CRAN Package Check Results for Package NameNeedle

Last updated on 2024-03-28 23:01:51 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.7 1.90 60.08 61.98 OK
r-devel-linux-x86_64-debian-gcc 1.2.7 1.58 43.49 45.07 OK
r-devel-linux-x86_64-fedora-clang 1.2.7 77.12 OK
r-devel-linux-x86_64-fedora-gcc 1.2.7 84.29 OK
r-devel-windows-x86_64 1.2.7 3.00 252.00 255.00 ERROR
r-patched-linux-x86_64 1.2.7 1.79 56.50 58.29 OK
r-release-linux-x86_64 1.2.7 1.93 56.81 58.74 OK
r-release-macos-arm64 1.2.7 36.00 OK
r-release-macos-x86_64 1.2.7 95.00 OK
r-release-windows-x86_64 1.2.7 5.00 76.00 81.00 OK
r-oldrel-macos-arm64 1.2.7 34.00 OK
r-oldrel-windows-x86_64 1.2.7 7.00 94.00 101.00 OK

Check Details

Version: 1.2.7
Check: tests
Result: 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 Flavor: r-devel-windows-x86_64