DESeq2 gives an error and R crashes
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Entering edit mode
Shefali • 0
@da3ffe4e
Last seen 5 weeks ago
Delhi

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
DESeq2 • 203 views
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Entering edit mode

Issue resolved after updating macOS to Sonoma 14.4.1. No additional changes were made.

The new sessionInfo() is as follows:

R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.4.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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/New_York
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] airway_1.22.0               DESeq2_1.42.1               SummarizedExperiment_1.32.0
 [4] Biobase_2.62.0              MatrixGenerics_1.14.0       matrixStats_1.2.0          
 [7] GenomicRanges_1.54.1        GenomeInfoDb_1.38.8         IRanges_2.36.0             
[10] S4Vectors_0.40.2            BiocGenerics_0.48.1        

loaded via a namespace (and not attached):
 [1] Matrix_1.6-5            gtable_0.3.4            dplyr_1.1.4             compiler_4.3.3         
 [5] crayon_1.5.2            tidyselect_1.2.1        Rcpp_1.0.12             bitops_1.0-7           
 [9] parallel_4.3.3          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          generics_0.1.3         
[17] S4Arrays_1.2.1          tibble_3.2.1            DelayedArray_0.28.0     munsell_0.5.1          
[21] GenomeInfoDbData_1.2.11 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          zlibbioc_1.48.2        
[29] locfit_1.5-9.9          grid_4.3.3              rstudioapi_0.16.0       lifecycle_1.0.4        
[33] vctrs_0.6.5             glue_1.7.0              codetools_0.2-20        abind_1.4-5            
[37] RCurl_1.98-1.14         fansi_1.0.6             colorspace_2.1-0        pkgconfig_2.0.3        
[41] tools_4.3.3
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