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@rv-18712
Last seen 5.7 years ago
I am trying to use oligo::rma for a HTA feature set from a linux environment and right after background correction, following is trace back – Background correcting
Error in basicRMA(pms, pnVec, normalize, background): ERROR; return code from pthread_create() is 22
Traceback:
1. oligo::rma(in_data, target = "core")
2. oligo::rma(in_data, target = "core")
3. .local(object, ...)
4. basicRMA(pms, pnVec, normalize, background)
When I run the same command for the same files in a windows Rstudio and it runs just fine. I have over 1500 samples, and need to use the linux env to process it all.
I appreciate your help!
Attached is the sessionInfo -
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)
Matrix products: default
BLAS/LAPACK: /home/linuxbrew/.linuxbrew/Cellar/openblas/0.3.4/lib/libopenblasp-r0.3.4.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] 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
[8] methods base
other attached packages:
[1] pd.hta.2.0_3.12.2 DBI_1.0.0 RSQLite_2.1.1
[4] oligo_1.46.0 Biostrings_2.50.2 XVector_0.22.0
[7] IRanges_2.16.0 S4Vectors_0.20.1 Biobase_2.42.0
[10] oligoClasses_1.44.0 BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 compiler_3.5.2
[3] BiocManager_1.30.4 GenomeInfoDb_1.18.1
[5] bitops_1.0-6 iterators_1.0.10
[7] tools_3.5.2 zlibbioc_1.28.0
[9] digest_0.6.18 bit_1.1-14
[11] memoise_1.1.0 preprocessCore_1.44.0
[13] lattice_0.20-38 ff_2.2-14
[15] pkgconfig_2.0.2 Matrix_1.2-15
[17] foreach_1.4.4 DelayedArray_0.8.0
[19] GenomeInfoDbData_1.2.0 affxparser_1.54.0
[21] bit64_0.9-7 grid_3.5.2
[23] BiocParallel_1.16.5 blob_1.1.1
[25] codetools_0.2-16 matrixStats_0.54.0
[27] GenomicRanges_1.34.0 splines_3.5.2
[29] SummarizedExperiment_1.12.0 RCurl_1.95-4.11
[31] affyio_1.52.0
If you're running it on a cluster environment (running Red Hat), then you may be up against restrictions in place by your system administrator. Are you just running it from the command line on the server?
Hi Kevin, Apologies for the delayed reply. No, I am running it in a Red Hat server. It works just fine on a local command line.
Thanks!
Hi Kevin, Apologies for the delayed reply. No, I am running it in a Red Hat server. It works just fine on a local command line.
Thanks!