Question: Minfi issue: return code from pthread_create() is 22
0
gravatar for jshouse
4 weeks ago by
jshouse0
jshouse0 wrote:

I went to estimate cell counts from a 450k RGSet with

    estimateCellCounts(RGSet, referencePlatform = c("IlluminaHumanMethylation450k"))

I got the following:

> cellCounts <- estimateCellCounts(RGSet, referencePlatform = c("IlluminaHumanMethylation450k")) 
[estimateCellCounts] Combining user data with reference (flow sorted) data. 'stringsAsFactors' is ignored
[estimateCellCounts] Processing user and reference data together.
[preprocessQuantile] Mapping to genome.
[preprocessQuantile] Fixing outliers.
[preprocessQuantile] Quantile normalizing. Error in normalize.quantiles(mat[Index2, ]) :   
 ERROR; return code from pthread_create() is 22

I tried to find this error but did not get anything that seemed helpful.

My sessionInfo:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 19.04

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 FlowSorted.Blood.450k_1.22.0                      
 [3] haven_2.1.1                                        gridExtra_2.3                                     
 [5] sva_3.32.1                                         genefilter_1.66.0                                 
 [7] mgcv_1.8-28                                        nlme_3.1-140                                      
 [9] lmtest_0.9-37                                      zoo_1.8-6                                         
[11] sandwich_2.5-1                                     MASS_7.3-51.1                                     
[13] data.table_1.12.2                                  R.utils_2.9.0                                     
[15] R.oo_1.22.0                                        R.methodsS3_1.7.1                                 
[17] foreign_0.8-71                                     IlluminaHumanMethylation450kmanifest_0.4.0        
[19] compare_0.2-6                                      minfi_1.30.0                                      
[21] bumphunter_1.26.0                                  locfit_1.5-9.1                                    
[23] iterators_1.0.10                                   foreach_1.4.4                                     
[25] Biostrings_2.52.0                                  XVector_0.24.0                                    
[27] SummarizedExperiment_1.14.0                        DelayedArray_0.10.0                               
[29] BiocParallel_1.18.0                                matrixStats_0.54.0                                
[31] Biobase_2.44.0                                     GenomicRanges_1.36.0                              
[33] GenomeInfoDb_1.20.0                                IRanges_2.18.1                                    
[35] S4Vectors_0.22.0                                   BiocGenerics_0.30.0                               
[37] forcats_0.4.0                                      stringr_1.4.0                                     
[39] dplyr_0.8.3                                        purrr_0.3.2                                       
[41] readr_1.3.1                                        tidyr_0.8.3                                       
[43] tibble_2.1.3                                       ggplot2_3.2.0                                     
[45] tidyverse_1.2.1                                    knitr_1.23    
minfi 450k • 83 views
ADD COMMENTlink modified 26 days ago by jdshih20 • written 4 weeks ago by jshouse0
Answer: Minfi issue: return code from pthread_create() is 22
1
gravatar for jdshih
26 days ago by
jdshih20
jdshih20 wrote:

I had the same error using oligo and affy, and the source of the error appears to be openblas >= 0.3.4. You can see in your R session history that you are using openblas 0.3.5.

For now, I'd replace openblas with blas until this problem is fixed upstream and the change is propagated to your OS distribution.

See https://support.bioconductor.org/p/117119/#123061

ADD COMMENTlink modified 26 days ago • written 26 days ago by jdshih20
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