* using log directory ‘/srv/hornik/tmp/CRAN/PatientProfiles.Rcheck’ * using R Under development (unstable) (2024-04-10 r86396) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘PatientProfiles/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PatientProfiles’ version ‘0.8.0’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/7s] Note_to_CRAN_maintainers Maintainer: ‘Marti Catala ’ * 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 ‘PatientProfiles’ can be installed ... [4s/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 ... [0s/0s] 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 ... [0s/0s] OK * checking loading without being on the library search path ... [0s/0s] 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 ... [8s/8s] 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 ... [2s/2s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [550s/272s] OK Running ‘spelling.R’ [0s/0s] Running ‘testthat.R’ [550s/272s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [53s/52s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘cohort-intersect.Rmd’ using rmarkdown ** Processing: /srv/hornik/tmp/CRAN/PatientProfiles.Rcheck/vign_test/PatientProfiles/vignettes/cohort-intersect_files/figure-html/unnamed-chunk-5-1.png 1344x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16730 bytes Input file size = 16832 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 = 14956 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 = 14956 Output IDAT size = 14956 bytes (1774 bytes decrease) Output file size = 15034 bytes (1798 bytes = 10.68% decrease) Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. --- finished re-building ‘cohort-intersect.Rmd’ Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. --- re-building ‘concept-intersect.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 at lines 43-65 [unnamed-chunk-3] (concept-intersect.Rmd) Error: processing vignette 'concept-intersect.Rmd' failed with diagnostics: invalid non-character version specification 'x' (type: double) --- failed re-building ‘concept-intersect.Rmd’ Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. --- re-building ‘demographics.rmd’ using rmarkdown --- finished re-building ‘demographics.rmd’ Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. --- re-building ‘summarise.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 at lines 85-138 [unnamed-chunk-4] (summarise.Rmd) Error: processing vignette 'summarise.Rmd' failed with diagnostics: invalid non-character version specification 'x' (type: double) --- failed re-building ‘summarise.Rmd’ Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. --- re-building ‘table-intersect.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 at lines 42-71 [unnamed-chunk-4] (table-intersect.Rmd) Error: processing vignette 'table-intersect.Rmd' failed with diagnostics: invalid non-character version specification 'x' (type: double) --- failed re-building ‘table-intersect.Rmd’ Warning: Connection is garbage-collected, use dbDisconnect() to avoid this. SUMMARY: processing the following files failed: ‘concept-intersect.Rmd’ ‘summarise.Rmd’ ‘table-intersect.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [4s/4s] OK * checking HTML version of manual ... [1s/1s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR