* using log directory 'd:/Rcompile/CRANpkg/local/4.4/NameNeedle.Rcheck' * using R Under development (unstable) (2024-03-22 r86169 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'NameNeedle/DESCRIPTION' ... OK * this is package 'NameNeedle' version '1.2.7' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'NameNeedle' 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 ... [0s] OK * checking whether the package can be loaded with stated dependencies ... [0s] OK * checking whether the package can be unloaded cleanly ... [0s] OK * checking whether the namespace can be loaded with stated dependencies ... [0s] OK * checking whether the namespace can be unloaded cleanly ... [0s] OK * checking loading without being on the library search path ... [0s] OK * checking use of S3 registration ... 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 ... [2s] OK * checking Rd files ... [0s] 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 ... [0s] OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [0s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [182s] ERROR Running 'needles.R' [182s] Running the tests in 'tests/needles.R' failed. Complete output: > ### > ### NEEDLES.R - Package test code > ### > > options(warn=1) > library(NameNeedle) > source("checkFuncs") > > extdata.dir <- system.file("extdata", package="NameNeedle") > data(cellLineNames) > > > ## Change the default settings... > needleParams <- defaultNeedleParams > needleParams$MISMATCH <- -2 > needleParams$MATCH <- 2 > > ## Match RPPA names to SF2 names > matchscore <- matchcode <- rep(NA, length(sf2Names)) > for (j in seq_along(sf2Names)) { + scores <- sapply(rppaNames, + function(x, y) { + needles(x, y, needleParams)$score + }, + y=sf2Names[j]) + matchcode[j] <- paste(which(scores == max(scores)), collapse=',') + matchscore[j] <- max(scores) + } > > rppaMatch <- sapply(matchcode, + function(x) { + y <- as.numeric(strsplit(x, ',')[[1]]) + paste(rppaNames[y], collapse="; ") + }) > > ## Match Illumina names to SF2 names > imatchscore <- imatchcode <- rep(NA, length(sf2Names)) > for (j in seq_along(sf2Names)) { + scores <- sapply(illuNames, + function(x, y) { + needles(x, y, needleParams)$score + }, + y=sf2Names[j]) + imatchcode[j] <- paste(which(scores == max(scores)), collapse=',') + imatchscore[j] <- max(scores) + } > > illuMatch <- sapply(imatchcode, + function(x) { + y <- as.numeric(strsplit(x, ',')[[1]]) + paste(illuNames[y], collapse="; ") + }) > > ## Collect aggregated output > matcher <- data.frame(rppaMatch=rppaMatch, + rppaScore=matchscore, + illuMatch=illuMatch, + illuScore=imatchscore, + stringsAsFactors = TRUE) > > ## Save results to disk (uncomment iff code changed) > prevResults.filename <- "namesMatched.tsv" > # uncomment iff code changed - replace existing results manually > #write.table(matcher, file=prevResults.filename, sep='\t', quote=FALSE, col.names=NA) > > ## Retrieve previous results > prevResults <- local({ + prevResults.pathname <- file.path(extdata.dir, prevResults.filename) + colClasses <- c("integer", rep(c("factor", "numeric"), 2)) + df <- read.delim(prevResults.pathname, colClasses=colClasses, + header=TRUE, stringsAsFactors = TRUE) + df[, -1] ## Toss unwanted first column (row numbers) + }) > > ## Verify against previous results > checkIdentical(matcher, prevResults) [1] TRUE > > > proc.time() user system elapsed 7.21 0.20 7.34 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [23s] OK * checking PDF version of manual ... [27s] OK * checking HTML version of manual ... [1s] OK * DONE Status: 1 ERROR