Rmd)
Error: processing vignette 'B-summarise_concept_set_counts.Rmd' failed with diagnostics:
could not find function "eunomia_is_available"
--- failed re-building ‘B-summarise_concept_set_counts.Rmd’
--- re-building ‘C-summarise_observation_period.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-7-1.png
1344x960 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15443 bytes
Input file size = 16310 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11852
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 11816
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 10566
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10475
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10475
Output IDAT size = 10475 bytes (4968 bytes decrease)
Output file size = 10553 bytes (5757 bytes = 35.30% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 18078 bytes
Input file size = 18960 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14224
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 11430
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11347
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11347
Output IDAT size = 11347 bytes (6731 bytes decrease)
Output file size = 11425 bytes (7535 bytes = 39.74% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-8-2.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 40170 bytes
Input file size = 40296 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 35109
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 35109
Output IDAT size = 35109 bytes (5061 bytes decrease)
Output file size = 35187 bytes (5109 bytes = 12.68% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-13-1.png
1344x960 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 40543 bytes
Input file size = 41449 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35240
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 34630
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 34630
Output IDAT size = 34630 bytes (5913 bytes decrease)
Output file size = 34708 bytes (6741 bytes = 16.26% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/C-summarise_observation_period_files/figure-html/unnamed-chunk-14-1.png
1344x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 189584 bytes
Input file size = 189938 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 146029
zc = 9 zm = 8 zs = 1 f = 0
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 146029
Output IDAT size = 146029 bytes (43555 bytes decrease)
Output file size = 146107 bytes (43831 bytes = 23.08% decrease)
--- finished re-building ‘C-summarise_observation_period.Rmd’
SUMMARY: processing the following files failed:
‘A-summarise_clinical_tables_records.Rmd’
‘B-summarise_concept_set_counts.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... [8s/19s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR