Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:45 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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" | 4415 |
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 603/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DrugVsDisease 2.47.0 (landing page) j. Saez-Rodriguez
| nebbiolo2 | Linux (Ubuntu 22.04.3 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 | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the DrugVsDisease package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DrugVsDisease.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: DrugVsDisease |
Version: 2.47.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DrugVsDisease.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DrugVsDisease_2.47.0.tar.gz |
StartedAt: 2024-08-26 20:59:41 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 21:00:45 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 63.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: DrugVsDisease.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DrugVsDisease.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DrugVsDisease_2.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DrugVsDisease.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DrugVsDisease/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DrugVsDisease’ version ‘2.47.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'affy', 'limma', 'biomaRt', 'ArrayExpress', 'GEOquery', 'DrugVsDiseasedata', 'cMap2data', 'qvalue' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘DrugVsDisease’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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 ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘ArrayExpress’ ‘DrugVsDiseasedata’ ‘GEOquery’ ‘affy’ ‘biomaRt’ ‘limma’ ‘qvalue’ Please remove these calls from your code. Namespaces in Imports field not imported from: ‘BiocGenerics’ ‘RUnit’ ‘annotate’ ‘hgu133a.db’ ‘hgu133a2.db’ ‘hgu133plus2.db’ ‘xtable’ All declared Imports should be used. Packages in Depends field not imported from: ‘ArrayExpress’ ‘DrugVsDiseasedata’ ‘GEOquery’ ‘affy’ ‘biomaRt’ ‘cMap2data’ ‘limma’ ‘qvalue’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .averagecluster: no visible binding for global variable ‘drugClusters’ .averagecluster: no visible binding for global variable ‘diseaseClusters’ .calculateES: no visible binding for global variable ‘drugRL’ .calculateES: no visible binding for global variable ‘diseaseRL’ .calculateES : <anonymous>: no visible global function definition for ‘qvalue’ .convertEnsembl: no visible binding for global variable ‘annotationlist’ .convertEnsembl: no visible global function definition for ‘useMart’ .convertEnsembl: no visible global function definition for ‘getBM’ .datafromAE: no visible global function definition for ‘ArrayExpress’ .datafromAE: no visible global function definition for ‘annotation’ .datafromAE: no visible global function definition for ‘pData’ .datafromGEO: no visible global function definition for ‘getGEO’ .datafromGEO: no visible global function definition for ‘GDS2eSet’ .datafromGEO: no visible global function definition for ‘pData’ .datafromGEO: no visible global function definition for ‘annotation’ .datafromGEO: no visible binding for global variable ‘GEOfactorvalues’ .datafromGEO: no visible global function definition for ‘exprs’ .findCluster: no visible binding for global variable ‘drugClusters’ .findCluster: no visible binding for global variable ‘diseaseClusters’ .findSignifCompounds: no visible global function definition for ‘qvalue’ .fitlms: no visible global function definition for ‘lmFit’ .multcontrast: no visible global function definition for ‘contrasts.fit’ .multcontrast: no visible global function definition for ‘eBayes’ .normalisedata: no visible global function definition for ‘rma’ .normalisedata: no visible global function definition for ‘mas5’ .readlocalAE: no visible global function definition for ‘ReadAffy’ .readlocalCEL: no visible global function definition for ‘ReadAffy’ .singlecontrast: no visible global function definition for ‘lmFit’ .singlecontrast: no visible global function definition for ‘contrasts.fit’ .singlecontrast: no visible global function definition for ‘eBayes’ .treatmentonlyfit: no visible global function definition for ‘lmFit’ .writecytoscape: no visible binding for global variable ‘drugClusters’ .writecytoscape: no visible binding for global variable ‘cytodrug’ .writecytoscape: no visible binding for global variable ‘druglabels’ .writecytoscape: no visible binding for global variable ‘diseaseClusters’ .writecytoscape: no visible binding for global variable ‘cytodisease’ .writecytoscape: no visible binding for global variable ‘diseaselabels’ generateprofiles: no visible binding for global variable ‘genelist’ generateprofiles: no visible global function definition for ‘exprs’ Undefined global functions or variables: ArrayExpress GDS2eSet GEOfactorvalues ReadAffy annotation annotationlist contrasts.fit cytodisease cytodrug diseaseClusters diseaseRL diseaselabels drugClusters drugRL druglabels eBayes exprs genelist getBM getGEO lmFit mas5 pData qvalue rma useMart * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed classifyprofile 7.538 1.772 9.315 selectrankedlists 5.281 1.498 6.794 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: 1 Test Suite : DrugVsDisease RUnit Tests - 2 test functions, 0 errors, 1 failure FAILURE in test_.KS.drug.disease: Error in checkTrue(sum(diag(DrugVsDisease:::.KS.drug.disease(d, d))) == : Test not TRUE Test files with failing tests test_.KS.drug.disease.R test_.KS.drug.disease Error in BiocGenerics:::testPackage("DrugVsDisease") : unit tests failed for package DrugVsDisease 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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/DrugVsDisease.Rcheck/00check.log’ for details.
DrugVsDisease.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DrugVsDisease ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘DrugVsDisease’ ... ** 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 (DrugVsDisease)
DrugVsDisease.Rcheck/tests/runTests.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-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. > require("DrugVsDisease")||stop("unable to load DrugVsDisease") Loading required package: DrugVsDisease Loading required package: affy Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: limma Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Loading required package: biomaRt Loading required package: ArrayExpress Loading required package: GEOquery Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Loading required package: DrugVsDiseasedata Loading required package: cMap2data Attaching package: 'cMap2data' The following object is masked from 'package:DrugVsDiseasedata': genelist Loading required package: qvalue [1] TRUE > library(BiocGenerics) > library(RUnit) > BiocGenerics:::testPackage("DrugVsDisease") Timing stopped at: 0.028 0.003 0.031 Error in checkTrue(sum(diag(DrugVsDisease:::.KS.drug.disease(d, d))) == : Test not TRUE RUNIT TEST PROTOCOL -- Mon Aug 26 21:00:42 2024 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 1 1 Test Suite : DrugVsDisease RUnit Tests - 2 test functions, 0 errors, 1 failure FAILURE in test_.KS.drug.disease: Error in checkTrue(sum(diag(DrugVsDisease:::.KS.drug.disease(d, d))) == : Test not TRUE Test files with failing tests test_.KS.drug.disease.R test_.KS.drug.disease Error in BiocGenerics:::testPackage("DrugVsDisease") : unit tests failed for package DrugVsDisease Execution halted
DrugVsDisease.Rcheck/DrugVsDisease-Ex.timings
name | user | system | elapsed | |
DrugVsDisease-package | 0 | 0 | 0 | |
classifyprofile | 7.538 | 1.772 | 9.315 | |
customClust | 0.001 | 0.000 | 0.001 | |
customdb | 0.000 | 0.001 | 0.000 | |
customedge | 0.000 | 0.001 | 0.000 | |
customsif | 0.001 | 0.000 | 0.000 | |
generateprofiles | 0 | 0 | 0 | |
profiles | 0.000 | 0.000 | 0.001 | |
selectrankedlists | 5.281 | 1.498 | 6.794 | |
selprofile | 0.000 | 0.001 | 0.001 | |