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alanocallaghan / scater

Clone of the Bioconductor repository for the scater package.
https://bioconductor.org/packages/devel/bioc/html/scater.html
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runPCA segfault #214

Closed wakelin-g closed 1 week ago

wakelin-g commented 1 week ago

Hi guys,

I am catching a segfault when using runPCA on essentially anything. Does anyone have any ideas what might be causing it?

library(scater)
m <- matrix(rnorm(10000), nrow=100, ncol=100)
sce <- SingleCellExperiment(assays=list(logcounts=log1p(m))
sce <- runPCA(sce)
Full trace ``` *** caught segfault *** address 0x1f5, cause 'invalid permissions' Traceback: 1: compute_center(ptr, nthreads) 2: .compute_center_and_scale(x, center, scale, nthreads = bpnworkers(BPPARAM)) 3: (function (x, k = 5, nu = k, nv = k, center = FALSE, scale = FALSE, deferred = FALSE, extra.work = 7, ..., fold = Inf, BPPARAM = SerialParam()) { if (nu == 0 && nv == 0 && k == 0) { return(list(d = numeric(0), u = matrix(0, nrow(x), 0), v = matrix(0, ncol(x), 0))) } checked <- check_numbers(k = k, nu = nu, nv = nv, limit = min(dim(x)) - 1L) k <- checked$k nv <- checked$nv nu <- checked$nu old <- getAutoBPPARAM() setAutoBPPARAM(BPPARAM) on.exit(setAutoBPPARAM(old)) if (!.bpisup2(BPPARAM)) { bpstart(BPPARAM) on.exit(bpstop(BPPARAM), add = TRUE) } args <- list(work = max(k, nu, nv) + extra.work, ...) if (use_crossprod(x, fold)) { x <- standardize_matrix(x, center = center, scale = scale, deferred = deferred, BPPARAM = BPPARAM) res <- do.call(svd_via_crossprod, c(list(x, k = k, nu = nu, nv = nv, FUN = irlba, BPPARAM = BPPARAM), args)) } else { args$nu <- nu args$nv <- max(k, nv) if (bpnworkers(BPPARAM) == 1L) { stats <- .compute_center_and_scale(x, center, scale, nthreads = bpnworkers(BPPARAM)) res <- do.call(irlba, c(args, list(A = x, center = stats$center, scale = stats$scale))) } else { x <- standardize_matrix(x, center = center, scale = scale, deferred = deferred, BPPARAM = BPPARAM) res <- do.call(irlba, c(list(A = x, fastpath = FALSE), args)) } res$v <- res$v[, seq_len(nv), drop = FALSE] res$d <- head(res$d, k) res <- standardize_output_SVD(res, x) } res})(x = c(1.52900083969766, 1.69205151985914, 1.82202974800099, 1.96022621958905, 1.83409765648279, 1.79641553159751, 1.74796080430389, 2.03524660777028, 1.85860828646435, 1.9638660484713, 1.75214514467655, 1.68889151415908, 1.70396069792009, 1.62313431196837, 1.92848501569001, 1.58091717690577, 1.44923927944104, 1.42635816355124, 2.00100565832429, 1.96852852324167, 1.7444218436406, 1.92601507377643, 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1.69051048172752, 1.86012146775696, 1.43400320128913, 2.00382878426777, 1.82989487461566, 1.82249935728805, 1.99180362002349, 2.01321881671772, 1.86229445616568, 2.0352808819345, 1.63479028890609, 1.60741473021141, 1.60470776711694, 1.69888282133067, 1.54764121750889, 1.68659545654008, 1.52072057306215, 1.74290323196414, 1.78974047887504, 1.82408526954678, 1.694422862131, 1.95457797994124, 2.03903717859932, 1.93884660810121, 1.54429945604118, 1.43791450982033, 1.94834564506793, 1.74209266887963, 1.84252388732508, 1.10066574710828, 1.73758803458635, 1.67373168400356, 1.83820164673867, 1.71884057591237, 2.02096843614129, 1.83279308688306, 1.78113831437404, 1.96006006080796, 1.98227726367144), k = 50, nu = 50, nv = 50, center = TRUE, scale = FALSE, BPPARAM = new("SerialParam", .xData = ), deferred = FALSE, fold = Inf, extra.work = 7L) 4: do.call(FUN, c(list(x = x, k = k, nu = nu, nv = nv, center = center, scale = scale, BPPARAM = BPPARAM, ...), ARGS(BSPARAM))) 5: runSVD(x, k = k, nu = nu, nv = nv, center = center, scale = scale, BPPARAM = BPPARAM, ..., BSPARAM = BSPARAMFUN(deferred = bsdeferred(BSPARAM), fold = bsfold(BSPARAM))) 6: runSVD(x, k = k, nu = nu, nv = nv, center = center, scale = scale, BPPARAM = BPPARAM, ..., BSPARAM = BSPARAMFUN(deferred = bsdeferred(BSPARAM), fold = bsfold(BSPARAM))) 7: runSVD(x, k = rank, nu = ifelse(get.pcs, rank, 0), nv = ifelse(get.rotation, rank, 0), center = center, scale = scale, ...) 8: runSVD(x, k = rank, nu = ifelse(get.pcs, rank, 0), nv = ifelse(get.rotation, rank, 0), center = center, scale = scale, ...) 9: .local(x, ...) 10: runPCA(x, rank = ncomponents, BSPARAM = BSPARAM, BPPARAM = BPPARAM) 11: runPCA(x, rank = ncomponents, BSPARAM = BSPARAM, BPPARAM = BPPARAM) 12: .calculate_pca(mat, transposed = !is.null(dimred), ...) 13: .local(x, ...) 14: calculatePCA(y, ...) 15: calculatePCA(y, ...) 16: .local(x, ...) 17: runPCA(sce) 18: runPCA(sce) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace ```
sessionInfo (before runPCA) ``` R version 4.4.1 (2024-06-14) Platform: aarch64-apple-darwin20 Running under: macOS 15.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: America/Halifax tzcode source: internal attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] scater_1.32.0 ggplot2_3.5.1 scuttle_1.14.0 SingleCellExperiment_1.26.0 [5] SummarizedExperiment_1.34.0 Biobase_2.64.0 GenomicRanges_1.56.1 GenomeInfoDb_1.40.1 [9] IRanges_2.38.0 S4Vectors_0.44.0 BiocGenerics_0.50.0 MatrixGenerics_1.16.0 [13] matrixStats_1.3.0 HSMMSingleCell_1.26.0 loaded via a namespace (and not attached): [1] gtable_0.3.5 beeswarm_0.4.0 ggrepel_0.9.5 lattice_0.22-6 vctrs_0.6.5 [6] tools_4.4.1 generics_0.1.3 parallel_4.4.1 tibble_3.2.1 fansi_1.0.6 [11] pkgconfig_2.0.3 BiocNeighbors_1.99.2 Matrix_1.7-0 sparseMatrixStats_1.16.0 lifecycle_1.0.4 [16] GenomeInfoDbData_1.2.12 compiler_4.4.1 munsell_0.5.1 codetools_0.2-20 vipor_0.4.7 [21] pillar_1.9.0 crayon_1.5.3 BiocParallel_1.38.0 DelayedArray_0.30.1 viridis_0.6.5 [26] abind_1.4-5 tidyselect_1.2.1 rsvd_1.0.5 BiocSingular_1.20.0 dplyr_1.1.4 [31] grid_4.4.1 colorspace_2.1-0 cli_3.6.3 SparseArray_1.6.0 magrittr_2.0.3 [36] S4Arrays_1.6.0 utf8_1.2.4 withr_3.0.0 DelayedMatrixStats_1.26.0 scales_1.3.0 [41] UCSC.utils_1.0.0 ggbeeswarm_0.7.2 XVector_0.44.0 httr_1.4.7 gridExtra_2.3 [46] ScaledMatrix_1.12.0 beachmat_2.21.6 irlba_2.3.5.1 viridisLite_0.4.2 rlang_1.1.4 [51] Rcpp_1.0.12 glue_1.7.0 jsonlite_1.8.8 R6_2.5.1 zlibbioc_1.50.0 ```
alanocallaghan commented 1 week ago

While I usually appreciate a good reprex, scrolling through the data in outlook to get to the "view on GitHub" link was a bit dizzying 🤣

Invalid permissions sounds like a security or file permissions issue. The error seems to be in irlba, can you run a basic irlba PCA without scater or biocsingular involved at all?

LTLA commented 1 week ago

Previous release version of scater with the previous devel version of beachmat, for starters. Advise updating both to the current release version.

wakelin-g commented 1 week ago

While I usually appreciate a good reprex, scrolling through the data in outlook to get to the "view on GitHub" link was a bit dizzying 🤣

Invalid permissions sounds like a security or file permissions issue. The error seems to be in irlba, can you run a basic irlba PCA without scater or biocsingular involved at all?

Hah... sorry, forgot that emails don't wrap text. And yes, versioning was the problem (sorry!) Thanks both for the quick help.

alanocallaghan commented 1 week ago

Great, thanks for the detailed report in any case