* using log directory 'C:/msys64/home/tomas/utf/ucrt64/inst_all/BioSeqClass.Rcheck' * using R Under development (unstable) (2020-06-23 r78739) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'BioSeqClass/DESCRIPTION' ... OK * this is package 'BioSeqClass' version '1.42.0' * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'BioSeqClass' can be installed ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Package listed in more than one of Depends, Imports, Suggests, Enhances: 'scatterplot3d' A package should be listed in only one of these fields. * 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 Package in Depends field not imported from: 'scatterplot3d' 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 ... OK * 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 data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ERROR Running examples in 'BioSeqClass-Ex.R' failed The error most likely occurred in: > ### Name: classify > ### Title: Classification with Specific Features and Cross-Validation > ### Aliases: classify > > ### ** Examples > > ## read positive/negative sequence from files. > tmpfile1 = file.path(path.package("BioSeqClass"), "example", "acetylation_K.pos40.pep") > tmpfile2 = file.path(path.package("BioSeqClass"), "example", "acetylation_K.neg40.pep") > posSeq = as.matrix(read.csv(tmpfile1,header=FALSE,sep="\t",row.names=1))[,1] > negSeq = as.matrix(read.csv(tmpfile2,header=FALSE,sep="\t",row.names=1))[,1] > seq=c(posSeq,negSeq) > classLable=c(rep("+1",length(posSeq)),rep("-1",length(negSeq)) ) > data = data.frame(featureBinary(seq),classLable) > > ## Use LibSVM and 5-cross-validation to classify. > LIBSVM_CV5 = classify(data,classifyMethod="libsvm",cv=5, + svm.kernel="linear",svm.scale=FALSE) > ## Features selection is done by envoking "CfsSubsetEval" method in WEKA. > FS_LIBSVM_CV5 = classify(data,classifyMethod="libsvm",cv=5,evaluator="CfsSubsetEval", + search="BestFirst",svm.kernel="linear",svm.scale=FALSE) Error in system(command, intern = TRUE) : '-cp' not found Calls: classify -> selectWeka -> system Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... 'BioSeqClass.Rnw'... failed ERROR Errors in running code in vignettes: when running code in 'BioSeqClass.Rnw' ... sp acc mcc pc 0.5616667 0.5616667 0.1243355 0.3918323 > FS_LIBSVM_CV5 = classify(data, classifyMethod = "libsvm", + cv = 5, evaluator = "CfsSubsetEval", search = "BestFirst", + svm.kernel = "lin ..." ... [TRUNCATED] When sourcing 'BioSeqClass.R': Error: '-cp' not found Execution halted * checking re-building of vignette outputs ... NOTE Error(s) in re-building vignettes: ... --- re-building 'BioSeqClass.Rnw' using Sweave Loading required package: scatterplot3d Error: processing vignette 'BioSeqClass.Rnw' failed with diagnostics: chunk 7 (label = classModel) Error in system(command, intern = TRUE) : '-cp' not found --- failed re-building 'BioSeqClass.Rnw' SUMMARY: processing the following file failed: 'BioSeqClass.Rnw' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 3 NOTEs See 'C:/msys64/home/tomas/utf/ucrt64/inst_all/BioSeqClass.Rcheck/00check.log' for details.