Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:45 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 470/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cTRAP 1.23.0 (landing page) Nuno Saraiva-Agostinho
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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: 1.23.0 |
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_1.23.0.tar.gz |
StartedAt: 2024-08-21 03:57:23 -0000 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 04:12:17 -0000 (Wed, 21 Aug 2024) |
EllapsedTime: 894.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cTRAP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.23.0.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 ‘1.23.0’ * 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 ... OK * 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotDrugSetEnrichment 256.760 1.225 258.511 plot.referenceComparison 25.747 0.426 26.223 analyseDrugSetEnrichment 18.867 1.515 75.199 convertGeneIdentifiers 18.521 1.142 30.607 plot.perturbationChanges 13.693 0.343 14.073 plotTargetingDrugsVSsimilarPerturbations 10.080 0.156 10.253 predictTargetingDrugs 8.422 0.103 8.541 filterCMapMetadata 7.633 0.243 18.256 prepareDrugSets 5.703 0.707 6.434 prepareCMapPerturbations 6.259 0.068 5.702 loadCMapData 4.128 0.085 9.088 downloadENCODEknockdownMetadata 2.977 0.521 69.974 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘spelling.R’ 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: 5 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 0.218 0.017 0.219
cTRAP.Rcheck/tests/testthat.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. > library(testthat) > library(cTRAP) > > test_check("cTRAP") trying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/expressionDrugSensitivityCorGDSC7.qs' downloaded 31.6 MB trying URL 'https://compbio.imm.medicina.ulisboa.pt/public/cTRAP/compound_descriptors_NCI60_2D.qs' downloaded 2.1 MB [ FAIL 0 | WARN 0 | SKIP 2 | PASS 243 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On Bioconductor (1): 'test_ENCODE.R:16:5' • empty test (1): 'test_drugSetEnrichment.R:88:1' [ FAIL 0 | WARN 0 | SKIP 2 | PASS 243 ] > > proc.time() user system elapsed 78.898 6.489 136.317
cTRAP.Rcheck/cTRAP-Ex.timings
name | user | system | elapsed | |
analyseDrugSetEnrichment | 18.867 | 1.515 | 75.199 | |
convertGeneIdentifiers | 18.521 | 1.142 | 30.607 | |
downloadENCODEknockdownMetadata | 2.977 | 0.521 | 69.974 | |
filterCMapMetadata | 7.633 | 0.243 | 18.256 | |
getCMapConditions | 0.003 | 0.000 | 0.003 | |
getCMapPerturbationTypes | 0 | 0 | 0 | |
listExpressionDrugSensitivityAssociation | 0 | 0 | 0 | |
loadCMapData | 4.128 | 0.085 | 9.088 | |
loadCMapZscores | 3.027 | 0.052 | 2.455 | |
loadDrugDescriptors | 0.064 | 0.004 | 0.068 | |
loadENCODEsamples | 0 | 0 | 0 | |
loadExpressionDrugSensitivityAssociation | 1.249 | 0.143 | 1.396 | |
parseCMapID | 0 | 0 | 0 | |
performDifferentialExpression | 0 | 0 | 0 | |
plot.perturbationChanges | 13.693 | 0.343 | 14.073 | |
plot.referenceComparison | 25.747 | 0.426 | 26.223 | |
plotDrugSetEnrichment | 256.760 | 1.225 | 258.511 | |
plotTargetingDrugsVSsimilarPerturbations | 10.080 | 0.156 | 10.253 | |
predictTargetingDrugs | 8.422 | 0.103 | 8.541 | |
prepareCMapPerturbations | 6.259 | 0.068 | 5.702 | |
prepareDrugSets | 5.703 | 0.707 | 6.434 | |
prepareENCODEgeneExpression | 0 | 0 | 0 | |
rankSimilarPerturbations | 2.465 | 0.032 | 2.501 | |