Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:06 -0400 (Sat, 30 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 1020/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
igblastr 0.99.14 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | ... NOT SUPPORTED ... | ||||||||||||
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: 0.99.14 |
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_0.99.14.tar.gz |
StartedAt: 2025-08-29 21:30:24 -0400 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 21:33:21 -0400 (Fri, 29 Aug 2025) |
EllapsedTime: 176.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: igblastr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_0.99.14.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/igblastr.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘igblastr/DESCRIPTION’ ... OK * this is package ‘igblastr’ version ‘0.99.14’ * 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 6.3Mb sub-directories of 1Mb or more: extdata 5.9Mb * 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 igblastn 19.346 0.624 7.931 bcr_browser 15.237 0.498 6.131 augment_germline_db 14.461 0.605 5.498 install_IMGT_germline_db 1.596 0.205 7.338 OAS-utils 0.650 0.065 5.687 * 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 ‘/Users/biocbuild/bbs-3.22-bioc/meat/igblastr.Rcheck/00check.log’ for details.
igblastr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL igblastr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘igblastr’ ... ** this is package ‘igblastr’ version ‘0.99.14’ ** 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 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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) > 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 > > 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 _IMGT.rat.IGH.202508 18 db_name C _IMGT.human.IGH+IGK+IGL.202412 76 _IMGT.mouse.IGH.202412 31 _IMGT.rabbit.IGH.202412 28 * _IMGT.rat.IGH.202508 18 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 210 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test-precompiled-igblast-utils.R:1:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 210 ] > > if (!is_bioc_build_machine) { + options(igblastr_cache=NULL) + } > > proc.time() user system elapsed 14.556 2.941 15.965
igblastr.Rcheck/igblastr-Ex.timings
name | user | system | elapsed | |
OAS-utils | 0.650 | 0.065 | 5.687 | |
augment_germline_db | 14.461 | 0.605 | 5.498 | |
auxiliary-data-utils | 0.111 | 0.020 | 0.148 | |
bcr_browser | 15.237 | 0.498 | 6.131 | |
get_igblast_root | 0.002 | 0.001 | 0.001 | |
igblast_info | 0.007 | 0.002 | 0.009 | |
igblastn | 19.346 | 0.624 | 7.931 | |
igblastr_usage_report | 0.000 | 0.001 | 0.001 | |
install_IMGT_germline_db | 1.596 | 0.205 | 7.338 | |
install_igblast | 0.005 | 0.001 | 0.006 | |
list_c_region_dbs | 0.090 | 0.013 | 0.106 | |
list_germline_dbs | 1.610 | 0.219 | 2.224 | |
outfmt7-utils | 2.852 | 0.213 | 2.883 | |