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This page was generated on 2023-02-08 01:15:12 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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To the developers/maintainers of the maPredictDSC package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maPredictDSC.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1077/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maPredictDSC 1.37.0 (landing page) Adi Laurentiu Tarca
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: maPredictDSC |
Version: 1.37.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:maPredictDSC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings maPredictDSC_1.37.0.tar.gz |
StartedAt: 2023-02-07 06:42:26 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 06:47:00 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 273.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: maPredictDSC.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:maPredictDSC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings maPredictDSC_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/maPredictDSC.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘maPredictDSC/DESCRIPTION’ ... OK * this is package ‘maPredictDSC’ version ‘1.37.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'MASS', 'affy', 'limma', 'gcrma', 'ROC', 'class', 'e1071', 'caret', 'hgu133plus2.db', 'ROCR', 'AnnotationDbi', 'LungCancerACvsSCCGEO' 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 ‘maPredictDSC’ 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 R 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: ‘ROC’ ‘ROCR’ ‘affy’ ‘caret’ ‘class’ ‘e1071’ ‘gcrma’ ‘limma’ Please remove these calls from your code. 'library' or 'require' call to ‘parallel’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘LungCancerACvsSCCGEO’ ‘ROC’ ‘ROCR’ ‘affy’ ‘caret’ ‘class’ ‘e1071’ ‘gcrma’ ‘hgu133plus2.db’ ‘limma’ 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 maPredictDSC: no visible global function definition for ‘installed.packages’ maPredictDSC: no visible global function definition for ‘ReadAffy’ maPredictDSC: no visible global function definition for ‘rma’ maPredictDSC: no visible global function definition for ‘mas5’ maPredictDSC: no visible global function definition for ‘gcrma’ maPredictDSC: no visible global function definition for ‘exprs’ maPredictDSC: no visible global function definition for ‘mas5calls’ maPredictDSC: no visible global function definition for ‘createFolds’ maPredictDSC : mff: no visible global function definition for ‘model.matrix’ maPredictDSC : mff: no visible global function definition for ‘formula’ maPredictDSC : mff: no visible global function definition for ‘lmFit’ maPredictDSC : mff: no visible global function definition for ‘makeContrasts’ maPredictDSC : mff: no visible global function definition for ‘contrasts.fit’ maPredictDSC : mff: no visible global function definition for ‘eBayes’ maPredictDSC : mff: no visible global function definition for ‘topTable’ maPredictDSC : mff: no visible global function definition for ‘pt’ maPredictDSC : mff : wf: no visible global function definition for ‘wilcox.test’ maPredictDSC : mff: no visible global function definition for ‘predict’ maPredictDSC : mff: no visible global function definition for ‘knn’ maPredictDSC : mff: no visible global function definition for ‘svm’ maPredictDSC : mff: no visible global function definition for ‘rocdemo.sca’ maPredictDSC : mff: no visible binding for global variable ‘dxrule.sca’ maPredictDSC : mff: no visible global function definition for ‘AUC’ maPredictDSC: no visible global function definition for ‘mclapply’ maPredictDSC: no visible global function definition for ‘sd’ maPredictDSC: no visible global function definition for ‘model.matrix’ maPredictDSC: no visible global function definition for ‘formula’ maPredictDSC: no visible global function definition for ‘lmFit’ maPredictDSC: no visible global function definition for ‘makeContrasts’ maPredictDSC: no visible global function definition for ‘contrasts.fit’ maPredictDSC: no visible global function definition for ‘eBayes’ maPredictDSC: no visible global function definition for ‘topTable’ maPredictDSC: no visible global function definition for ‘pt’ maPredictDSC : wf: no visible global function definition for ‘wilcox.test’ maPredictDSC: no visible global function definition for ‘predict’ maPredictDSC: no visible global function definition for ‘knn’ maPredictDSC: no visible global function definition for ‘svm’ perfDSC: no visible global function definition for ‘prediction’ perfDSC: no visible global function definition for ‘performance’ perfDSC: no visible global function definition for ‘na.omit’ perfDSC: no visible global function definition for ‘trapezint’ perfDSC: no visible global function definition for ‘rocdemo.sca’ perfDSC: no visible binding for global variable ‘dxrule.sca’ perfDSC: no visible global function definition for ‘AUC’ Undefined global functions or variables: AUC ReadAffy contrasts.fit createFolds dxrule.sca eBayes exprs formula gcrma installed.packages knn lmFit makeContrasts mas5 mas5calls mclapply model.matrix na.omit performance predict prediction pt rma rocdemo.sca sd svm topTable trapezint wilcox.test Consider adding importFrom("stats", "formula", "model.matrix", "na.omit", "predict", "pt", "sd", "wilcox.test") importFrom("utils", "installed.packages") to your NAMESPACE file. * 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 ... ERROR Running examples in ‘maPredictDSC-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: predictDSC > ### Title: Phenotype prediction using microarray data: approach of the best > ### overall team in the IMPROVER Diagnostic Signature Challenge > ### Aliases: predictDSC > ### Keywords: parametric methods > > ### ** Examples > > > library(maPredictDSC) > library(LungCancerACvsSCCGEO) > data(LungCancerACvsSCCGEO) > anoLC files group 1 GSM137916.CEL.gz AC 2 GSM258560.CEL.gz AC 3 GSM258579.CEL.gz AC 4 GSM258589.CEL.gz AC 5 GSM258598.CEL.gz AC 6 GSM353885.CEL.gz AC 7 GSM467021.CEL.gz AC 8 GSM152624.CEL.gz SCC 9 GSM258580.CEL.gz SCC 10 GSM277678.CEL.gz SCC 11 GSM466956.CEL.gz SCC 12 GSM466980.CEL.gz SCC 13 GSM466989.CEL.gz SCC 14 GSM467023.CEL.gz SCC 15 GSM46976.CEL.gz SCC 16 lung_100.CEL Test 17 lung_107.CEL Test 18 lung_111.CEL Test 19 lung_15.CEL Test 20 lung_150.CEL Test 21 lung_29.CEL Test 22 lung_30.CEL Test 23 lung_35.CEL Test 24 lung_40.CEL Test 25 lung_41.CEL Test 26 lung_50.CEL Test 27 lung_51.CEL Test 28 lung_59.CEL Test 29 lung_62.CEL Test 30 lung_8.CEL Test > gsLC SCC AC lung_15.CEL 1 0 lung_29.CEL 0 1 lung_30.CEL 0 1 lung_59.CEL 0 1 lung_51.CEL 1 0 lung_100.CEL 1 0 lung_62.CEL 1 0 lung_8.CEL 1 0 lung_41.CEL 0 1 lung_40.CEL 1 0 lung_150.CEL 1 0 lung_111.CEL 1 0 lung_35.CEL 0 1 lung_107.CEL 1 0 lung_50.CEL 0 1 > table(anoLC$group) AC SCC Test 7 8 15 > > #run a series of methods combinations > modlist=predictDSC(ano=anoLC,celfile.path=system.file("extdata/lungcancer",package="LungCancerACvsSCCGEO"), + annotation="hgu133plus2.db", + preprocs=c("rma"),filters=c("mttest","wilcox"),FCT=1.0,classifiers=c("LDA","kNN"), + CVP=2,NF=4, NR=1) Loading required package: parallel Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu133plus2cdf’ Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu133plus2cdf’ Killed * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘maPredictDSC.Rnw’... failed to complete the test ERROR Errors in running code in vignettes: when running code in ‘maPredictDSC.Rnw’ ... > modlist = predictDSC(ano = anoLC, celfile.path = system.file("extdata/lungcancer", + package = "LungCancerACvsSCCGEO"), annotation = "hgu133plu ..." ... [TRUNCATED] Loading required package: parallel Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu133plus2cdf’ Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu133plus2cdf’ Background correcting Killed ... incomplete output. Crash? * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: --- re-building ‘maPredictDSC.Rnw’ using Sweave Loading required package: MASS 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, sort, 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: gcrma Loading required package: ROC Loading required package: class Loading required package: e1071 Loading required package: caret Loading required package: ggplot2 Loading required package: lattice Loading required package: hgu133plus2.db Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Attaching package: ‘AnnotationDbi’ The following object is masked from ‘package:MASS’: select Loading required package: org.Hs.eg.db Loading required package: ROCR Loading required package: LungCancerACvsSCCGEO Loading required package: parallel Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu133plus2cdf’ Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu133plus2cdf’ Killed * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/maPredictDSC.Rcheck/00check.log’ for details.
maPredictDSC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL maPredictDSC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘maPredictDSC’ ... ** using staged installation ** R ** 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 (maPredictDSC)
maPredictDSC.Rcheck/maPredictDSC-Ex.timings
name | user | system | elapsed | |
aggregateDSC | 0 | 0 | 0 | |
perfDSC | 0.030 | 0.000 | 0.031 | |