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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:igblastr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings igblastr_1.1.20.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/igblastr.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘igblastr/DESCRIPTION’ ... OK
* this is package ‘igblastr’ version ‘1.1.20’
* 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 ‘igblastr’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    extdata   8.1Mb
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘jsonlite:::simplifyDataFrame’
  See the note in ?`:::` about the use of this operator.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘igblastr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: install_custom_germline_db
> ### Title: Install a germline db from user-supplied gene allele sequences
> ### Aliases: install_custom_germline_db
> ### Keywords: utilities
> 
> ### ** Examples
> 
> if (!has_igblast()) install_igblast()
> 
> ## ---------------------------------------------------------------------
> ## A. WITH UNGAPPED GERMLINE V GENE ALLELE SEQUENCES
> ## ---------------------------------------------------------------------
> 
> ## In this admittedly artificial example, we're going to create and
> ## install a germline db from the gene allele sequences in built-in
> ## germline db _AIRR.human.IGH+IGK+IGL.202410. More precisely, we're
> ## going to:
> ##   1. Dump built-in germline db _AIRR.human.IGH+IGK+IGL.202410
> ##      in 7 FASTA files.
> ##   2. Use these FASTA files to create and install a new germline db.
> ##   3. Check that the new db contains the same sequences as the
> ##      original db.
> 
> ## --- 1. Dump _AIRR.human.IGH+IGK+IGL.202410 in 7 FASTA files ---
> 
> dump_germline_db <- function(db_name, destdir) {
+   for (region_type in c("V", "D", "J")) {
+     alleles <- load_germline_db(db_name, region_types=region_type)
+     for (locus in c("IGH", "IGK", "IGL")) {
+       loc_alleles <- alleles[grep(locus, names(alleles))]
+       if (length(loc_alleles) == 0L)
+         next
+       fasta_file <- paste0(locus, region_type, ".fasta")
+       writeXStringSet(loc_alleles, file.path(destdir, fasta_file))
+     }
+   }
+ }
> 
> db_name0 <- "_AIRR.human.IGH+IGK+IGL.202410"
> dir.create(exA_fasta_dir <- tempfile())
> 
> dump_germline_db(db_name0, exA_fasta_dir)
> 
> list.files(exA_fasta_dir)  # 7 FASTA files
[1] "IGHD.fasta" "IGHJ.fasta" "IGHV.fasta" "IGKJ.fasta" "IGKV.fasta"
[6] "IGLJ.fasta" "IGLV.fasta"
> 
> ## --- 2. Use FASTA files to install new germline db ---
> 
> exA_db_name <- "cus.exA.human.IGH+IGK+IGL"
> install_custom_germline_db(exA_db_name, exA_fasta_dir)
Error in .stop_on_existing_cached_germline_db(db_name) : 
  Germline db cus.exA.human.IGH+IGK+IGL is already installed in igblastr's
  persistent cache.
  Use list_germline_dbs() to list all the germline dbs currently installed in
  the cache (see '?list_germline_dbs').
  Use 'overwrite=TRUE' to reinstall.
Calls: install_custom_germline_db ... install_germline_db -> .stop_on_existing_cached_germline_db
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
igblastn            29.068  1.858  11.882
augment_germline_db  7.893  0.412   3.409
igbrowser            6.534  0.242   3.022
OAS-utils            0.277  0.024   5.599
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/igblastr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL igblastr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘igblastr’ ...
** this is package ‘igblastr’ version ‘1.1.20’
** using staged installation
** R
** 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 (igblastr)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-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)
> 
> is_bioc_build_machine <- isTRUE(as.logical(Sys.getenv("IS_BIOC_BUILD_MACHINE")))
> if (!is_bioc_build_machine) {
+     ## We temporarily set the cache to a different (non-persistent)
+     ## location to prevent the tests from messing up the real cache
+     ## located at 'R_user_dir("igblastr", "cache")'. Additionally, this
+     ## allows running the tests in different R sessions without the
+     ## concurrent runs stepping on each other's toes.
+     ## Make sure to do this BEFORE loading igblastr.
+     tmp_cache <- tempfile("igblastr_tests_cache_")
+     options(igblastr_cache=tmp_cache)
+ }
> 
> library(igblastr)
Loading required package: tibble
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: Seqinfo

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

igblastr tip: More than 30 days have passed since the last time you ran
  'update_live_igdata()'. Time to run it again!
> 
> if (!has_igblast()) install_igblast()
> test_check("igblastr")
 db_name                                 C
 _IMGT.human.IGH+IGK+IGL.202412         76
 _IMGT.human.TRA+TRB+TRG+TRD.202509     12
 _IMGT.mouse.IGH.202509                 56
 _IMGT.mouse.TRA+TRB+TRG+TRD.202509      9
 _IMGT.rabbit.IGH.202412                28
 _IMGT.rat.IGH.202508                   18
 _IMGT.rhesus_monkey.IGH+IGK+IGL.202509 40
 db_name                                 C  
 _IMGT.human.IGH+IGK+IGL.202412         76  
 _IMGT.human.TRA+TRB+TRG+TRD.202509     12  
 _IMGT.mouse.IGH.202509                 56  
 _IMGT.mouse.TRA+TRB+TRG+TRD.202509      9  
 _IMGT.rabbit.IGH.202412                28 *
 _IMGT.rat.IGH.202508                   18  
 _IMGT.rhesus_monkey.IGH+IGK+IGL.202509 40  
 db_name                                            V  D  J intdata  
 _AIRR.human.IGH+IGK+IGL.202309                   342 31 23    TRUE  
 _AIRR.human.IGH+IGK+IGL.202309.src               354 33 24   FALSE  
 _AIRR.human.IGH+IGK+IGL.202401                   342 31 23    TRUE  
 _AIRR.human.IGH+IGK+IGL.202401.src               354 33 24   FALSE  
 _AIRR.human.IGH+IGK+IGL.202410                   342 31 23    TRUE *
 _AIRR.human.IGH+IGK+IGL.202410.src               354 33 24   FALSE  
 _AIRR.mouse.CAST_EiJ.IGH+IGK+IGL.202501          184  9 22   FALSE  
 _AIRR.mouse.LEWES_EiJ.IGH+IGK+IGL.202501         169 11 22   FALSE  
 _AIRR.mouse.MSM_MsJ.IGH+IGK+IGL.202501           172  9 22   FALSE  
 _AIRR.mouse.NOD_ShiLtJ.IGH+IGK+IGL.202501        149  9 22   FALSE  
 _AIRR.mouse.PWD_PhJ.IGH+IGK+IGL.202501           184 10 22   FALSE  
 _AIRR.rhesus_monkey.IGH+IGK+IGL.202601          2294 72 39    TRUE  
 IMGT-202518-3.Homo_sapiens.IGH+IGK+IGL           698 47 34    TRUE  
 IMGT-202518-3.Homo_sapiens.TRA+TRB               266  3 87    TRUE  
 IMGT-202518-3.Homo_sapiens.TRA+TRB+TRG+TRD       291  6 97    TRUE  
 IMGT-202518-3.Mus_musculus.IGH+IGK+IGL           862 61 27    TRUE  
 IMGT-202518-3.Mus_musculus.TRA+TRB+TRG+TRD       387  5 96    TRUE  
 IMGT-202518-3.Sus_scrofa.IGH+IGK+IGL              65  5 19   FALSE  
 IMGT-202531-1.Mus_musculus.IGH+IGK+IGL           865 61 27    TRUE  
 IMGT-202531-1.Mus_musculus.TRA+TRB+TRG+TRD       387  5 96    TRUE  
 IMGT-202531-1.Oryctolagus_cuniculus.IGH+IGK+IGL  148 11 34    TRUE  
 IMGT-202531-1.Rattus_norvegicus.IGH+IGK+IGL      403 37 15    TRUE  
 cus.exA.human.IGH+IGK+IGL                        342 31 23   FALSE  
 cus.exB.human.IGH+IGK+IGL                        342 31 23   FALSE  
 cus.exC.human.IGH+IGK+IGL                        342 31 23    TRUE  
[ FAIL 0 | WARN 11 | SKIP 1 | PASS 477 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-precompiled-igblast-utils.R:1:1'

[ FAIL 0 | WARN 11 | SKIP 1 | PASS 477 ]
> 
> if (!is_bioc_build_machine) {
+     options(igblastr_cache=NULL)
+ }
> 
> 
> proc.time()
   user  system elapsed 
 43.779   8.817  55.178