| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-26 11:57 -0500 (Thu, 26 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4891 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1038/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| igblastr 1.0.17 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for igblastr in R Universe. | ||||||||||||||
|
To the developers/maintainers of the igblastr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/igblastr.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: igblastr |
| Version: 1.0.17 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:igblastr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings igblastr_1.0.17.tar.gz |
| StartedAt: 2026-02-26 01:04:16 -0500 (Thu, 26 Feb 2026) |
| EndedAt: 2026-02-26 01:11:53 -0500 (Thu, 26 Feb 2026) |
| EllapsedTime: 456.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: igblastr.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:igblastr.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings igblastr_1.0.17.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/igblastr.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘igblastr/DESCRIPTION’ ... OK
* this is package ‘igblastr’ version ‘1.0.17’
* 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 9.1Mb
sub-directories of 1Mb or more:
extdata 8.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
urlExists: no visible global function definition for ‘wsmg’
Undefined global functions or variables:
wsmg
* 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)
> list_germline_dbs()
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
>
> ## --- 3. Check that new and original dbs have the same sequences ---
>
> stopifnot(identical(
+ as.character(load_germline_db(db_name0)),
+ as.character(load_germline_db(exA_db_name))
+ ))
>
> ## ---------------------------------------------------------------------
> ## B. WITH GAPPED GERMLINE V GENE ALLELE SEQUENCES
> ## ---------------------------------------------------------------------
>
> ## In this example, we're going to download human germline gene allele
> ## **gapped** sequences from AIRR-community/OGRDB and use them to create
> ## and install a new germline db. More precisely, we're going to:
> ## 1. Download the gapped sequences for the following "Reference Sets"
> ## from AIRR-community/OGRDB:
> ## - IGH_VDJ version 9
> ## - IGKappa_VJ version 4
> ## - IGLambda_VJ version 3
> ## Each "Reference Set" corresponds to a BCR germline locus. For each
> ## set, AIRR-community/OGRDB provides a FASTA file containing the
> ## gapped allele sequences for that locus. We'll also split each file
> ## to produce one FASTA file per region type for that locus, so we'll
> ## end up with 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 built-in germline db _AIRR.human.IGH+IGK+IGL.202410.
>
> ## --- 1. Download human gapped sequences from AIRR-community/OGRDB ---
>
> download_AIRR_gapped_germline_sets <- function(organism, sets, destdir) {
+ base_url <- "https://ogrdb.airr-community.org/download_germline_set/"
+ for (i in seq_along(germline_sets)) {
+ set <- names(sets)[[i]]
+ version <- sets[[i]]
+ url <- sprintf("%s%s/%s/%s/gapped_ex", base_url,
+ organism, set, version)
+ tmpfile <- tempfile()
+ download.file(URLencode(url), tmpfile)
+ alleles <- readDNAStringSet(tmpfile)
+ locus_regions <- strsplit(set, "_")[[1L]]
+ locus <- substr(locus_regions[[1L]], 1L, 3L)
+ region_types <- strsplit(locus_regions[[2L]], "")[[1L]]
+ ## Split the downloaded FASTA file by region type.
+ for (region_type in region_types) {
+ group <- paste0(locus, region_type)
+ reg_alleles <- alleles[grep(group, names(alleles))]
+ fasta_file <- paste0(group, ".fasta")
+ writeXStringSet(reg_alleles, file.path(destdir, fasta_file))
+ }
+ }
+ }
>
> dir.create(exB_fasta_dir <- tempfile())
> germline_sets <- c(IGH_VDJ=9, IGKappa_VJ=4, IGLambda_VJ=3)
>
> download_AIRR_gapped_germline_sets("Homo sapiens", germline_sets,
+ exB_fasta_dir)
trying URL 'https://ogrdb.airr-community.org/download_germline_set/Homo%20sapiens/IGH_VDJ/9/gapped_ex'
Content type 'application/octet-stream' length 68833 bytes (67 KB)
==================================================
downloaded 67 KB
trying URL 'https://ogrdb.airr-community.org/download_germline_set/Homo%20sapiens/IGKappa_VJ/4/gapped_ex'
Content type 'application/octet-stream' length 23012 bytes (22 KB)
==================================================
downloaded 22 KB
trying URL 'https://ogrdb.airr-community.org/download_germline_set/Homo%20sapiens/IGLambda_VJ/3/gapped_ex'
Content type 'application/octet-stream' length 29109 bytes (28 KB)
==================================================
downloaded 28 KB
>
> list.files(exB_fasta_dir) # 7 FASTA files
[1] "IGHD.fasta" "IGHJ.fasta" "IGHV.fasta" "IGKJ.fasta" "IGKV.fasta"
[6] "IGLJ.fasta" "IGLV.fasta"
>
> ## Note that the V allele sequences have gaps:
> IGKV_alleles <- readDNAStringSet(file.path(exB_fasta_dir, "IGKV.fasta"))
> as.character(IGKV_alleles[1:3])
IGKV1-12*01
"GACATCCAGATGACCCAGTCTCCATCTTCCGTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATT..................AGCAGCTGGTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCA.....................TCCAGTTTGCAAAGTGGGGTCCCA...TCAAGGTTCAGCGGCAGTGGA......TCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTACTATTGTCAACAGGCTAACAGTTTCCCTCC"
IGKV1-13*01
"GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATT..................AGCAGTGCTTTAGCCTGATATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCC.....................TCCAGTTTGGAAAGTGGGGTCCCA...TCAAGGTTCAGCGGCAGTGGA......TCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAATTACCCTCA"
IGKV1-16*02
"GACATCCAGATGACCCAGTCTCCATCCTCACTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGCATT..................AGCAATTATTTAGCCTGGTTTCAGCAGAAACCAGGGAAAGCCCCTAAGTCCCTGATCTATGCTGCA.....................TCCAGTTTGCAAAGTGGGGTCCCA...TCAAAGTTCAGCGGCAGTGGA......TCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGCCAACAGTATAATAGTTACCCTCC"
>
> ## --- 2. Use FASTA files to install new germline db ---
>
> exB_db_name <- "cus.exB.human.IGH+IGK+IGL"
> install_custom_germline_db(exB_db_name, exB_fasta_dir, gapped=TRUE)
> list_germline_dbs()
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
>
> ## --- 3. Check that the new db contains the same sequences ---
> ## --- as _AIRR.human.IGH+IGK+IGL.202410 ---
>
> ## The Reference Sets we used to populate the new db (IGH_VDJ version 9,
> ## IGKappa_VJ version 4, IGLambda_VJ version 3) are the same that were
> ## used to populate built-in germline db _AIRR.human.IGH+IGK+IGL.202410.
> ## Let's check that the two dbs contain the same sequences:
> stopifnot(identical(
+ as.character(load_germline_db(db_name0)),
+ as.character(load_germline_db(exB_db_name))
+ ))
>
> ## ---------------------------------------------------------------------
> ## C. CREATE AND INSTALL GERMLINE DB WITH COMPUTED "INTERNAL DATA"
> ## ---------------------------------------------------------------------
>
> ## The gaps that germline gene allele sequence providers like IMGT and
> ## AIRR-community/OGRDB inject in the V allele sequences reflect their
> ## FWR/CDR boundaries. When the 'with.intdata' argument is set to TRUE,
> ## install_custom_germline_db() takes advantage of this to compute and
> ## add the "internal data" associated with the V alleles to the new db:
> exC_db_name <- "cus.exC.human.IGH+IGK+IGL"
> install_custom_germline_db(exC_db_name, exB_fasta_dir, gapped=TRUE,
+ with.intdata=TRUE)
> list_germline_dbs() # 'intdata' col indicates presence of "internal data"
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
>
> ## Note that the "internal data" in a germline db can be loaded with
> ## load_intdata() (see '?load_intdata' for more information):
> intdataC <- load_intdata(exC_db_name)
> head(intdataC)
allele_name fwr1_start fwr1_end cdr1_start cdr1_end fwr2_start fwr2_end
1 IGHV1-18*01 1 75 76 99 100 150
2 IGHV1-18*03 1 75 76 99 100 150
3 IGHV1-18*04 1 75 76 99 100 150
4 IGHV1-2*02 1 75 76 99 100 150
5 IGHV1-2*04 1 75 76 99 100 150
6 IGHV1-2*05 1 75 76 99 100 150
cdr2_start cdr2_end fwr3_start fwr3_end chain_type coding_frame_start
1 151 174 175 288 VH 0
2 151 174 175 288 VH 0
3 151 174 175 288 VH 0
4 151 174 175 288 VH 0
5 151 174 175 288 VH 0
6 151 174 175 288 VH 0
>
> ## Check that the "internal data" in the new db is the same as in
> ## _AIRR.human.IGH+IGK+IGL.202410:
> stopifnot(identical(intdataC, load_intdata(db_name0)))
Error: identical(intdataC, load_intdata(db_name0)) is not TRUE
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
igblastn 38.942 1.966 16.911
igbrowser 9.069 0.236 4.659
augment_germline_db 7.875 0.454 3.549
install_IMGT_germline_db 7.877 0.268 9.865
OAS-utils 0.779 0.131 6.024
* 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, 3 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/igblastr.Rcheck/00check.log’
for details.
igblastr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL igblastr ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘igblastr’ ... ** this is package ‘igblastr’ version ‘1.0.17’ ** 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)
igblastr.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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")
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 469 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-precompiled-igblast-utils.R:1:1'
[ FAIL 0 | WARN 11 | SKIP 1 | PASS 469 ]
>
> if (!is_bioc_build_machine) {
+ options(igblastr_cache=NULL)
+ }
>
>
> proc.time()
user system elapsed
88.601 5.112 89.783
igblastr.Rcheck/igblastr-Ex.timings
| name | user | system | elapsed | |
| OAS-utils | 0.779 | 0.131 | 6.024 | |
| allele2gene | 0.091 | 0.091 | 0.188 | |
| augment_germline_db | 7.875 | 0.454 | 3.549 | |
| auxdata-utils | 1.397 | 0.063 | 1.463 | |
| compute_auxdata | 0.131 | 0.003 | 0.135 | |
| compute_imgt_intdata | 0 | 0 | 0 | |
| get_igblast_root | 0.001 | 0.000 | 0.001 | |
| igblast_info | 0.005 | 0.001 | 0.007 | |
| igblastn | 38.942 | 1.966 | 16.911 | |
| igblastr_usage_report | 0 | 0 | 0 | |
| igbrowser | 9.069 | 0.236 | 4.659 | |
| install_IMGT_germline_db | 7.877 | 0.268 | 9.865 | |