Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:40 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 1030/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
immunotation 1.12.0 (landing page) Katharina Imkeller
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the immunotation package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/immunotation.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: immunotation |
Version: 1.12.0 |
Command: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immunotation.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings immunotation_1.12.0.tar.gz |
StartedAt: 2024-08-12 02:06:33 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 02:11:26 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 293.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: immunotation.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:immunotation.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings immunotation_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/immunotation.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'immunotation/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'immunotation' version '1.12.0' * 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 'immunotation' can be installed ... OK * checking installed package size ... NOTE installed size is 5.5Mb sub-directories of 1Mb or more: R 3.2Mb extdata 2.2Mb * 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 dependencies in R code ... OK * 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 plot_allele_frequency 2.45 0.34 12.61 query_haplotype_frequencies 0.70 0.02 31.40 * 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 'E:/biocbuild/bbs-3.19-bioc/meat/immunotation.Rcheck/00check.log' for details.
immunotation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL immunotation ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'immunotation' ... ** 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 (immunotation)
immunotation.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 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(immunotation) > > test_check("immunotation") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 146 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 146 ] > > > proc.time() user system elapsed 56.76 3.95 191.67
immunotation.Rcheck/immunotation-Ex.timings
name | user | system | elapsed | |
assemble_protein_complex | 3.05 | 0.19 | 3.31 | |
build_allele_group | 1.45 | 0.04 | 1.50 | |
decode_MAC | 0.03 | 0.04 | 0.36 | |
encode_MAC | 0.00 | 0.00 | 0.06 | |
get_G_group | 0.01 | 0.00 | 0.02 | |
get_P_group | 0 | 0 | 0 | |
get_mhcpan_input | 0.11 | 0.00 | 0.11 | |
get_serotypes | 0.02 | 0.00 | 0.02 | |
get_valid_organisms | 0.01 | 0.00 | 0.01 | |
human_protein_complex_table | 1.29 | 0.36 | 1.64 | |
plot_allele_frequency | 2.45 | 0.34 | 12.61 | |
query_allele_frequencies | 0.11 | 0.02 | 3.16 | |
query_haplotype_frequencies | 0.70 | 0.02 | 31.40 | |
query_population_detail | 0.02 | 0.00 | 0.33 | |
retrieve_chain_lookup_table | 1.78 | 0.00 | 1.78 | |