* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/TCGA2STAT.Rcheck’ * using R Under development (unstable) (2020-03-29 r78100) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘TCGA2STAT/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TCGA2STAT’ version ‘1.2’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘TCGA2STAT’ 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 ... OK * 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 line widths ... 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 ... OK * checking examples with --run-donttest ... ERROR Running examples in ‘TCGA2STAT-Ex.R’ failed The error most likely occurred in: > ### Name: SampleSplit > ### Title: Split the Data by Sample Types. > ### Aliases: SampleSplit > > ### ** Examples > > ## No test: > library(TCGA2STAT) > lusc.rnaseq2 <- getTCGA(disease="LUSC", data.type="RNASeq2") RNASeqV2 data will be imported! This may take some time! 20501 genes have been imported! > lusc.rnaseq2.bytype <- SampleSplit(lusc.rnaseq2$dat) ----------- FAILURE REPORT -------------- --- failure: the condition has length > 1 --- --- srcref --- : --- package (from environment) --- TCGA2STAT --- call from context --- SampleSplit(lusc.rnaseq2$dat) --- call from argument --- if (class(temp) == "data.frame" | class(temp) == "matrix") { if (sum(colnames(temp)[1:3] == c("Gene_Symbol", "Chromosome", "Genomic_Coordinate")) == 3) { annot <- temp[, 1:3] temp <- temp[, -c(1:3)] temp.type <- sapply(colnames(temp), function(s) unlist(strsplit(s, "-"))[4]) primary.tumor <- cbind(annot, temp[, grep("^01", temp.type)]) recurrent.tumor <- cbind(annot, temp[, grep("^02", temp.type)]) normal <- cbind(annot, temp[, c(grep("^10", temp.type), grep("^11", temp.type), grep("^12", temp.type))]) } else { temp.type <- sapply(colnames(temp), function(s) unlist(strsplit(s, "-"))[4]) primary.tumor <- temp[, grep("^01", temp.type)] recurrent.tumor <- temp[, grep("^02", temp.type)] normal <- temp[, c(grep("^10", temp.type), grep("^11", temp.type), grep("^12", temp.type))] } return(list(primary.tumor = primary.tumor, recurrent.tumor = recurrent.tumor, normal = normal)) } --- R stacktrace --- where 1: SampleSplit(lusc.rnaseq2$dat) --- value of length: 2 type: logical --- [1] TRUE FALSE --- function from context --- function (dat) { temp <- dat if (is.null(temp)) { message("Empy data object") return(NULL) } if (class(temp) == "data.frame" | class(temp) == "matrix") { if (sum(colnames(temp)[1:3] == c("Gene_Symbol", "Chromosome", "Genomic_Coordinate")) == 3) { annot <- temp[, 1:3] temp <- temp[, -c(1:3)] temp.type <- sapply(colnames(temp), function(s) unlist(strsplit(s, "-"))[4]) primary.tumor <- cbind(annot, temp[, grep("^01", temp.type)]) recurrent.tumor <- cbind(annot, temp[, grep("^02", temp.type)]) normal <- cbind(annot, temp[, c(grep("^10", temp.type), grep("^11", temp.type), grep("^12", temp.type))]) } else { temp.type <- sapply(colnames(temp), function(s) unlist(strsplit(s, "-"))[4]) primary.tumor <- temp[, grep("^01", temp.type)] recurrent.tumor <- temp[, grep("^02", temp.type)] normal <- temp[, c(grep("^10", temp.type), grep("^11", temp.type), grep("^12", temp.type))] } return(list(primary.tumor = primary.tumor, recurrent.tumor = recurrent.tumor, normal = normal)) } } --- function search by body --- Function SampleSplit in namespace TCGA2STAT has this body. ----------- END OF FAILURE REPORT -------------- Error in if (class(temp) == "data.frame" | class(temp) == "matrix") { : the condition has length > 1 Calls: SampleSplit Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR See ‘/data/blackswan/ripley/R/packages/tests-devel/TCGA2STAT.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:08.94, 55.92 + 4.16