• 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 the install log 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
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• checking for missing documentation entries ... OK
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• 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