• using R Under development (unstable) (2025-02-28 r87848)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 20.1.0-rc3     flang version 20.1.0-rc3
• 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/17s] OK See the install log for details.
• checking installed package size ... OK
• 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 ... [18s/24s] 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/18s] OK   Running ‘testthat.R’ [17s/17s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [8m/10m] 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_txc) AS counts_number_subjects FROM (   SELECT q01.*, 1.0 AS id_txc   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_1740783801     ) 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_txc) 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-clang/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-clang/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 = 18516 bytes Input file size = 19398 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14778   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 = 12230   zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 12128   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 = 12128 Output IDAT size = 12128 bytes (6388 bytes decrease) Output file size = 12206 bytes (7192 bytes = 37.08% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/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 = 40010 bytes Input file size = 40136 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 = 34980   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 = 34980 Output IDAT size = 34980 bytes (5030 bytes decrease) Output file size = 35058 bytes (5078 bytes = 12.65% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/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 = 41503 bytes Input file size = 42421 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36155   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 35623   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 = 35623 Output IDAT size = 35623 bytes (5880 bytes decrease) Output file size = 35701 bytes (6720 bytes = 15.84% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/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 = 183043 bytes Input file size = 183385 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 139576   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 = 139576 Output IDAT size = 139576 bytes (43467 bytes decrease) Output file size = 139654 bytes (43731 bytes = 23.85% 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 ... 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