Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 205/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the biodbKegg package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbKegg.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: biodbKegg |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbKegg_1.12.0.tar.gz |
StartedAt: 2024-12-20 12:38:23 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 13:10:47 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1944.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbKegg.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbKegg_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbKegg.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘biodbKegg/DESCRIPTION’ ... OK * this is package ‘biodbKegg’ 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 for sufficient/correct file permissions ... OK * checking whether package ‘biodbKegg’ can be installed ... OK * checking installed package size ... OK * checking package 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 ... 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 KeggEnzymeConn 8.455 0.709 200.292 KeggPathwayConn 2.852 0.198 76.002 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ── Failure ('test_700_reaction.R:16:1'): We can search for an entry by name. ─── id %in% ids is not TRUE `actual`: FALSE `expected`: TRUE While searching for entry R00105 by name "ATP:NADH 2'-phosphotransferase". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`) 3. └─testthat::expect_true(id %in% ids, msg) [ FAIL 12 | WARN 0 | SKIP 0 | PASS 1470 ] Error: Test failures Execution halted * 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 ERROR See ‘/Users/biocbuild/bbs-3.20-bioc/meat/biodbKegg.Rcheck/00check.log’ for details.
biodbKegg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbKegg ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘biodbKegg’ ... ** 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 Warning in fun(libname, pkgname) : Package 'biodbKegg' is deprecated and will be removed from Bioconductor version 3.21 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'biodbKegg' is deprecated and will be removed from Bioconductor version 3.21 ** testing if installed package keeps a record of temporary installation path * DONE (biodbKegg)
biodbKegg.Rcheck/tests/testthat.Rout.fail
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-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. > # vi: fdm=marker > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbKegg) Warning message: In fun(libname, pkgname) : Package 'biodbKegg' is deprecated and will be removed from Bioconductor version 3.21 > Sys.setenv(TESTTHAT_REPORTER = "summary") > test_check("biodbKegg") trying URL 'https://www.kegg.jp/kegg/pathway/map/map00260.png?1734718069985772' downloaded 158 KB [ FAIL 12 | WARN 0 | SKIP 0 | PASS 1470 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_100_compound.R:184:1'): ppm tolerance works in annotateMzValues() ── c("mz", id.col) not identical to colnames(ret). Lengths differ: 2 is not 1 Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`) 3. └─testthat::expect_identical(c("mz", id.col), colnames(ret)) ── Failure ('test_300_genes.R:32:1'): We can search for an entry by searchable field ── length(ids) > 0 is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`) 3. └─testthat::expect_true(length(ids) > 0) ── Failure ('test_300_genes.R:32:1'): We can search for an entry by searchable field ── c(`mmu%3A14635` = "mmu:14635") %in% character(0) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`) 3. └─testthat::expect_true(!!id %in% !!ids) ── Failure ('test_400_module.R:16:1'): We can search for an entry by searchable field ── length(ids) > 0 is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`) 3. └─testthat::expect_true(length(ids) > 0) ── Failure ('test_400_module.R:16:1'): We can search for an entry by searchable field ── c(M00009 = "M00009") %in% character(0) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`) 3. └─testthat::expect_true(!!id %in% !!ids) ── Failure ('test_400_module.R:16:1'): We can search for an entry by name. ───── length(ids) > 0 is not TRUE `actual`: FALSE `expected`: TRUE While searching for entry M00009 by name "Citrate cycle (TCA cycle, Krebs cycle)". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`) 3. └─testthat::expect_true(length(ids) > 0, msg) ── Failure ('test_400_module.R:16:1'): We can search for an entry by name. ───── id %in% ids is not TRUE `actual`: FALSE `expected`: TRUE While searching for entry M00009 by name "Citrate cycle (TCA cycle, Krebs cycle)". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`) 3. └─testthat::expect_true(id %in% ids, msg) ── Failure ('test_600_pathway.R:103:1'): extractPathwayMapShapes() works correctly. ── `shapes` has length 2, not length 1. Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodbKegg (local) `<fn>`(conn = `<KggPthwC>`) 3. └─testthat::expect_length(shapes, items[[i]]) at test_600_pathway.R:68:9 ── Failure ('test_700_reaction.R:16:1'): We can search for an entry by searchable field ── length(ids) > 0 is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`) 3. └─testthat::expect_true(length(ids) > 0) ── Failure ('test_700_reaction.R:16:1'): We can search for an entry by searchable field ── c(R00105 = "R00105") %in% character(0) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`) 3. └─testthat::expect_true(!!id %in% !!ids) ── Failure ('test_700_reaction.R:16:1'): We can search for an entry by name. ─── length(ids) > 0 is not TRUE `actual`: FALSE `expected`: TRUE While searching for entry R00105 by name "ATP:NADH 2'-phosphotransferase". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`) 3. └─testthat::expect_true(length(ids) > 0, msg) ── Failure ('test_700_reaction.R:16:1'): We can search for an entry by name. ─── id %in% ids is not TRUE `actual`: FALSE `expected`: TRUE While searching for entry R00105 by name "ATP:NADH 2'-phosphotransferase". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`) 3. └─testthat::expect_true(id %in% ids, msg) [ FAIL 12 | WARN 0 | SKIP 0 | PASS 1470 ] Error: Test failures Execution halted
biodbKegg.Rcheck/biodbKegg-Ex.timings
name | user | system | elapsed | |
KeggCircle | 0.009 | 0.001 | 0.010 | |
KeggCompoundConn | 2.619 | 0.655 | 3.299 | |
KeggCompoundEntry | 0.212 | 0.011 | 0.226 | |
KeggConn | 0.254 | 0.013 | 0.271 | |
KeggEntry | 0.417 | 0.024 | 2.732 | |
KeggEnzymeConn | 8.455 | 0.709 | 200.292 | |
KeggEnzymeEntry | 0.429 | 0.025 | 2.763 | |
KeggGenesConn | 0.445 | 0.022 | 2.704 | |
KeggGenesEntry | 0.382 | 0.016 | 0.400 | |
KeggGlycanConn | 0.346 | 0.015 | 0.364 | |
KeggGlycanEntry | 0.673 | 0.024 | 2.968 | |
KeggModuleConn | 0.392 | 0.024 | 2.688 | |
KeggModuleEntry | 0.330 | 0.017 | 0.351 | |
KeggOrthologyConn | 0.478 | 0.026 | 3.404 | |
KeggOrthologyEntry | 0.425 | 0.016 | 0.443 | |
KeggPathwayConn | 2.852 | 0.198 | 76.002 | |
KeggPathwayEntry | 0.451 | 0.023 | 2.717 | |
KeggReactionConn | 0.411 | 0.023 | 2.741 | |
KeggReactionEntry | 0.364 | 0.018 | 0.385 | |
KeggRect | 0.004 | 0.000 | 0.004 | |
KeggShape | 0.001 | 0.000 | 0.001 | |