* using log directory ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/OmopSketch.Rcheck’
* using R version 4.4.3 RC (2025-02-20 r87839)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc-14 (Debian 14.2.0-16) 14.2.0
GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* 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 ... OK
See 'https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/OmopSketch-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [11s/14s] OK
* checking Rd files ... [0s/1s] 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 ... [1s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [10s/9s] OK
Running ‘testthat.R’ [10s/9s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [285s/390s] 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_gwk) AS counts_number_subjects
FROM (
SELECT q01.*, 1.0 AS id_gwk
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_1740763374
) 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_gwk) 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: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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 = 15522 bytes
Input file size = 16389 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11819
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 = 10600
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 10555
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 = 10555
Output IDAT size = 10555 bytes (4967 bytes decrease)
Output file size = 10633 bytes (5756 bytes = 35.12% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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 = 19281 bytes
Input file size = 20163 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14264
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 = 11607
zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11553
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 = 11553
Output IDAT size = 11553 bytes (7728 bytes decrease)
Output file size = 11631 bytes (8532 bytes = 42.32% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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 = 39870 bytes
Input file size = 39996 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 = 36055
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 = 36055
Output IDAT size = 36055 bytes (3815 bytes decrease)
Output file size = 36133 bytes (3863 bytes = 9.66% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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 = 41068 bytes
Input file size = 41986 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36532
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 36000
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 = 36000
Output IDAT size = 36000 bytes (5068 bytes decrease)
Output file size = 36078 bytes (5908 bytes = 14.07% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/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 = 185380 bytes
Input file size = 185722 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 147327
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 = 147327
Output IDAT size = 147327 bytes (38053 bytes decrease)
Output file size = 147405 bytes (38317 bytes = 20.63% 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 ... [4s/7s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR