* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OmopSketch.Rcheck’ * using R Under development (unstable) (2025-02-26 r87830) * 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-devel-linux-x86_64-debian-gcc/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 ... [0s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] 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 ... [7s/9s] OK * checking Rd files ... [0s/0s] 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/1s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [8s/6s] OK Running ‘testthat.R’ [7s/6s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [211s/285s] 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_bdz) AS counts_number_subjects FROM ( SELECT q01.*, 1.0 AS id_bdz 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_1740665509 ) 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_bdz) 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-devel-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-devel-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 = 19488 bytes Input file size = 20370 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14464 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 = 11760 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11715 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 = 11715 Output IDAT size = 11715 bytes (7773 bytes decrease) Output file size = 11793 bytes (8577 bytes = 42.11% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-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 = 40271 bytes Input file size = 40397 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 = 36430 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 = 36430 Output IDAT size = 36430 bytes (3841 bytes decrease) Output file size = 36508 bytes (3889 bytes = 9.63% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-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 = 43154 bytes Input file size = 44072 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38657 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 38258 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 = 38258 Output IDAT size = 38258 bytes (4896 bytes decrease) Output file size = 38336 bytes (5736 bytes = 13.02% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-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 = 185540 bytes Input file size = 185882 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 149910 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 = 149910 Output IDAT size = 149910 bytes (35630 bytes decrease) Output file size = 149988 bytes (35894 bytes = 19.31% 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/5s] OK * checking HTML version of manual ... [0s/1s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR