Check results for 'LDcorSV'

using R Under development (unstable) (2026-02-12 r89409)
using platform: aarch64-apple-darwin23
R was compiled by Apple clang version 17.0.0 (clang-1700.3.19.1) GNU Fortran (GCC) 14.2.0
running under: macOS Sequoia 15.7.1
using session charset: UTF-8 * current time: 2026-02-13 01:59:14 UTC
checking for file ‘LDcorSV/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘LDcorSV’ version ‘1.3.4’
package encoding: UTF-8
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 ‘LDcorSV’ can be installed ... [1s/1s] OK See the install log for details.
checking installed package size ... OK
checking package 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/0s] OK
checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
checking whether the package can be unloaded cleanly ... [0s/0s] OK
checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
checking loading without being on the library search path ... [0s/0s] 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 ... [1s/1s] OK
checking Rd files ... [0s/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/0s] OK
checking data for ASCII and uncompressed saves ... OK
checking examples ... [0s/0s] ERROR Running examples in ‘LDcorSV-Ex.R’ failed The error most likely occurred in: > ### Name: LD.Measures > ### Title: LD Measures > ### Aliases: LD.Measures > > ### ** Examples > > data(data.test) > Geno <- data.test[[1]] > V.WAIS <- data.test[[2]] > S.2POP <- data.test[[3]] > > LD <- LD.Measures(Geno, V = V.WAIS, S = S.2POP, data = "G", supinfo = TRUE, na.presence = TRUE) *** caught segfault *** address 0x110, cause 'invalid permissions' Traceback: 1: Inv.proj.matrix.sdp(V) 2: Measure.R2V(biloci = lij, V = V, na.presence = na.presence) 3: FUN(X[[i]], ...) 4: lapply(X = X, FUN = FUN, ...) 5: sapply((i + 1):(ncol(donnees)), function(j) { li <- donnees[, i] lj <- donnees[, j] lij <- cbind(li, lj) loc1 <- c(loc1, mark[i]) loc2 <- c(loc2, mark[j]) M.r2 <- Measure.R2(biloci = lij, na.presence = na.presence) if (!S.yes) M.r2s <- Measure.R2S(biloci = lij, struc = S, na.presence = na.presence) if (!V.yes) { if (!na.presence) M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence, V_inv = V_inv) else M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence) } if (!S.yes & !V.yes) { if (!na.presence) M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence, V_inv = V_inv) else M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence) } r2 <- c(r2, M.r2) r2s <- c(r2s, M.r2s) r2v <- c(r2v, M.r2v) r2vs <- c(r2vs, M.r2vs) if (supinfo) { M.MAF.loc1 <- NA M.heterofreq.loc1 <- NA M.NAfreq.loc1 <- NA M.MAF.loc2 <- NA M.heterofreq.loc2 <- NA M.NAfreq.loc2 <- NA supinfo.li <- info[, which(colnames(info) == mark[i])] supinfo.lj <- info[, which(colnames(info) == mark[j])] M.MAF.loc1 <- supinfo.li[1] M.heterofreq.loc1 <- supinfo.li[2] M.NAfreq.loc1 <- supinfo.li[3] M.MAF.loc2 <- supinfo.lj[1] M.heterofreq.loc2 <- supinfo.lj[2] M.NAfreq.loc2 <- supinfo.lj[3] MAF.loc1 <- c(MAF.loc1, M.MAF.loc1) heterofreq.loc1 <- c(heterofreq.loc1, M.heterofreq.loc1) NAfreq.loc1 <- c(NAfreq.loc1, M.NAfreq.loc1) MAF.loc2 <- c(MAF.loc2, M.MAF.loc2) heterofreq.loc2 <- c(heterofreq.loc2, M.heterofreq.loc2) NAfreq.loc2 <- c(NAfreq.loc2, M.NAfreq.loc2) } res <- c(as.matrix(loc1), as.matrix(loc2), r2, r2s, r2v, r2vs, MAF.loc1, heterofreq.loc1, NAfreq.loc1, MAF.loc2, heterofreq.loc2, NAfreq.loc2)}) 6: FUN(X[[i]], ...) 7: lapply(X = S, FUN = FUN, ...) 8: doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) 11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 14: FUN(X[[i]], ...) 15: lapply(seq_len(cores), inner.do) 16: mclapply(1:(ncol(donnees) - 1), function(i) { res <- sapply((i + 1):(ncol(donnees)), function(j) { li <- donnees[, i] lj <- donnees[, j] lij <- cbind(li, lj) loc1 <- c(loc1, mark[i]) loc2 <- c(loc2, mark[j]) M.r2 <- Measure.R2(biloci = lij, na.presence = na.presence) if (!S.yes) M.r2s <- Measure.R2S(biloci = lij, struc = S, na.presence = na.presence) if (!V.yes) { if (!na.presence) M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence, V_inv = V_inv) else M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence) } if (!S.yes & !V.yes) { if (!na.presence) M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence, V_inv = V_inv) else M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence) } *** caught segfault *** address 0x110, cause 'invalid permissions' r2 <- c(r2, M.r2) r2s <- c(r2s, M.r2s) r2v <- c(r2v, M.r2v) r2vs <- c(r2vs, M.r2vs) if (supinfo) { M.MAF.loc1 <- NA M.heterofreq.loc1 <- NA M.NAfreq.loc1 <- NA M.MAF.loc2 <- NA M.heterofreq.loc2 <- NA M.NAfreq.loc2 <- NA supinfo.li <- info[, which(colnames(info) == mark[i])] supinfo.lj <- info[, which(colnames(info) == mark[j])] M.MAF.loc1 <- supinfo.li[1] M.heterofreq.loc1 <- supinfo.li[2] M.NAfreq.loc1 <- supinfo.li[3] M.MAF.loc2 <- supinfo.lj[1] M.heterofreq.loc2 <- supinfo.lj[2] M.NAfreq.loc2 <- supinfo.lj[3] MAF.loc1 <- c(MAF.loc1, M.MAF.loc1) heterofreq.loc1 <- c(heterofreq.loc1, M.heterofreq.loc1) NAfreq.loc1 <- c(NAfreq.loc1, M.NAfreq.loc1) MAF.loc2 <- c(MAF.loc2, M.MAF.loc2) heterofreq.loc2 <- c(heterofreq.loc2, M.heterofreq.loc2) NAfreq.loc2 <- c(NAfreq.loc2, M.NAfreq.loc2) } res <- c(as.matrix(loc1), as.matrix(loc2), r2, r2s, r2v, r2vs, MAF.loc1, heterofreq.loc1, NAfreq.loc1, MAF.loc2, heterofreq.loc2, NAfreq.loc2) }) RES <- cbind(RES, res)}) 17: LD.Measures(Geno, V = V.WAIS, S = S.2POP, data = "G", supinfo = TRUE, na.presence = TRUE) An irrecoverable exception occurred. R is aborting now ... Traceback: 1: Inv.proj.matrix.sdp(V) 2: Measure.R2V(biloci = lij, V = V, na.presence = na.presence) 3: FUN(X[[i]], ...) 4: lapply(X = X, FUN = FUN, ...) 5: sapply((i + 1):(ncol(donnees)), function(j) { li <- donnees[, i] lj <- donnees[, j] lij <- cbind(li, lj) loc1 <- c(loc1, mark[i]) loc2 <- c(loc2, mark[j]) M.r2 <- Measure.R2(biloci = lij, na.presence = na.presence) if (!S.yes) M.r2s <- Measure.R2S(biloci = lij, struc = S, na.presence = na.presence) if (!V.yes) { if (!na.presence) M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence, V_inv = V_inv) else M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence) } if (!S.yes & !V.yes) { if (!na.presence) M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence, V_inv = V_inv) else M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence) } r2 <- c(r2, M.r2) r2s <- c(r2s, M.r2s) r2v <- c(r2v, M.r2v) r2vs <- c(r2vs, M.r2vs) if (supinfo) { M.MAF.loc1 <- NA M.heterofreq.loc1 <- NA M.NAfreq.loc1 <- NA M.MAF.loc2 <- NA M.heterofreq.loc2 <- NA M.NAfreq.loc2 <- NA supinfo.li <- info[, which(colnames(info) == mark[i])] supinfo.lj <- info[, which(colnames(info) == mark[j])] M.MAF.loc1 <- supinfo.li[1] M.heterofreq.loc1 <- supinfo.li[2] M.NAfreq.loc1 <- supinfo.li[3] M.MAF.loc2 <- supinfo.lj[1] M.heterofreq.loc2 <- supinfo.lj[2] M.NAfreq.loc2 <- supinfo.lj[3] MAF.loc1 <- c(MAF.loc1, M.MAF.loc1) heterofreq.loc1 <- c(heterofreq.loc1, M.heterofreq.loc1) NAfreq.loc1 <- c(NAfreq.loc1, M.NAfreq.loc1) MAF.loc2 <- c(MAF.loc2, M.MAF.loc2) heterofreq.loc2 <- c(heterofreq.loc2, M.heterofreq.loc2) NAfreq.loc2 <- c(NAfreq.loc2, M.NAfreq.loc2) } res <- c(as.matrix(loc1), as.matrix(loc2), r2, r2s, r2v, r2vs, MAF.loc1, heterofreq.loc1, NAfreq.loc1, MAF.loc2, heterofreq.loc2, NAfreq.loc2)}) 6: FUN(X[[i]], ...) 7: lapply(X = S, FUN = FUN, ...) 8: doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) 11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 14: FUN(X[[i]], ...) 15: lapply(seq_len(cores), inner.do) 16: mclapply(1:(ncol(donnees) - 1), function(i) { res <- sapply((i + 1):(ncol(donnees)), function(j) { li <- donnees[, i] lj <- donnees[, j] lij <- cbind(li, lj) loc1 <- c(loc1, mark[i]) loc2 <- c(loc2, mark[j]) M.r2 <- Measure.R2(biloci = lij, na.presence = na.presence) if (!S.yes) M.r2s <- Measure.R2S(biloci = lij, struc = S, na.presence = na.presence) if (!V.yes) { if (!na.presence) M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence, V_inv = V_inv) else M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence) } if (!S.yes & !V.yes) { if (!na.presence) M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence, V_inv = V_inv) else M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence) } r2 <- c(r2, M.r2) r2s <- c(r2s, M.r2s) r2v <- c(r2v, M.r2v) r2vs <- c(r2vs, M.r2vs) if (supinfo) { M.MAF.loc1 <- NA M.heterofreq.loc1 <- NA M.NAfreq.loc1 <- NA M.MAF.loc2 <- NA M.heterofreq.loc2 <- NA M.NAfreq.loc2 <- NA supinfo.li <- info[, which(colnames(info) == mark[i])] supinfo.lj <- info[, which(colnames(info) == mark[j])] M.MAF.loc1 <- supinfo.li[1] M.heterofreq.loc1 <- supinfo.li[2] M.NAfreq.loc1 <- supinfo.li[3] M.MAF.loc2 <- supinfo.lj[1] M.heterofreq.loc2 <- supinfo.lj[2] M.NAfreq.loc2 <- supinfo.lj[3] MAF.loc1 <- c(MAF.loc1, M.MAF.loc1) heterofreq.loc1 <- c(heterofreq.loc1, M.heterofreq.loc1) NAfreq.loc1 <- c(NAfreq.loc1, M.NAfreq.loc1) MAF.loc2 <- c(MAF.loc2, M.MAF.loc2) heterofreq.loc2 <- c(heterofreq.loc2, M.heterofreq.loc2) NAfreq.loc2 <- c(NAfreq.loc2, M.NAfreq.loc2) } res <- c(as.matrix(loc1), as.matrix(loc2), r2, r2s, r2v, r2vs, MAF.loc1, heterofreq.loc1, NAfreq.loc1, MAF.loc2, heterofreq.loc2, NAfreq.loc2) }) RES <- cbind(RES, res)}) 17: LD.Measures(Geno, V = V.WAIS, S = S.2POP, data = "G", supinfo = TRUE, na.presence = TRUE) An irrecoverable exception occurred. R is aborting now ... Warning in mclapply(1:(ncol(donnees) - 1), function(i) { : scheduled cores 1, 2 did not deliver results, all values of the jobs will be affected Error in matrix(unlist(RES), nrow = length(RES[[1]][, 1])) : 'data' must be of a vector type, was 'NULL' Calls: LD.Measures -> matrix Execution halted
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [0s/0s] ERROR Running ‘testthat.R’ [0s/0s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(LDcorSV) > > test_check("LDcorSV") *** caught segfault *** address 0x110, cause 'invalid permissions' *** caught segfault *** address 0x110, cause 'invalid permissions' Traceback: 1: Inv.proj.matrix.sdp(V) 2: Measure.R2V(biloci = lij, V = V, na.presence = na.presence) 3: FUN(X[[i]], ...) 4: lapply(X = X, FUN = FUN, ...) 5: sapply((i + 1):(ncol(donnees)), function(j) { li <- donnees[, i] lj <- donnees[, j] lij <- cbind(li, lj) loc1 <- c(loc1, mark[i]) loc2 <- c(loc2, mark[j]) M.r2 <- Measure.R2(biloci = lij, na.presence = na.presence) if (!S.yes) M.r2s <- Measure.R2S(biloci = lij, struc = S, na.presence = na.presence) if (!V.yes) { if (!na.presence) M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence, V_inv = V_inv) else M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence) } if (!S.yes & !V.yes) { if (!na.presence) M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence, V_inv = V_inv) else M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence) } r2 <- c(r2, M.r2) r2s <- c(r2s, M.r2s) r2v <- c(r2v, M.r2v) r2vs <- c(r2vs, M.r2vs) if (supinfo) { M.MAF.loc1 <- NA M.heterofreq.loc1 <- NA M.NAfreq.loc1 <- NA M.MAF.loc2 <- NA M.heterofreq.loc2 <- NA M.NAfreq.loc2 <- NA supinfo.li <- info[, which(colnames(info) == mark[i])] supinfo.lj <- info[, which(colnames(info) == mark[j])] M.MAF.loc1 <- supinfo.li[1] M.heterofreq.loc1 <- supinfo.li[2] M.NAfreq.loc1 <- supinfo.li[3] M.MAF.loc2 <- supinfo.lj[1] M.heterofreq.loc2 <- supinfo.lj[2] M.NAfreq.loc2 <- supinfo.lj[3] MAF.loc1 <- c(MAF.loc1, M.MAF.loc1) heterofreq.loc1 <- c(heterofreq.loc1, M.heterofreq.loc1) NAfreq.loc1 <- c(NAfreq.loc1, M.NAfreq.loc1) MAF.loc2 <- c(MAF.loc2, M.MAF.loc2) heterofreq.loc2 <- c(heterofreq.loc2, M.heterofreq.loc2) NAfreq.loc2 <- c(NAfreq.loc2, M.NAfreq.loc2) } res <- c(as.matrix(loc1), as.matrix(loc2), r2, r2s, r2v, r2vs, MAF.loc1, heterofreq.loc1, NAfreq.loc1, MAF.loc2, heterofreq.loc2, NAfreq.loc2)}) 6: FUN(X[[i]], ...) 7: lapply(X = S, FUN = FUN, ...) 8: doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10: tryCatchList(expr, classes, parentenv, handlers) Traceback: 1: Inv.proj.matrix.sdp(V) 2: Measure.R2V(biloci = lij, V = V, na.presence = na.presence) 3: FUN(X[[i]], ...) 4: lapply(X = X, FUN = FUN, ...) 5: sapply((i + 1):(ncol(donnees)), function(j) { li <- donnees[, i]11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) lj <- donnees[, j] lij <- cbind(li, lj) loc1 <- c(loc1, mark[i]) loc2 <- c(loc2, mark[j]) M.r2 <- Measure.R2(biloci = lij, na.presence = na.presence) if (!S.yes) M.r2s <- Measure.R2S(biloci = lij, struc = S, na.presence = na.presence) if (!V.yes) { if (!na.presence) M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence, V_inv = V_inv) else M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence) } if (!S.yes & !V.yes) { if (!na.presence) M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } na.presence = na.presence, V_inv = V_inv) else M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence) } r2 <- c(r2, M.r2) r2s <- c(r2s, M.r2s) r2v <- c(r2v, M.r2v) r2vs <- c(r2vs, M.r2vs) if (supinfo) { M.MAF.loc1 <- NA M.heterofreq.loc1 <- NA M.NAfreq.loc1 <- NA M.MAF.loc2 <- NA M.heterofreq.loc2 <- NA M.NAfreq.loc2 <- NA invisible(structure(msg, class = "try-error", condition = e))}) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 14: FUN(X[[i]], ...) 15: lapply(seq_len(cores), inner.do) 16: mclapply(1:(ncol(donnees) - 1), function(i) { res <- sapply((i + 1):(ncol(donnees)), function(j) { li <- donnees[, i] lj <- donnees[, j] lij <- cbind(li, lj) loc1 <- c(loc1, mark[i]) loc2 <- c(loc2, mark[j]) M.r2 <- Measure.R2(biloci = lij, na.presence = na.presence) if (!S.yes) supinfo.li <- info[, which(colnames(info) == mark[i])] supinfo.lj <- info[, which(colnames(info) == mark[j])] M.MAF.loc1 <- supinfo.li[1] M.heterofreq.loc1 <- supinfo.li[2] M.NAfreq.loc1 <- supinfo.li[3] M.MAF.loc2 <- supinfo.lj[1] M.heterofreq.loc2 <- supinfo.lj[2] M.NAfreq.loc2 <- supinfo.lj[3] MAF.loc1 <- c(MAF.loc1, M.MAF.loc1) heterofreq.loc1 <- c(heterofreq.loc1, M.heterofreq.loc1) NAfreq.loc1 <- c(NAfreq.loc1, M.NAfreq.loc1) MAF.loc2 <- c(MAF.loc2, M.MAF.loc2) heterofreq.loc2 <- c(heterofreq.loc2, M.heterofreq.loc2) NAfreq.loc2 <- c(NAfreq.loc2, M.NAfreq.loc2) } res <- c(as.matrix(loc1), as.matrix(loc2), r2, r2s, r2v, r2vs, MAF.loc1, heterofreq.loc1, NAfreq.loc1, MAF.loc2, heterofreq.loc2, NAfreq.loc2)}) M.r2s <- Measure.R2S(biloci = lij, struc = S, na.presence = na.presence) if (!V.yes) { if (!na.presence) M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence, V_inv = V_inv) else M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence) } if (!S.yes & !V.yes) { if (!na.presence) M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence, V_inv = V_inv) else M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence) } r2 <- c(r2, M.r2) r2s <- c(r2s, M.r2s) r2v <- c(r2v, M.r2v) r2vs <- c(r2vs, M.r2vs) if (supinfo) { M.MAF.loc1 <- NA M.heterofreq.loc1 <- NA M.NAfreq.loc1 <- NA M.MAF.loc2 <- NA M.heterofreq.loc2 <- NA M.NAfreq.loc2 <- NA supinfo.li <- info[, which(colnames(info) == mark[i])] 6: FUN(X[[i]], ...) 7: lapply(X = S, FUN = FUN, ...) 8: doTryCatch(return(expr), name, parentenv, handler) 9: tryCatchOne(expr, names, parentenv, handlers[[1L]]) supinfo.lj <- info[, which(colnames(info) == mark[j])] M.MAF.loc1 <- supinfo.li[1] M.heterofreq.loc1 <- supinfo.li[2] M.NAfreq.loc1 <- supinfo.li[3] M.MAF.loc2 <- supinfo.lj[1]10: tryCatchList(expr, classes, parentenv, handlers) 11: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) M.heterofreq.loc2 <- supinfo.lj[2] M.NAfreq.loc2 <- supinfo.lj[3] MAF.loc1 <- c(MAF.loc1, M.MAF.loc1) heterofreq.loc1 <- c(heterofreq.loc1, M.heterofreq.loc1) NAfreq.loc1 <- c(NAfreq.loc1, M.NAfreq.loc1) MAF.loc2 <- c(MAF.loc2, M.MAF.loc2) heterofreq.loc2 <- c(heterofreq.loc2, M.heterofreq.loc2) NAfreq.loc2 <- c(NAfreq.loc2, M.NAfreq.loc2) } res <- c(as.matrix(loc1), as.matrix(loc2), r2, r2s, r2v, r2vs, MAF.loc1, heterofreq.loc1, NAfreq.loc1, MAF.loc2, prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 12: try(lapply(X = S, FUN = FUN, ...), silent = TRUE) heterofreq.loc2, NAfreq.loc2) }) RES <- cbind(RES, res)}) 17: LD.Measures(Geno, V = V.WAIS, S = S.2POP, data = "G", supinfo = TRUE, na.presence = TRUE) 18: eval(code, test_env) 19: eval(code, test_env) 20: withCallingHandlers({ eval(code, test_env) 13: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) 14: FUN(X[[i]], ...) 15: lapply(seq_len(cores), inner.do) 16: new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, mclapply(1:(ncol(donnees) - 1), function(i) { res <- sapply((i + 1):(ncol(donnees)), function(j) { li <- donnees[, i] lj <- donnees[, j] lij <- cbind(li, lj) loc1 <- c(loc1, mark[i]) loc2 <- c(loc2, mark[j]) M.r2 <- Measure.R2(biloci = lij, na.presence = na.presence) if (!S.yes) error = handle_error, interrupt = handle_interrupt) 21: doTryCatch(return(expr), name, parentenv, handler) 22: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 23: tryCatchList(expr, classes, parentenv, handlers) 24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { M.r2s <- Measure.R2S(biloci = lij, struc = S, na.presence = na.presence) if (!V.yes) { if (!na.presence) M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence, V_inv = V_inv) else M.r2v <- Measure.R2V(biloci = lij, V = V, na.presence = na.presence) } if (!S.yes & !V.yes) { if (!na.presence) M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence, V_inv = V_inv) else M.r2vs <- Measure.R2VS(biloci = lij, V = V, struc = S, na.presence = na.presence) } r2 <- c(r2, M.r2) r2s <- c(r2s, M.r2s) r2v <- c(r2v, M.r2v) snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 25: doWithOneRestart(return(expr), restart) 26: withOneRestart(expr, restarts[[1L]]) 27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { r2vs <- c(r2vs, M.r2vs) if (supinfo) { M.MAF.loc1 <- NA M.heterofreq.loc1 <- NA M.NAfreq.loc1 <- NA M.MAF.loc2 <- NA M.heterofreq.loc2 <- NA M.NAfreq.loc2 <- NA supinfo.li <- info[, which(colnames(info) == mark[i])] supinfo.lj <- info[, which(colnames(info) == mark[j])] M.MAF.loc1 <- supinfo.li[1] M.heterofreq.loc1 <- supinfo.li[2] M.NAfreq.loc1 <- supinfo.li[3] M.MAF.loc2 <- supinfo.lj[1] M.heterofreq.loc2 <- supinfo.lj[2] snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { }) 28: test_code(code, parent.frame()) 29: test_that("LD measures", { data(data.test) Geno <- data.test[[1]] V.WAIS <- data.test[[2]] S.2POP <- data.test[[3]] LD <- LD.Measures(Geno, V = V.WAIS, S = S.2POP, data = "G", supinfo = TRUE, na.presence = TRUE) expect_equal(LD[173, 3], 0.00736549685246069, tolerance = 1e-06) expect_equal(LD[173, 4], 0.0096994662565902, tolerance = 1e-06) expect_equal(LD[173, 5], 0.0115996465046284, tolerance = 1e-06) expect_equal(LD[173, 6], 0.0103672763202665, tolerance = 1e-06) expect_equal(LD[173, 7], 0.021978021978022, tolerance = 1e-06) expect_equal(LD[173, 8], 0.043956043956044, tolerance = 1e-06) expect_equal(LD[173, 9], 0, tolerance = 1e-06) expect_equal(LD[173, 10], 0.0934065934065934, tolerance = 1e-06) M.NAfreq.loc2 <- supinfo.lj[3] MAF.loc1 <- c(MAF.loc1, M.MAF.loc1) heterofreq.loc1 <- c(heterofreq.loc1, M.heterofreq.loc1) NAfreq.loc1 <- c(NAfreq.loc1, M.NAfreq.loc1) MAF.loc2 <- c(MAF.loc2, M.MAF.loc2) heterofreq.loc2 <- c(heterofreq.loc2, M.heterofreq.loc2) NAfreq.loc2 <- c(NAfreq.loc2, M.NAfreq.loc2) } res <- c(as.matrix(loc1), as.matrix(loc2), r2, r2s, r2v, r2vs, MAF.loc1, heterofreq.loc1, NAfreq.loc1, MAF.loc2, heterofreq.loc2, NAfreq.loc2) }) RES <- cbind(RES, res)}) 17: LD.Measures(Geno, V = V.WAIS, S = S.2POP, data = "G", supinfo = TRUE, expect_equal(LD[173, 11], 0.120879120879121, tolerance = 1e-06) expect_equal(LD[173, 12], 0, tolerance = 1e-06)}) 30: eval(code, test_env) 31: eval(code, test_env) 32: withCallingHandlers({ na.presence = TRUE) 18: eval(code, test_env) 19: eval(code, test_env) 20: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) 21: doTryCatch(return(expr), name, parentenv, handler) 22: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 23: tryCatchList(expr, classes, parentenv, handlers) 24: tryCatch(withCallingHandlers({ eval(code, test_env) eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) 33: doTryCatch(return(expr), name, parentenv, handler) 34: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 35: tryCatchList(expr, classes, parentenv, handlers) 36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 25: doWithOneRestart(return(expr), restart) 26: withOneRestart(expr, restarts[[1L]]) if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) } 27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) {}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 37: doWithOneRestart(return(expr), restart) 38: withOneRestart(expr, restarts[[1L]]) 39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { }) 28: test_code(code, parent.frame()) 29: test_that("LD measures", { data(data.test) Geno <- data.test[[1]] V.WAIS <- data.test[[2]] S.2POP <- data.test[[3]] skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), LD <- LD.Measures(Geno, V = V.WAIS, S = S.2POP, data = "G", supinfo = TRUE, na.presence = TRUE) expect_equal(LD[173, 3], 0.00736549685246069, tolerance = 1e-06) expect_equal(LD[173, 4], 0.0096994662565902, tolerance = 1e-06) expect_equal(LD[173, 5], 0.0115996465046284, tolerance = 1e-06) expect_equal(LD[173, 6], 0.0103672763202665, tolerance = 1e-06) expect_equal(LD[173, 7], 0.021978021978022, tolerance = 1e-06) expect_equal(LD[173, 8], 0.043956043956044, tolerance = 1e-06) expect_equal(LD[173, 9], 0, tolerance = 1e-06) expect_equal(LD[173, 10], 0.0934065934065934, tolerance = 1e-06) expect_equal(LD[173, 11], 0.120879120879121, tolerance = 1e-06) expect_equal(LD[173, 12], 0, tolerance = 1e-06)}) 30: eval(code, test_env) 31: eval(code, test_env) 32: end_test = function() { }) 40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) 41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) 42: FUN(X[[i]], ...) 43: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) 44: doTryCatch(return(expr), name, parentenv, handler) 45: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 46: tryCatchList(expr, classes, parentenv, handlers) 47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt) 33: doTryCatch(return(expr), name, parentenv, handler) NULL}) 48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) 49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call) 50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle) 51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 52: test_check("LDcorSV")34: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 35: tryCatchList(expr, classes, parentenv, handlers) 36: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { An irrecoverable exception occurred. R is aborting now ... skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal) 37: doWithOneRestart(return(expr), restart) 38: withOneRestart(expr, restarts[[1L]]) 39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { }) 40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) 41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call) 42: FUN(X[[i]], ...) 43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call) 44: doTryCatch(return(expr), name, parentenv, handler) 45: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 46: tryCatchList(expr, classes, parentenv, handlers) 47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 48: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)) 49: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call) 50: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle) 51: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 52: test_check("LDcorSV") An irrecoverable exception occurred. R is aborting now ... Saving _problems/test-LDcorSV-17.R [ FAIL 1 | WARN 1 | SKIP 0 | PASS 4 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-LDcorSV.R:17:5'): LD measures ────────────────────────────────── Error in `matrix(unlist(RES), nrow = length(RES[[1]][, 1]))`: 'data' must be of a vector type, was 'NULL' Backtrace: ▆ 1. └─LDcorSV::LD.Measures(...) at test-LDcorSV.R:17:5 2. └─base::matrix(unlist(RES), nrow = length(RES[[1]][, 1])) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 4 ] Error: ! Test failures. Execution halted
checking PDF version of manual ... [2s/2s] OK
DONE Status: 2 ERRORs
using check arguments '--no-clean-on-error '