Last updated on 2020-07-02 02:09:43 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.3.0 | 184.13 | 344.81 | 528.94 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.3.0 | 130.36 | 256.36 | 386.72 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.3.0 | 672.98 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.3.0 | 636.14 | OK | |||
| r-devel-windows-ix86+x86_64 | 1.3.0 | 518.00 | 597.00 | 1115.00 | OK | |
| r-patched-linux-x86_64 | 1.3.0 | 106.39 | 314.35 | 420.74 | OK | |
| r-patched-solaris-x86 | 1.3.0 | 551.30 | ERROR | |||
| r-release-linux-x86_64 | 1.3.0 | 107.95 | 318.81 | 426.76 | OK | |
| r-release-osx-x86_64 | 1.3.0 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 1.3.0 | 371.00 | 626.00 | 997.00 | OK | |
| r-oldrel-osx-x86_64 | 1.3.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.3.0 | 449.00 | 920.00 | 1369.00 | OK |
Version: 1.3.0
Check: installed package size
Result: NOTE
installed size is 9.2Mb
sub-directories of 1Mb or more:
libs 7.5Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 1.3.0
Check: Rd cross-references
Result: NOTE
Undeclared package ‘RSpectra’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.3.0
Check: examples
Result: ERROR
Running examples in ‘bigsnpr-Ex.R’ failed
The error most likely occurred in:
> ### Name: snp_fastImputeSimple
> ### Title: Fast imputation
> ### Aliases: snp_fastImputeSimple
>
> ### ** Examples
>
> bigsnp <- snp_attachExtdata("example-missing.bed")
> G <- bigsnp$genotypes
> G[, 2] # some missing values
[1] NA NA 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 0
[26] 0 0 0 0 1 0 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 1 0
[51] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[76] 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA
[101] 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 NA 0 0 0 0 0
[126] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 NA 0
[151] 1 0 0 0 0 0 0 0 0 0 0 NA 0 0 0 0 0 0 0 0 0 0 1 0 0
[176] 0 0 0 0 0 0 NA 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0
> G2 <- snp_fastImputeSimple(G)
*** caught segfault ***
address f7dcc000, cause 'invalid permissions'
Traceback:
1: impute(X, rows_along(X), ind, method)
2: FUN(ind = ind.part, ...)
3: eval(xpr, envir = envir)
4: eval(xpr, envir = envir)
5: doTryCatch(return(expr), name, parentenv, handler)
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatch(eval(xpr, envir = envir), error = function(e) e)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch({ repeat { args <- nextElem(it) if (obj$verbose) { cat(sprintf("evaluation # %d:\n", i)) print(args) } for (a in names(args)) assign(a, args[[a]], pos = envir, inherits = FALSE) r <- tryCatch(eval(xpr, envir = envir), error = function(e) e) if (obj$verbose) { cat("result of evaluating expression:\n") print(r) } tryCatch(accumulator(list(r), i), error = function(e) { cat("error calling combine function:\n") print(e) NULL }) i <- i + 1 }}, error = function(e) { if (!identical(conditionMessage(e), "StopIteration")) stop(simpleError(conditionMessage(e), expr))})
13: e$fun(obj, substitute(ex), parent.frame(), e$data)
14: foreach(ic = rows_along(intervals)) %dopar% { ind.part <- ind[seq(intervals[ic, "lower"], intervals[ic, "upper"])] FUN(ind = ind.part, ...)}
15: bigparallelr::split_parapply(p.FUN, ind, X, ..., .combine = p.combine, ncores = ncores, opts_cluster = list(type = getOption("bigstatsr.cluster.type")))
16: big_parallelize(Gna, p.FUN = part_impute, ncores = ncores, method = method)
17: snp_fastImputeSimple(G)
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86
Version: 1.3.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [190s/187s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(bigsnpr)
Loading required package: bigstatsr
>
> test_check("bigsnpr", filter = "7-")
── 1. Failure: parallel bed_prodVec() works (@test-7-OpenMP.R#39) ─────────────
all(sapply(test, all.equal, current = true)) isn't true.
*** caught segfault ***
address f8660ffc, cause 'invalid permissions'
*** caught segfault ***
address f8660ffc, cause 'invalid permissions'
Traceback:
1: clumping_chr_cached(G, keep, spcor.chr, spInd = ind.sp.grp, rowInd = ind.row, colInd = ind.chr.grp, ordInd = ord.chr.grp, rankInd = rank.chr.grp, pos = pos.chr.grp, sumX = sumX.chr.grp, denoX = deno.chr.grp, size = 1000 * base.size.clmp/thr.clmp, thr = thr.clmp, ncores = ncores)
2: FUN(X[[i]], ...)
3: lapply(split(ind.noexcl, infos.chr[ind.noexcl]), function(ind.chr) { ind.keep <- list() info.chr <- infos.imp[ind.chr] S.chr <- lpS[ind.chr] pos.chr <- infos.pos[ind.chr] stats <- snp_colstats(G, ind.row, ind.chr, ncores) sumX.chr <- stats$sumX denoX.chr <- stats$denoX spcor.chr <- sparseMatrix(i = integer(), j = integer(), x = double(), dims = rep(length(ind.chr), 2)) assert_sorted(pos.chr) for (thr.imp in THR_IMP) { ind <- which(info.chr >= thr.imp) ind.chr <- ind.chr[ind] spcor.chr <- spcor.chr[ind, ind, drop = FALSE] info.chr <- info.chr[ind] pos.chr <- pos.chr[ind] S.chr <- S.chr[ind] sumX.chr <- sumX.chr[ind] denoX.chr <- denoX.chr[ind] for (group in groups) { ind2 <- which(ind.chr %in% group) if (length(ind2) == 0) { for (thr.clmp in THR_CLMP) { for (base.size.clmp in BASE_SIZE_CLMP) { ind.keep[[length(ind.keep) + 1L]] <- integer() } } } else { ind.sp.grp <- ind2 - 1L ind.chr.grp <- ind.chr[ind2] ord.chr.grp <- order(S.chr[ind2], decreasing = TRUE) rank.chr.grp <- match(seq_along(ord.chr.grp), ord.chr.grp) pos.chr.grp <- pos.chr[ind2] sumX.chr.grp <- sumX.chr[ind2] deno.chr.grp <- denoX.chr[ind2] keep <- FBM(1, length(ind.chr.grp), type = "integer") for (thr.clmp in THR_CLMP) { for (base.size.clmp in BASE_SIZE_CLMP) { keep[] <- -1 spcor.chr <- clumping_chr_cached(G, keep, spcor.chr, spInd = ind.sp.grp, rowInd = ind.row, colInd = ind.chr.grp, ordInd = ord.chr.grp, rankInd = rank.chr.grp, pos = pos.chr.grp, sumX = sumX.chr.grp, denoX = deno.chr.grp, size = 1000 * base.size.clmp/thr.clmp, thr = thr.clmp, ncores = ncores) stopifnot(all(keep[] %in% 0:1)) ind.keep[[length(ind.keep) + 1L]] <- ind.chr.grp[keep[] == 1] } } } } } ind.keep})
4: snp_grid_clumping(G, ind.row = rows, lpS = lpS, ncores = 2, infos.chr = rep(1, ncol(G)), infos.pos = cols_along(G), grid.base.size = 0.1, grid.thr.r2 = c(0.05, 0.5))
5: FUN(X[[i]], ...)
6: lapply(X = X, FUN = FUN, ...)
7: sapply(integer(n), eval.parent(substitute(function(...) expr)), simplify = simplify)
8: replicate(5, simplify = FALSE, { snp_grid_clumping(G, ind.row = rows, lpS = lpS, ncores = 2, infos.chr = rep(1, ncol(G)), infos.pos = cols_along(G), grid.base.size = 0.1, grid.thr.r2 = c(0.05, 0.5))})
9: eval(code, test_env)
10: eval(code, test_env)
11: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
19: test_code(desc, code, env = parent.frame())
20: test_that("parallel snp_grid_clumping() works", { G <- snp_attachExtdata()$genotypes rows <- sample(nrow(G), replace = TRUE) lpS <- runif(ncol(G)) test <- replicate(5, simplify = FALSE, { snp_grid_clumping(G, ind.row = rows, lpS = lpS, ncores = 2, infos.chr = rep(1, ncol(G)), infos.pos = cols_along(G), grid.base.size = 0.1, grid.thr.r2 = c(0.05, 0.5)) }) true <- snp_grid_clumping(G, ind.row = rows, lpS = lpS, ncores = 1, infos.chr = rep(1, ncol(G)), infos.pos = cols_along(G), grid.base.size = 0.1, grid.thr.r2 = c(0.05, 0.5)) expect_true(all(sapply(test, identical, y = true)))})
21: eval(code, test_env)
22: eval(code, test_env)
23: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
31: test_code(NULL, exprs, env)
32: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
33: force(code)
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(expr, restarts[[1L]])
36: withRestarts(testthat_abort_reporter = function() NULL, force(code))
37: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { reporter$start_file(basename(path)) lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) reporter$.end_context() reporter$end_file() })
38: FUN(X[[i]], ...)
39: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
40: force(code)
41: doWithOneRestart(return(expr), restart)
42: withOneRestart(expr, restarts[[1L]])
43: withRestarts(testthat_abort_reporter = function() NULL, force(code))
44: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
45: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
46: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
47: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
48: test_check("bigsnpr", filter = "7-")
An irrecoverable exception occurred. R is aborting now ...
Traceback:
1: clumping_chr_cached(G, keep, spcor.chr, spInd = ind.sp.grp, rowInd = ind.row, colInd = ind.chr.grp, ordInd = ord.chr.grp, rankInd = rank.chr.grp, pos = pos.chr.grp, sumX = sumX.chr.grp, denoX = deno.chr.grp, size = 1000 * base.size.clmp/thr.clmp, thr = thr.clmp, ncores = ncores)
2: FUN(X[[i]], ...)
3: lapply(split(ind.noexcl, infos.chr[ind.noexcl]), function(ind.chr) { ind.keep <- list() info.chr <- infos.imp[ind.chr] S.chr <- lpS[ind.chr] pos.chr <- infos.pos[ind.chr] stats <- snp_colstats(G, ind.row, ind.chr, ncores) sumX.chr <- stats$sumX denoX.chr <- stats$denoX spcor.chr <- sparseMatrix(i = integer(), j = integer(), x = double(), dims = rep(length(ind.chr), 2)) assert_sorted(pos.chr) for (thr.imp in THR_IMP) { ind <- which(info.chr >= thr.imp) ind.chr <- ind.chr[ind] spcor.chr <- spcor.chr[ind, ind, drop = FALSE] info.chr <- info.chr[ind] pos.chr <- pos.chr[ind] S.chr <- S.chr[ind] sumX.chr <- sumX.chr[ind] denoX.chr <- denoX.chr[ind] for (group in groups) { ind2 <- which(ind.chr %in% group) if (length(ind2) == 0) { for (thr.clmp in THR_CLMP) { for (base.size.clmp in BASE_SIZE_CLMP) { ind.keep[[length(ind.keep) + 1L]] <- integer() } } } else { ind.sp.grp <- ind2 - 1L ind.chr.grp <- ind.chr[ind2] ord.chr.grp <- order(S.chr[ind2], decreasing = TRUE) rank.chr.grp <- match(seq_along(ord.chr.grp), ord.chr.grp) pos.chr.grp <- pos.chr[ind2] sumX.chr.grp <- sumX.chr[ind2] deno.chr.grp <- denoX.chr[ind2] keep <- FBM(1, length(ind.chr.grp), type = "integer") for (thr.clmp in THR_CLMP) { for (base.size.clmp in BASE_SIZE_CLMP) { keep[] <- -1e+00 spcor.chr <- clumping_chr_cached(G, keep, spcor.chr, spInd = ind.sp.grp, rowInd = ind.row, colInd = ind.chr.grp, ordInd = ord.chr.grp, rankInd = rank.chr.grp, pos = pos.chr.grp, sumX = sumX.chr.grp, denoX = deno.chr.grp, size = 1000 * base.size.clmp/thr.clmp, thr = thr.clmp, ncores = ncores) stopifnot(all(keep[] %in% 0:1)) ind.keep[[length(ind.keep) + 1L]] <- ind.chr.grp[keep[] == 1] } } } } } ind.keep})
4: snp_grid_clumping(G, ind.row = rows, lpS = lpS, ncores = 2, infos.chr = rep(1, ncol(G)), infos.pos = cols_along(G), grid.base.size = 0.1, grid.thr.r2 = c(0.05, 0.5))
5: FUN(X[[i]], ...)
6: lapply(X = X, FUN = FUN, ...)
7: sapply(integer(n), eval.parent(substitute(function(...) expr)), simplify = simplify)
8: replicate(5, simplify = FALSE, { snp_grid_clumping(G, ind.row = rows, lpS = lpS, ncores = 2, infos.chr = rep(1, ncol(G)), infos.pos = cols_along(G), grid.base.size = 0.1, grid.thr.r2 = c(0.05, 0.5))})
9: eval(code, test_env)
10: eval(code, test_env)
11: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
19: test_code(desc, code, env = parent.frame())
20: test_that("parallel snp_grid_clumping() works", { G <- snp_attachExtdata()$genotypes rows <- sample(nrow(G), replace = TRUE) lpS <- runif(ncol(G)) test <- replicate(5, simplify = FALSE, { snp_grid_clumping(G, ind.row = rows, lpS = lpS, ncores = 2, infos.chr = rep(1, ncol(G)), infos.pos = cols_along(G), grid.base.size = 0.1, grid.thr.r2 = c(0.05, 0.5)) }) true <- snp_grid_clumping(G, ind.row = rows, lpS = lpS, ncores = 1, infos.chr = rep(1, ncol(G)), infos.pos = cols_along(G), grid.base.size = 0.1, grid.thr.r2 = c(0.05, 0.5)) expect_true(all(sapply(test, identical, y = true)))})
21: eval(code, test_env)
22: eval(code, test_env)
23: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
24: doTryCatch(return(expr), name, parentenv, handler)
25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
26: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
29: tryCatchList(expr, classes, parentenv, handlers)
30: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
31: test_code(NULL, exprs, env)
32: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
33: force(code)
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(expr, restarts[[1L]])
36: withRestarts(testthat_abort_reporter = function() NULL, force(code))
37: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { reporter$start_file(basename(path)) lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) reporter$.end_context() reporter$end_file() })
38: FUN(X[[i]], ...)
39: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
40: force(code)
41: doWithOneRestart(return(expr), restart)
42: withOneRestart(expr, restarts[[1L]])
43: withRestarts(testthat_abort_reporter = function() NULL, force(code))
44: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
45: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
46: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
47: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
48: test_check("bigsnpr", filter = "7-")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86