• using R Under development (unstable) (2025-02-21 r87787)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 20.1.0-rc2     flang version 20.1.0-rc2
• 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/26s] 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 ... [19s/46s] 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 ... [16s/31s] OK   Running ‘testthat.R’ [16s/30s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [9m/23m] ERROR Error(s) in re-building vignettes: --- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-clang/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-9-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 55182 bytes Input file size = 56112 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48331   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 47971   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 = 47778   zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 47083   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 = 47083 Output IDAT size = 47083 bytes (8099 bytes decrease) Output file size = 47161 bytes (8951 bytes = 15.95% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-10-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 61172 bytes Input file size = 62114 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 54748   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 = 54189   zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 53691   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 = 53691 Output IDAT size = 53691 bytes (7481 bytes decrease) Output file size = 53769 bytes (8345 bytes = 13.43% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-11-1.png 1344x960 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 54349 bytes Input file size = 55279 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 48921   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 = 48921 Output IDAT size = 48921 bytes (5428 bytes decrease) Output file size = 48999 bytes (6280 bytes = 11.36% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-13-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 211407 bytes Input file size = 211785 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 171189   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 = 171189 Output IDAT size = 171189 bytes (40218 bytes decrease) Output file size = 171267 bytes (40518 bytes = 19.13% decrease) --- finished 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 = 18266 bytes Input file size = 19148 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14316   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 = 11602   zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 11506   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 = 11506 Output IDAT size = 11506 bytes (6760 bytes decrease) Output file size = 11584 bytes (7564 bytes = 39.50% 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 = 39923 bytes Input file size = 40049 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 = 34935   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 = 34935 Output IDAT size = 34935 bytes (4988 bytes decrease) Output file size = 35013 bytes (5036 bytes = 12.57% 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 = 41284 bytes Input file size = 42202 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35928   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 35370   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 = 35370 Output IDAT size = 35370 bytes (5914 bytes decrease) Output file size = 35448 bytes (6754 bytes = 16.00% 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 = 184514 bytes Input file size = 184856 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 142167   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 = 142167 Output IDAT size = 142167 bytes (42347 bytes decrease) Output file size = 142245 bytes (42611 bytes = 23.05% decrease) --- finished re-building ‘C-summarise_observation_period.Rmd’ SUMMARY: processing the following file failed:   ‘B-summarise_concept_set_counts.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [8s/18s] 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