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On running the following DESeq2 code, R crashes with the shown error message. I have tried creating the DESeqDataSet object in multiple ways and it always gets created successfully, but all functions that require dispersion estimates lead to R crashing and quitting.
library("airway")
library("DESeq2")
data("airway")
se <- airway
dds <- DESeqDataSet(se, design = ~ cell + dex)
dds <- DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
*** caught bus error ***
address 0x100000cfeedfacf, cause 'invalid alignment'
Traceback:
1: fitBeta(ySEXP = ySEXP, xSEXP = xSEXP, nfSEXP = nfSEXP, alpha_hatSEXP = alpha_hatSEXP, contrastSEXP = contrastSEXP, beta_matSEXP = beta_matSEXP, lambdaSEXP = lambdaSEXP, weightsSEXP = weightsSEXP, useWeightsSEXP = useWeightsSEXP, tolSEXP = tolSEXP, maxitSEXP = maxitSEXP, useQRSEXP = useQRSEXP, minmuSEXP = minmuSEXP)
2: fitBetaWrapper(ySEXP = counts(object), xSEXP = modelMatrix, nfSEXP = normalizationFactors, alpha_hatSEXP = alpha_hat, beta_matSEXP = beta_mat, lambdaSEXP = lambdaNatLogScale, weightsSEXP = weights, useWeightsSEXP = useWeights, tolSEXP = betaTol, maxitSEXP = maxit, useQRSEXP = useQR, minmuSEXP = minmu)
3: fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], modelMatrix = modelMatrix, type = type)
4: estimateDispersionsGeneEst(object, maxit = maxit, useCR = useCR, weightThreshold = weightThreshold, quiet = quiet, modelMatrix = modelMatrix, minmu = minmu, type = dispersionEstimator)
5: .local(object, ...)
6: estimateDispersions(object, fitType = fitType, quiet = quiet, modelMatrix = modelMatrix, minmu = minmu)
7: estimateDispersions(object, fitType = fitType, quiet = quiet, modelMatrix = modelMatrix, minmu = minmu)
8: DESeq(dds)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
sessionInfo( )
R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.5.2
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] DESeq2_1.42.1 airway_1.22.0
[3] SummarizedExperiment_1.32.0 Biobase_2.62.0
[5] GenomicRanges_1.54.1 GenomeInfoDb_1.38.8
[7] IRanges_2.36.0 S4Vectors_0.40.2
[9] BiocGenerics_0.48.1 MatrixGenerics_1.14.0
[11] matrixStats_1.2.0
loaded via a namespace (and not attached):
[1] Matrix_1.6-5 gtable_0.3.4 dplyr_1.1.4
[4] compiler_4.3.3 crayon_1.5.2 tidyselect_1.2.1
[7] Rcpp_1.0.12 bitops_1.0-7 parallel_4.3.3
[10] scales_1.3.0 BiocParallel_1.36.0 lattice_0.22-6
[13] ggplot2_3.5.0 R6_2.5.1 XVector_0.42.0
[16] generics_0.1.3 S4Arrays_1.2.1 tibble_3.2.1
[19] DelayedArray_0.28.0 munsell_0.5.1 GenomeInfoDbData_1.2.11
[22] pillar_1.9.0 rlang_1.1.3 utf8_1.2.4
[25] SparseArray_1.2.4 cli_3.6.2 magrittr_2.0.3
[28] zlibbioc_1.48.2 locfit_1.5-9.9 grid_4.3.3
[31] lifecycle_1.0.4 vctrs_0.6.5 glue_1.7.0
[34] codetools_0.2-20 abind_1.4-5 RCurl_1.98-1.14
[37] fansi_1.0.6 colorspace_2.1-0 pkgconfig_2.0.3
[40] tools_4.3.3
Issue resolved after updating macOS to Sonoma 14.4.1. No additional changes were made.
The new sessionInfo() is as follows: