* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/Platypus.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘Platypus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Platypus’ version ‘3.5.0’
* 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 ‘Platypus’ can be installed ... [62s/95s] 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 ... [114s/155s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [13s/18s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/41s] ERROR
Running examples in ‘Platypus-Ex.R’ failed
The error most likely occurred in:

> ### Name: VDJ_clonotype
> ### Title: Platypus V3 clonotyping wrapper
> ### Aliases: VDJ_clonotype
> 
> ### ** Examples
> 
> reclonotyped_vgm <- VDJ_clonotype(VDJ=Platypus::small_vgm[[1]],
+ clone.strategy="cdr3.nt",
+ hierarchical = "none", global.clonotype = TRUE)
Clonotyping strategy: cdr3.nt
Processing sample 1 of 1
Backing up 10x default clonotyping in columns clonotype_id_10x and clonotype_frequency_10x before updating clonotype_id and clonotype_frequency columns
> 
> reclonotyped_vgm <- VDJ_clonotype(VDJ=Platypus::small_vgm[[1]],
+ clone.strategy="cdr3.homology", homology.threshold = 0.5,
+ hierarchical = "single.chains", global.clonotype = TRUE)
Clonotyping strategy: cdr3.homology
Hierarchical clonotyping is specifically designed to incorporate cells with abberand numbers of chains. Filtering for 1VDJ 1VJ chain thereby defeats its purpose. Function will continue without filtering.
Filtered out 1 cells containing more than one VDJ AND VJ chain or two VDJ chains, as these likely correspond to doublets
Processing sample 1 of 1
Error in loadNamespace(x) : there is no package called ‘stringdist’
Calls: VDJ_clonotype ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [7s/12s] OK
* checking PDF version of manual ... [12s/17s] 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
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/Platypus.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 8:58.07, 360.04 + 23.41