* using log directory ‘/home/hornik/tmp/CRAN_special_noSuggests/OmopSketch.Rcheck’ * using R Under development (unstable) (2024-11-11 r87319) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (Debian 14.2.0-1) 14.2.0 GNU Fortran (Debian 14.2.0-1) 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 ‘0.1.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [6s/7s] OK * 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 serialization versions ... OK * checking whether package ‘OmopSketch’ can be installed ... [3s/4s] OK * 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 ... [0s/0s] OK * checking whether the package can be unloaded cleanly ... [0s/0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s/0s] 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 ... [5s/5s] 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 ... [5s/3s] OK Running ‘testthat.R’ [4s/3s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [69s/67s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘A-summarise_clinical_tables_records.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/CRAN_special_noSuggests/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-9-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 72804 bytes Input file size = 72978 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 72518 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 = 70118 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 = 70118 Output IDAT size = 70118 bytes (2686 bytes decrease) Output file size = 70196 bytes (2782 bytes = 3.81% decrease) ** Processing: /home/hornik/tmp/CRAN_special_noSuggests/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-10-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 67763 bytes Input file size = 67937 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66501 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 = 65026 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 = 65026 Output IDAT size = 65026 bytes (2737 bytes decrease) Output file size = 65104 bytes (2833 bytes = 4.17% decrease) ** Processing: /home/hornik/tmp/CRAN_special_noSuggests/OmopSketch.Rcheck/vign_test/OmopSketch/vignettes/A-summarise_clinical_tables_records_files/figure-html/unnamed-chunk-11-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 169898 bytes Input file size = 170216 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 141052 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 = 141052 Output IDAT size = 141052 bytes (28846 bytes decrease) Output file size = 141130 bytes (29086 bytes = 17.09% decrease) ** Processing: /home/hornik/tmp/CRAN_special_noSuggests/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 = 162533 bytes Input file size = 162839 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 = 158015 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 = 158015 Output IDAT size = 158015 bytes (4518 bytes decrease) Output file size = 158093 bytes (4746 bytes = 2.91% decrease) --- finished re-building ‘A-summarise_clinical_tables_records.Rmd’ --- re-building ‘B-summarise_concept_counts.Rmd’ using rmarkdown trying URL 'https://example-data.ohdsi.dev/GiBleed.zip' Content type 'application/zip' length 6754786 bytes (6.4 MB) ================================================== downloaded 6.4 MB Quitting from lines 37-51 [unnamed-chunk-2] (B-summarise_concept_counts.Rmd) Error: processing vignette 'B-summarise_concept_counts.Rmd' failed with diagnostics: there is no package called 'CodelistGenerator' --- failed re-building ‘B-summarise_concept_counts.Rmd’ SUMMARY: processing the following file failed: ‘B-summarise_concept_counts.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [3s/3s] OK * checking HTML version of manual ... [0s/0s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR