Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 200/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
biodbKegg 1.11.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.4 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: 1.11.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbKegg.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings biodbKegg_1.11.0.tar.gz |
StartedAt: 2024-06-10 00:18:47 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 00:44:37 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 1550.2 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbKegg.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbKegg.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings biodbKegg_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/biodbKegg.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 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 'biodbKegg/DESCRIPTION' ... OK * this is package 'biodbKegg' version '1.11.0' * 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 '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 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 7.17 0.54 12.90 KeggCompoundConn 4.15 1.74 10.92 * 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 26 | WARN 0 | SKIP 0 | PASS 1512 ] 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 'F:/biocbuild/bbs-3.20-bioc/meat/biodbKegg.Rcheck/00check.log' for details.
biodbKegg.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL biodbKegg ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbKegg)
biodbKegg.Rcheck/tests/testthat.Rout.fail
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 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. > # vi: fdm=marker > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbKegg) > Sys.setenv(TESTTHAT_REPORTER = "summary") > test_check("biodbKegg") trying URL 'https://www.kegg.jp/kegg/pathway/map/map00260.png?17179945592127479' downloaded 158 KB [ FAIL 26 | WARN 0 | SKIP 0 | PASS 1512 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_200_enzyme.R:74:1'): 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 = `<KggEnzyC>`, opt = `<named list>`) 3. └─testthat::expect_true(length(ids) > 0) ── Failure ('test_200_enzyme.R:74:1'): We can search for an entry by searchable field ── c(`1.1.1.165` = "1.1.1.165") %in% character(0) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`) 3. └─testthat::expect_true(!!id %in% !!ids) ── Failure ('test_200_enzyme.R:74:1'): We can search for an entry by name. ───── length(ids) > 0 is not TRUE `actual`: FALSE `expected`: TRUE While searching for entry 1.1.1.165 by name "2-alkyn-1-ol dehydrogenase". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`) 3. └─testthat::expect_true(length(ids) > 0, msg) ── Failure ('test_200_enzyme.R:74:1'): We can search for an entry by name. ───── id %in% ids is not TRUE `actual`: FALSE `expected`: TRUE While searching for entry 1.1.1.165 by name "2-alkyn-1-ol dehydrogenase". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`) 3. └─testthat::expect_true(id %in% ids, msg) ── 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_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_300_genes.R:32:1'): We can search for an entry by name. ────── length(ids) > 0 is not TRUE `actual`: FALSE `expected`: TRUE While searching for entry mmu:14635 by name "(RefSeq) galactokinase 1". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`) 3. └─testthat::expect_true(length(ids) > 0, msg) ── Failure ('test_300_genes.R:32:1'): We can search for an entry by name. ────── id %in% ids is not TRUE `actual`: FALSE `expected`: TRUE While searching for entry mmu:14635 by name "(RefSeq) galactokinase 1". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`) 3. └─testthat::expect_true(id %in% ids, msg) ── Failure ('test_350_glycan.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 = `<KggGlycC>`, opt = `<named list>`) 3. └─testthat::expect_true(length(ids) > 0) ── Failure ('test_350_glycan.R:16:1'): We can search for an entry by searchable field ── c(G00018 = "G00018") %in% character(0) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`) 3. └─testthat::expect_true(!!id %in% !!ids) ── Failure ('test_350_glycan.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 G00018 by name "DS 3". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`) 3. └─testthat::expect_true(length(ids) > 0, msg) ── Failure ('test_350_glycan.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 G00018 by name "DS 3". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`) 3. └─testthat::expect_true(id %in% ids, msg) ── 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:88:1'): 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 = `<KggPthwC>`, opt = `<named list>`) 3. └─testthat::expect_true(length(ids) > 0) ── Failure ('test_600_pathway.R:88:1'): We can search for an entry by searchable field ── c(map00053 = "map00053") %in% character(0) is not TRUE `actual`: FALSE `expected`: TRUE Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`) 3. └─testthat::expect_true(!!id %in% !!ids) ── Failure ('test_600_pathway.R:88:1'): We can search for an entry by name. ──── length(ids) > 0 is not TRUE `actual`: FALSE `expected`: TRUE While searching for entry map00053 by name "Ascorbate and aldarate metabolism". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`) 3. └─testthat::expect_true(length(ids) > 0, msg) ── Failure ('test_600_pathway.R:88:1'): We can search for an entry by name. ──── id %in% ids is not TRUE `actual`: FALSE `expected`: TRUE While searching for entry map00053 by name "Ascorbate and aldarate metabolism". Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`) 3. └─testthat::expect_true(id %in% ids, msg) ── 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 26 | WARN 0 | SKIP 0 | PASS 1512 ] Error: Test failures Execution halted
biodbKegg.Rcheck/biodbKegg-Ex.timings
name | user | system | elapsed | |
KeggCircle | 0 | 0 | 0 | |
KeggCompoundConn | 4.15 | 1.74 | 10.92 | |
KeggCompoundEntry | 0.69 | 0.04 | 0.75 | |
KeggConn | 0.65 | 0.04 | 2.72 | |
KeggEntry | 0.68 | 0.03 | 0.78 | |
KeggEnzymeConn | 7.17 | 0.54 | 12.90 | |
KeggEnzymeEntry | 0.80 | 0.05 | 0.86 | |
KeggGenesConn | 0.87 | 0.04 | 0.94 | |
KeggGenesEntry | 0.75 | 0.05 | 0.81 | |
KeggGlycanConn | 0.75 | 0.02 | 0.76 | |
KeggGlycanEntry | 0.81 | 0.03 | 0.88 | |
KeggModuleConn | 0.89 | 0.03 | 0.95 | |
KeggModuleEntry | 0.58 | 0.03 | 0.61 | |
KeggOrthologyConn | 0.61 | 0.05 | 0.66 | |
KeggOrthologyEntry | 0.58 | 0.01 | 0.59 | |
KeggPathwayConn | 3.08 | 0.03 | 3.53 | |
KeggPathwayEntry | 0.65 | 0.03 | 0.71 | |
KeggReactionConn | 0.66 | 0.02 | 0.68 | |
KeggReactionEntry | 0.62 | 0.02 | 0.66 | |
KeggRect | 0 | 0 | 0 | |
KeggShape | 0 | 0 | 0 | |