############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:maPredictDSC.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings maPredictDSC_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/maPredictDSC.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 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 ‘maPredictDSC/DESCRIPTION’ ... OK * this is package ‘maPredictDSC’ version ‘1.40.0’ * 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 loading without being on the library search path ... 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 trying URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu133plus2cdf_2.18.0.tar.gz' Content type 'application/x-gzip' length 4353300 bytes (4.2 MB) ================================================== downloaded 4.2 MB * installing *source* package ‘hgu133plus2cdf’ ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu133plus2cdf’ Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu133plus2cdf’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu133plus2cdf’ Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu133plus2cdf’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hgu133plus2cdf’ Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hgu133plus2cdf’ ** testing if installed package keeps a record of temporary installation path * DONE (hgu133plus2cdf) The downloaded source packages are in ‘/home/biocbuild/tmp/Rtmp2tkPDO/downloaded_packages’ 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 Normalizing Calculating Expression Getting probe level data... Computing p-values Making P/M/A Calls Warning in mclapply(ml, mff) : scheduled cores 1, 2 did not deliver results, all values of the jobs will be affected Warning in mean.default(poolres) : argument is not numeric or logical: returning NA * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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 ‘/home/biocbuild/bbs-3.18-bioc/meat/maPredictDSC.Rcheck/00check.log’ for details.