- using R version 4.3.3 (2024-02-29)
- using platform: aarch64-apple-darwin20 (64-bit)
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.4
- 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 whether package ‘CohortSymmetry’ can be installed ... [1s/1s] 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 R 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 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 ... [1s/1s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... 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 ... [0s/0s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [68s/67s] OK
Running ‘testthat.R’ [68s/67s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking running R code from vignettes ... [39s/42s] ERROR
Errors in running code in vignettes:
when running code in ‘a01_Introduction.Rmd’
...
> library(here)
here() starts at /private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/Rtmp5b9ZoQ/file6f753fd27311/vignettes
> knitr::include_graphics(here("vignettes/workflow.png"))
When sourcing ‘a01_Introduction.R’:
Error: Cannot find the file(s): "/private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/Rtmp5b9ZoQ/file6f753fd27311/vignettes/vignettes/workflow.png"
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
when running code in ‘a02_Generate_a_sequence_cohort_set.Rmd’
...
> library(here)
here() starts at /private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/RtmpdLVgJ3/file6f7b29f563da/vignettes
> knitr::include_graphics(here("vignettes/1-NoRestrictions.png"))
When sourcing ‘a02_Generate_a_sequence_cohort_set.R’:
Error: Cannot find the file(s): "/private/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T/RtmpdLVgJ3/file6f7b29f563da/vignettes/vignettes/1-NoRestrictions.png"
Execution halted
Warning: Connection is garbage-collected, use dbDisconnect() to avoid this.
‘a01_Introduction.Rmd’ using ‘UTF-8’... failed
‘a02_Generate_a_sequence_cohort_set.Rmd’ using ‘UTF-8’... failed
‘a03_Summarise_sequence_ratios.Rmd’ using ‘UTF-8’... [8s/8s] OK
‘a04_Visualise_sequence_ratios.Rmd’ using ‘UTF-8’... [8s/9s] OK
‘a05_Summarise_temporal_symmetry.Rmd’ using ‘UTF-8’... [7s/8s] OK
‘a06_Visualise_temporal_symmetry.Rmd’ using ‘UTF-8’... [7s/8s] OK
- checking re-building of vignette outputs ... [70s/72s] OK
- checking PDF version of manual ... [2s/2s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '