Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-19 12:45 -0500 (Tue, 19 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4765 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 474/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cTRAP 1.24.0 (landing page) Nuno Saraiva-Agostinho
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the cTRAP package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cTRAP.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: cTRAP |
Version: 1.24.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cTRAP_1.24.0.tar.gz |
StartedAt: 2024-11-19 06:49:44 -0000 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 06:55:45 -0000 (Tue, 19 Nov 2024) |
EllapsedTime: 361.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: cTRAP.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cTRAP_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/cTRAP.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cTRAP/DESCRIPTION’ ... OK * this is package ‘cTRAP’ version ‘1.24.0’ * 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 ... NOTE Found the following hidden files and directories: .devcontainer These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘cTRAP’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: data 4.3Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 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 ... NOTE Found the following possibly unsafe calls: File ‘cTRAP/R/shinyInterface_session.R’: assignInNamespace("dataTablesFilter", dt_mod, "DT") plotComparison: no visible binding for global variable ‘.data’ plotMetricDistribution: no visible binding for global variable ‘.data’ plotSingleCorr: no visible binding for global variable ‘.data’ plotTargetingDrug: no visible binding for global variable ‘.data’ plotTargetingDrugsVSsimilarPerturbations: no visible binding for global variable ‘.data’ Undefined global functions or variables: .data * 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 ... NOTE Documented arguments not in \usage in Rd file 'compareWithAllMethods.Rd': ‘rankByAscending’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘cTRAP-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: analyseDrugSetEnrichment > ### Title: Analyse drug set enrichment > ### Aliases: analyseDrugSetEnrichment > > ### ** Examples > > descriptors <- loadDrugDescriptors() compound_descriptors_NCI60_2D.qs not found: downloading data... trying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/compound_descriptors_NCI60_2D.qs' Warning in download.file(link, file, mode = mode) : URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/compound_descriptors_NCI60_2D.qs': status was 'Could not resolve hostname' Error in download.file(link, file, mode = mode) : cannot open URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/compound_descriptors_NCI60_2D.qs' Calls: loadDrugDescriptors ... loadRemotePreProcessedData -> downloadIfNotFound -> download.file Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: • On Bioconductor (1): 'test_ENCODE.R:16:5' • empty test (1): 'test_drugSetEnrichment.R:88:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_drugSensitivity.R:4:1'): (code run outside of `test_that()`) ─── Error in `download.file(link, file, mode = mode)`: cannot open URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/expressionDrugSensitivityCorGDSC7.qs' Backtrace: ▆ 1. └─cTRAP::loadExpressionDrugSensitivityAssociation("GDSC 7") at test_drugSensitivity.R:4:1 2. └─cTRAP:::downloadIfNotFound(link, file) 3. └─utils::download.file(link, file, mode = mode) [ FAIL 1 | WARN 1 | SKIP 2 | PASS 221 ] 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: 2 ERRORs, 6 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/cTRAP.Rcheck/00check.log’ for details.
cTRAP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL cTRAP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘cTRAP’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (cTRAP)
cTRAP.Rcheck/tests/spelling.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.323 0.010 0.235
cTRAP.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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) > library(cTRAP) > > test_check("cTRAP") trying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/expressionDrugSensitivityCorGDSC7.qs' trying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/compound_descriptors_NCI60_2D.qs' downloaded 2.1 MB trying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/expressionDrugSensitivityCorGDSC7.qs' downloaded 31.6 MB [ FAIL 1 | WARN 1 | SKIP 2 | PASS 221 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On Bioconductor (1): 'test_ENCODE.R:16:5' • empty test (1): 'test_drugSetEnrichment.R:88:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_drugSensitivity.R:4:1'): (code run outside of `test_that()`) ─── Error in `download.file(link, file, mode = mode)`: cannot open URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/expressionDrugSensitivityCorGDSC7.qs' Backtrace: ▆ 1. └─cTRAP::loadExpressionDrugSensitivityAssociation("GDSC 7") at test_drugSensitivity.R:4:1 2. └─cTRAP:::downloadIfNotFound(link, file) 3. └─utils::download.file(link, file, mode = mode) [ FAIL 1 | WARN 1 | SKIP 2 | PASS 221 ] Error: Test failures Execution halted
cTRAP.Rcheck/cTRAP-Ex.timings
name | user | system | elapsed |