Last updated on 2026-02-12 05:51:11 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| ade4 | 5 | 9 | |
| ade4TkGUI | 14 | ||
| adegraphics | 2 | 12 | |
| adephylo | 14 | ||
| adespatial | 14 | ||
| aods3 | 14 | ||
| CINID | 14 | ||
| DRomics | 3 | 11 | |
| fitdistrplus | 14 | ||
| Interatrix | 14 | ||
| LDcorSV | 1 | 13 | |
| LifemapR | 14 | ||
| MareyMap | 14 | ||
| Mondrian | 14 | ||
| nlsMicrobio | 14 | ||
| nlstools | 14 | ||
| OnAge | 14 | ||
| phylter | 14 | ||
| ssd4mosaic | 14 |
Current CRAN status: NOTE: 5, OK: 9
Version: 1.7-23
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘sp’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.7-23
Check: installed package size
Result: NOTE
installed size is 9.3Mb
sub-directories of 1Mb or more:
R 2.0Mb
data 2.9Mb
libs 2.6Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: OK: 14
Current CRAN status: NOTE: 2, OK: 12
Version: 1.0-22
Check: installed package size
Result: NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
R 2.1Mb
doc 2.7Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: NOTE: 3, OK: 11
Version: 2.6-2
Check: installed package size
Result: NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
doc 2.5Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: ERROR: 1, OK: 13
Version: 1.3.4
Check: examples
Result: 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'
*** 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) } 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
Flavor: r-devel-macos-arm64
Version: 1.3.4
Check: tests
Result: 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]
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) { 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) if (!na.presence) NAfreq.loc1 <- c(NAfreq.loc1, M.NAfreq.loc1) MAF.loc2 <- c(MAF.loc2, M.MAF.loc2) 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) 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: } 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])]FUN(X[[i]], ...)
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] 7: lapply(X = S, FUN = FUN, ...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
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) }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"))) { 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()) 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) 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))
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]14: FUN(X[[i]], ...)
M.NAfreq.loc1 <- supinfo.li[3] M.MAF.loc2 <- supinfo.lj[1] M.heterofreq.loc2 <- supinfo.lj[2]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.NAfreq.loc2 <- supinfo.lj[3] MAF.loc1 <- c(MAF.loc1, M.MAF.loc1) heterofreq.loc1 <- c(heterofreq.loc1, M.heterofreq.loc1) M.MAF.loc2 <- NA M.heterofreq.loc2 <- NA M.NAfreq.loc2 <- NA 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, 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) 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, heterofreq.loc2 <- c(heterofreq.loc2, M.heterofreq.loc2) na.presence = TRUE)
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)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:
18: eval(code, test_env)
19: eval(code, test_env)
20: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN")withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
21: } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$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)doTryCatch(return(expr), name, parentenv, handler)
22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
23: tryCatchList(expr, classes, parentenv, handlers)
24: tryCatch(withCallingHandlers({
25: doWithOneRestart(return(expr), restart)
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
25: doWithOneRestart(return(expr), restart) if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) {
26: withOneRestart(expr, restarts[[1L]])
27: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), skip(paste0("{", e$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]] 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: 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)eval(code, test_env)
31: eval(code, test_env)
32: 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)withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations expect_equal(LD[173, 10], 0.0934065934065934, tolerance = 1e-06) expect_equal(LD[173, 11], 0.120879120879121, tolerance = 1e-06) expect_equal(LD[173, 12], 0, tolerance = 1e-06)})
30: eval(code, test_env)
31: eval(code, test_env)
32: withCallingHandlers({ eval(code, test_env) new_expectations <- the$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$package, "} is not installed.")) if (snapshot_skipped) { skip("On CRAN") } }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE else if (!new_expectations && skip_on_empty) { skip_empty() } invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed."))
33: doTryCatch(return(expr), name, parentenv, handler) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE
34: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 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:
35: tryCatchList(expr, classes, parentenv, handlers)
36: tryCatch(withCallingHandlers({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 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)
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)
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(expr, restarts[[1L]])
39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) {38: withOneRestart(expr, restarts[[1L]])
skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) {39: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) if (on_cran()) { skip(paste0("{", e$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$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
42: FUN(X[[i]], ...) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN")
43: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { error_call = error_call)
44: doTryCatch(return(expr), name, parentenv, handler)
})
40: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
41: source_file(path, env = env(env), desc = desc, shuffle = shuffle, 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 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]])})
48:
46: tryCatchList(expr, classes, parentenv, handlers)with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
47: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
48: with_reporter(reporters$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 ...
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
Flavor: r-devel-macos-arm64
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14
Current CRAN status: OK: 14