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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClustIRR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClustIRR_1.3.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ClustIRR.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClustIRR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClustIRR’ version ‘1.3.7’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ClustIRR’ can be installed ... OK
* 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 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 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 ... NOTE
check_custom_db: no visible binding for global variable ‘tcr3d’
Undefined global functions or variables:
  tcr3d
* checking Rd files ... NOTE
checkRd: (-1) clust_irr-class.Rd:30-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clust_irr-class.Rd:81: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘mcpas’ ‘tcr3d’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
  Warning: found non-ASCII strings
  'LGTGNQFYF<a0>' in object 'mcpas'
  'YQLTF<a0>' in object 'mcpas'
  'PYSSASKIIF<a0>' in object 'mcpas'
  'STSFGSNYGQNFVF<a0>' in object 'mcpas'
  'Inflammatory bowel disease (IBD)<a0>' in object 'mcpas'
  'Flagellin<a0>' in object 'mcpas'
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ClustIRR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clust_irr-class
> ### Title: clust_irr class
> ### Aliases: clust_irr class:clust_irr clust_irr-class
> ###   get_clustirr_clust,clust_irr-method
> ###   get_clustirr_inputs,clust_irr-method get_clustirr_clust
> ###   get_clustirr_inputs
> 
> ### ** Examples
> 
> # inputs
> data("CDR3ab")
> s <- data.frame(CDR3b = CDR3ab[1:1000, "CDR3b"])
> r <- data.frame(CDR3b = CDR3ab[1:5000, "CDR3b"])
> 
> # controls: auxiliary inputs
> control <- list(global_smart = TRUE,
+                 global_max_hdist = 1,
+                 local_max_fdr = 0.05,
+                 local_min_ove = 2,
+                 local_min_o = 1,
+                 trim_flank_aa = 3,
+                 global_pairs = NULL,
+                 low_mem = FALSE)
> 
> # clust_irr S4 object generated by function cluster_irr
> clust_irr_output <- cluster_irr(s = s, r = r,ks = 4,cores = 1,control = control)


Analyze database: 100.0% (1000.0)                    
  Index database: 100.0% (1000.0)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
    Read queries: 100.0% (20 kB)                    
 Search database: 4.0% (40.0)                    
 Search database: 48.8% (488.0)                    
 Search database: 93.6% (936.0)                    
 Search database: 100.0% (1000.0)                    
      Write hits: 100.0% (1360.0)                    
Warning in data("BLOSUM62", envir = data_env, package = "Biostrings") :
  data set ‘BLOSUM62’ not found
Warning in .call_fun_in_pwalign("stringDist", ...) :
  stringDist() has moved to the pwalign package. Please call
  pwalign::stringDist() to get rid of this warning.
Error in XStringSet.stringDist(x = BStringSet(x), method = method, ignoreCase = ignoreCase,  : 
  'substitutionMatrix' must be a numeric matrix
Calls: cluster_irr ... <Anonymous> -> <Anonymous> -> .local -> XStringSet.stringDist
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      Read queries: 100.0% (10231.0 Bytes)                    
   Search database: 23.2% (116.0)                    
   Search database: 100.0% (500.0)                    
        Write hits: 100.0% (600.0)                    
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 87 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-cluster.R:443:5'): cluster works with correct input and global smart mode ──
  Expected `cluster_irr(s = s, r = r, ks = ks, cores = cores, control = control_input_tmp)` to run without any errors.
  ℹ Actually got a <simpleError> with text:
    'substitutionMatrix' must be a numeric matrix
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 87 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/ClustIRR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ClustIRR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘ClustIRR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ClustIRR)

R version 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ClustIRR)
> test_check("ClustIRR")


Analyze database: 100.0% (500.0)                    
  Index database: 100.0% (500.0)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
 Search database: 23.2% (116.0)                    
 Search database: 100.0% (500.0)                    
      Write hits: 100.0% (600.0)                    
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 87 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-cluster.R:443:5'): cluster works with correct input and global smart mode ──
Expected `cluster_irr(s = s, r = r, ks = ks, cores = cores, control = control_input_tmp)` to run without any errors.
ℹ Actually got a <simpleError> with text:
  'substitutionMatrix' must be a numeric matrix

[ FAIL 1 | WARN 2 | SKIP 0 | PASS 87 ]
Error: Test failures
Execution halted