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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:igblastr.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings igblastr_1.1.29.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/igblastr.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-27 04:33:25 UTC
* checking for file ‘igblastr/DESCRIPTION’ ... OK
* this is package ‘igblastr’ version ‘1.1.29’
* 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 10.3Mb
  sub-directories of 1Mb or more:
    extdata   9.5Mb
* 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 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: OAS-utils
> ### Title: Download and manipulate OAS data
> ### Aliases: OAS-utils OAS_utils read_OAS_csv_metadata read_OAS_csv
> ###   extract_sequences_from_paired_OAS_df list_paired_OAS_studies
> ###   list_paired_OAS_units download_paired_OAS_units
> ###   extract_metadata_from_OAS_units
> ###   extract_sequences_from_paired_OAS_units OAS_is_up
> ### Keywords: utilities
> 
> ### ** Examples
> 
> if (OAS_is_up()) {
+   list_paired_OAS_studies()
+ 
+   list_paired_OAS_units("Eccles_2020")
+ 
+   ## Import all the pairs of antibody sequences from the Eccles_2020 study:
+ 
+   download_dir <- tempdir()
+   download_paired_OAS_units("Eccles_2020", destdir=download_dir)
+ 
+   metadata <- extract_metadata_from_OAS_units(download_dir)
+   metadata  # data.frame with 1 row per unit file
+ 
+   sequences <- extract_sequences_from_paired_OAS_units(download_dir)
+   sequences  # DNAStringSet object
+ 
+   ## Odd indices correspond to heavy chain sequences and even indices
+   ## to light chain sequences:
+ 
+   head(names(sequences))
+ 
+   sequences[1:2]  # 1st pair
+   sequences[3:4]  # 2nd pair
+   sequences[5:6]  # 3rd pair
+   # etc...
+ }
Error in getUrlContent(url, type = "text", encoding = "UTF-8", ...) : 
  Bad Gateway (HTTP 502).
Calls: list_paired_OAS_studies ... scrape_html_dir_index -> getUrlContent -> stop_for_status
Execution halted
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/igblastr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL igblastr
###
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘igblastr’ ...
** this is package ‘igblastr’ version ‘1.1.29’
** 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 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

> 
> if (!has_igblast()) install_igblast()
> test_check("igblastr")
trying URL 'https://www.imgt.org/download/V-QUEST/archives/IMGT_vquest_release202530-1.zip'
Content type 'application/zip' length 1146132 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

 db_name                                 C
 _IMGT.human.IGH+IGK+IGL.202412         76
 _IMGT.human.TRA+TRB+TRG+TRD.202509     12
 _IMGT.mouse.IGH.202509                 55
 _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                 55  
 _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 auxdata  
 _OGRDB.human.IGH+IGK+IGL.202410                  342 31 23    TRUE    TRUE *
 _OGRDB.human.IGH+IGK+IGL.202410.src              354 33 24    TRUE    TRUE  
 _OGRDB.mouse.CAST_EiJ.IGH+IGK+IGL.202603         184  9 22    TRUE    TRUE  
 _OGRDB.mouse.LEWES_EiJ.IGH+IGK+IGL.202603        169 11 22    TRUE    TRUE  
 _OGRDB.mouse.MSM_MsJ.IGH+IGK+IGL.202603          172  9 22    TRUE    TRUE  
 _OGRDB.mouse.NOD_ShiLtJ.IGH+IGK+IGL.202205       149  9 22    TRUE    TRUE  
 _OGRDB.mouse.PWD_PhJ.IGH+IGK+IGL.202410          184 10 22    TRUE    TRUE  
 _OGRDB.rhesus_monkey.IGH+IGK+IGL.202602         2294 72 39    TRUE    TRUE  
 IMGT-202614-2.Bos_taurus.IGH+IGK+IGL              89 23 33   FALSE   FALSE  
 IMGT-202614-2.Mus_musculus.IGH+IGK+IGL           865 61 27    TRUE   FALSE  
 IMGT-202614-2.Mus_musculus.TRA+TRB+TRG+TRD       387  5 96    TRUE   FALSE  
 IMGT-202614-2.Oryctolagus_cuniculus.IGH+IGK+IGL  148 11 34    TRUE   FALSE  
 IMGT-202614-2.Rattus_norvegicus.IGH+IGK+IGL      403 37 15    TRUE   FALSE  
 IMGT-202614-2.Sus_scrofa.IGH+IGK+IGL              65  5 19    TRUE    TRUE  
[ FAIL 0 | WARN 1 | SKIP 2 | PASS 503 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• empty test (2): , 'test-precompiled-igblast-utils.R:1:1'

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 503 ]
> 
> if (!is_bioc_build_machine) {
+     options(igblastr_cache=NULL)
+ }
> 
> 
> proc.time()
   user  system elapsed 
110.559   4.971 117.923