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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:igblastr.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings igblastr_0.99.11.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/igblastr.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'igblastr/DESCRIPTION' ... OK
* this is package 'igblastr' version '0.99.11'
* 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 whether package 'igblastr' 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
bcr_browser              3.34   0.32    8.09
outfmt7-utils            1.62   0.17    5.28
augment_germline_db      0.53   0.25   10.26
igblastn                 0.49   0.26   13.20
list_germline_dbs        0.30   0.17    8.70
install_IMGT_germline_db 0.23   0.11    9.91
* 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 NOTE
See
  'F:/biocbuild/bbs-3.22-bioc/meat/igblastr.Rcheck/00check.log'
for details.

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### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL igblastr
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'igblastr' ...
** this is package 'igblastr' version '0.99.11'
** 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 version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(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

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector
Loading required package: Seqinfo

Attaching package: 'Biostrings'

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

    strsplit

> 
> 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")'.
+     test_cache <- file.path(tempdir(), "igblastr_test_cache")
+     options(igblastr_cache=test_cache)
+ }
> 
> if (!has_igblast()) install_igblast()
> test_check("igblastr")
 db_name                         C
 _IMGT.human.IGH+IGK+IGL.202412 76
 _IMGT.mouse.IGH.202412         31
 _IMGT.rabbit.IGH.202412        28
 db_name                         C  
 _IMGT.human.IGH+IGK+IGL.202412 76  
 _IMGT.mouse.IGH.202412         31  
 _IMGT.rabbit.IGH.202412        28 *
 db_name                                     V  D  J  
 _AIRR.human.IGH+IGK+IGL.202501            354 33 24 *
 _AIRR.mouse.CAST_EiJ.IGH+IGK+IGL.202501   184  9 22  
 _AIRR.mouse.LEWES_EiJ.IGH+IGK+IGL.202501  169 11 22  
 _AIRR.mouse.MSM_MsJ.IGH+IGK+IGL.202501    172  9 22  
 _AIRR.mouse.NOD_ShiLtJ.IGH+IGK+IGL.202501 149  9 22  
 _AIRR.mouse.PWD_PhJ.IGH+IGK+IGL.202501    184 10 22  
 IMGT-202506-1.Homo_sapiens.IGH+IGK+IGL    700 47 34  
 IMGT-202506-1.Mus_musculus.IGH+IGK+IGL    862 61 27  
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 177 ]

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

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 177 ]
> 
> if (!is_bioc_build_machine) {
+     options(igblastr_cache=NULL)
+ }
> 
> proc.time()
   user  system elapsed 
   7.85    1.20   17.71