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This page was generated on 2024-05-07 11:32:32 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
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 479/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cTRAP 1.22.0 (landing page) Nuno Saraiva-Agostinho
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the cTRAP package: - 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: cTRAP |
Version: 1.22.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cTRAP_1.22.0.tar.gz |
StartedAt: 2024-05-06 20:48:43 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 20:54:14 -0400 (Mon, 06 May 2024) |
EllapsedTime: 331.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: cTRAP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cTRAP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cTRAP_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/cTRAP.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cTRAP/DESCRIPTION’ ... OK * this is package ‘cTRAP’ version ‘1.22.0’ * 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 5.0Mb 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 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 53.847 0.686 54.607 convertGeneIdentifiers 6.944 0.633 8.558 plot.referenceComparison 6.875 0.425 7.306 analyseDrugSetEnrichment 5.318 0.647 55.460 filterCMapMetadata 2.798 0.083 5.824 downloadENCODEknockdownMetadata 1.246 0.209 50.343 * 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: 6 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/cTRAP.Rcheck/00check.log’ for details.
cTRAP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cTRAP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.0 (2024-04-24) -- "Puppy Cup" 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. > if(requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.072 0.019 0.087
cTRAP.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" 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. > 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) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_drugSetEnrichment.R:88:1' • On Bioconductor (1): 'test_ENCODE.R:16:5' [ FAIL 0 | WARN 0 | SKIP 2 | PASS 243 ] > > proc.time() user system elapsed 23.193 3.119 64.371
cTRAP.Rcheck/cTRAP-Ex.timings
name | user | system | elapsed | |
analyseDrugSetEnrichment | 5.318 | 0.647 | 55.460 | |
convertGeneIdentifiers | 6.944 | 0.633 | 8.558 | |
downloadENCODEknockdownMetadata | 1.246 | 0.209 | 50.343 | |
filterCMapMetadata | 2.798 | 0.083 | 5.824 | |
getCMapConditions | 0.001 | 0.000 | 0.001 | |
getCMapPerturbationTypes | 0 | 0 | 0 | |
listExpressionDrugSensitivityAssociation | 0 | 0 | 0 | |
loadCMapData | 1.225 | 0.041 | 1.556 | |
loadCMapZscores | 0.922 | 0.052 | 0.974 | |
loadDrugDescriptors | 0.025 | 0.002 | 0.028 | |
loadENCODEsamples | 0.000 | 0.001 | 0.000 | |
loadExpressionDrugSensitivityAssociation | 0.192 | 0.190 | 0.384 | |
parseCMapID | 0 | 0 | 0 | |
performDifferentialExpression | 0 | 0 | 0 | |
plot.perturbationChanges | 4.234 | 0.270 | 4.508 | |
plot.referenceComparison | 6.875 | 0.425 | 7.306 | |
plotDrugSetEnrichment | 53.847 | 0.686 | 54.607 | |
plotTargetingDrugsVSsimilarPerturbations | 2.278 | 0.246 | 2.526 | |
predictTargetingDrugs | 1.509 | 0.249 | 1.757 | |
prepareCMapPerturbations | 1.983 | 0.042 | 2.032 | |
prepareDrugSets | 2.019 | 1.440 | 3.468 | |
prepareENCODEgeneExpression | 0 | 0 | 0 | |
rankSimilarPerturbations | 0.836 | 0.054 | 0.890 | |