- using R version 4.4.1 (2024-06-14)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.3.0-1) 13.3.0
GNU Fortran (Debian 13.3.0-1) 13.3.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘CohortSymmetry/DESCRIPTION’ ... OK
- this is package ‘CohortSymmetry’ version ‘0.1.1’
- 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 serialization versions ... OK
- checking whether package ‘CohortSymmetry’ can be installed ... OK
See the install log 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 ... [0s/1s] OK
- checking whether the package can be unloaded cleanly ... [0s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/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 ... [8s/9s] OK
- checking Rd files ... [0s/1s] 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 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 ... [13m/15m] OK
Running ‘testthat.R’ [13m/15m]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [147s/181s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Introduction.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortSymmetry.Rcheck/vign_test/CohortSymmetry/vignettes/a01_Introduction_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14573 bytes
Input file size = 14663 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12889
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 = 12889
Output IDAT size = 12889 bytes (1684 bytes decrease)
Output file size = 12967 bytes (1696 bytes = 11.57% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CohortSymmetry.Rcheck/vign_test/CohortSymmetry/vignettes/a01_Introduction_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 252 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6402 bytes
Input file size = 7248 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4816
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 = 4816
Output IDAT size = 4816 bytes (1586 bytes decrease)
Output file size = 4894 bytes (2354 bytes = 32.48% decrease)
--- finished re-building ‘a01_Introduction.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a02_Generate_a_sequence_cohort_set.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 57-74 [unnamed-chunk-4] (a02_Generate_a_sequence_cohort_set.Rmd)
Error: processing vignette 'a02_Generate_a_sequence_cohort_set.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a02_Generate_a_sequence_cohort_set.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a03_Summarise_sequence_ratios.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 32-59 [unnamed-chunk-3] (a03_Summarise_sequence_ratios.Rmd)
Error: processing vignette 'a03_Summarise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a03_Summarise_sequence_ratios.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a04_Visualise_sequence_ratios.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 36-71 [unnamed-chunk-3] (a04_Visualise_sequence_ratios.Rmd)
Error: processing vignette 'a04_Visualise_sequence_ratios.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a04_Visualise_sequence_ratios.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a05_Summarise_temporal_symmetry.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 32-59 [unnamed-chunk-3] (a05_Summarise_temporal_symmetry.Rmd)
Error: processing vignette 'a05_Summarise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a05_Summarise_temporal_symmetry.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
--- re-building ‘a06_Visualise_temporal_symmetry.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 36-71 [unnamed-chunk-3] (a06_Visualise_temporal_symmetry.Rmd)
Error: processing vignette 'a06_Visualise_temporal_symmetry.Rmd' failed with diagnostics:
unused argument (withConceptDetails = FALSE)
--- failed re-building ‘a06_Visualise_temporal_symmetry.Rmd’
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
SUMMARY: processing the following files failed:
‘a02_Generate_a_sequence_cohort_set.Rmd’
‘a03_Summarise_sequence_ratios.Rmd’
‘a04_Visualise_sequence_ratios.Rmd’
‘a05_Summarise_temporal_symmetry.Rmd’
‘a06_Visualise_temporal_symmetry.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [5s/6s] OK
- checking HTML version of manual ... [0s/1s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR