##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:immLynx.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings immLynx_0.99.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/immLynx.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-25 00:21:37 UTC
* using option ‘--no-vignettes’
* checking for file ‘immLynx/DESCRIPTION’ ... OK
* this is package ‘immLynx’ version ‘0.99.4’
* 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 ... NOTE
Found the following hidden files and directories:
  .claude
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘immLynx’ can be installed ... NOTE
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Users/biocbuild/bbs-3.23-bioc/meat/immLynx.Rcheck/00install.out’ 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 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 OK
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/immLynx.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL immLynx
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘immLynx’ ...
** this is package ‘immLynx’ version ‘0.99.4’
** using non-staged installation via StagedInstall field
** 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
* DONE (immLynx)

R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.078   0.028   0.101 

R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(immLynx)
> 
> test_check("immLynx")
Testing associations for 2 metaclones and 1 HLA alleles
Testing associations for 2 metaclones and 2 HLA alleles
Testing associations for 2 metaclones and 2 HLA alleles
Testing associations for 2 metaclones and 1 HLA alleles
Testing associations for 2 metaclones and 1 HLA alleles
Testing associations for 2 metaclones and 1 HLA alleles
Testing associations for 3 metaclones and 1 HLA alleles
Testing associations for 1 metaclones and 1 HLA alleles
Extracting TCR sequences from object...
[ FAIL 0 | WARN 0 | SKIP 82 | PASS 332 ]

══ Skipped tests (82) ══════════════════════════════════════════════════════════
• Skipping Python tests on Bioconductor build machine (82):
  'test-calculate_helpers.R:30:3', 'test-calculate_helpers.R:45:3',
  'test-calculate_helpers.R:62:3', 'test-calculate_helpers.R:77:3',
  'test-calculate_helpers.R:104:3', 'test-calculate_helpers.R:134:3',
  'test-huggingModel.R:28:3', 'test-huggingModel.R:42:3',
  'test-huggingModel.R:52:3', 'test-huggingModel.R:64:3',
  'test-huggingModel.R:76:3', 'test-huggingModel.R:88:3',
  'test-huggingModel.R:100:3', 'test-huggingModel.R:108:3',
  'test-huggingModel.R:122:3', 'test-proteinEmbeddings.R:79:3',
  'test-proteinEmbeddings.R:97:3', 'test-proteinEmbeddings.R:114:3',
  'test-proteinEmbeddings.R:131:3', 'test-proteinEmbeddings.R:151:3',
  'test-proteinEmbeddings.R:175:3', 'test-proteinEmbeddings.R:191:3',
  'test-proteinEmbeddings.R:208:3', 'test-proteinEmbeddings.R:224:3',
  'test-proteinEmbeddings.R:242:3', 'test-proteinEmbeddings.R:259:3',
  'test-runClustTCR.R:65:3', 'test-runClustTCR.R:77:3',
  'test-runClustTCR.R:93:3', 'test-runClustTCR.R:105:3',
  'test-runClustTCR.R:118:3', 'test-runClustTCR.R:130:3',
  'test-runClustTCR.R:146:3', 'test-runClustTCR.R:158:3',
  'test-runEmbeddings.R:90:3', 'test-runEmbeddings.R:103:3',
  'test-runEmbeddings.R:122:3', 'test-runEmbeddings.R:136:3',
  'test-runEmbeddings.R:149:3', 'test-runEmbeddings.R:162:3',
  'test-runEmbeddings.R:174:3', 'test-runEmbeddings.R:188:3',
  'test-runEmbeddings.R:201:3', 'test-runEmbeddings.R:214:3',
  'test-runEmbeddings.R:230:3', 'test-runEmbeddings.R:245:3',
  'test-runEmbeddings.R:258:3', 'test-runEmbeddings.R:273:3',
  'test-runEmbeddings.R:288:3', 'test-runEmbeddings.R:301:3',
  'test-runEmbeddings.R:315:3', 'test-runMetaclonotypist.R:95:3',
  'test-runMetaclonotypist.R:108:3', 'test-runMetaclonotypist.R:124:3',
  'test-runMetaclonotypist.R:136:3', 'test-runMetaclonotypist.R:155:3',
  'test-runOLGA.R:85:3', 'test-runOLGA.R:98:3', 'test-runOLGA.R:115:3',
  'test-runOLGA.R:128:3', 'test-runOLGA.R:143:3', 'test-runOLGA.R:166:3',
  'test-runOLGA.R:175:3', 'test-runOLGA.R:188:3', 'test-runSoNNia.R:71:3',
  'test-runSoNNia.R:99:3', 'test-runSoNNia.R:122:3', 'test-runSoNNia.R:145:3',
  'test-runTCRdist.R:100:3', 'test-runTCRdist.R:114:3',
  'test-runTCRdist.R:127:3', 'test-runTCRdist.R:140:3',
  'test-runTCRdist.R:152:3', 'test-runTCRdist.R:170:3',
  'test-tokenizeSequences.R:42:3', 'test-tokenizeSequences.R:55:3',
  'test-tokenizeSequences.R:67:3', 'test-tokenizeSequences.R:79:3',
  'test-tokenizeSequences.R:91:3', 'test-tokenizeSequences.R:103:3',
  'test-tokenizeSequences.R:115:3', 'test-tokenizeSequences.R:131:3'

[ FAIL 0 | WARN 0 | SKIP 82 | PASS 332 ]
> 
> proc.time()
   user  system elapsed 
  4.814   0.353   5.198