When calling a function which uses mclapply() with Rscript myFuction.R --json=config.json the mclapply functions fails with message
all scheduled cores encountered errors in user code
However when I run the code within RStudio it runs fine. I'm developing on RStudio AWS AMI and testing in RStudio, and executing Rscript from the terminal of RStudio AWS machine, and the environments are the same between RStudio and the terminal.
Does anyone have an idea of extra parameters I might need to give to mclapply or other environment parameters I need to define when running mclapply with Rscript?
I've tried changing all the mclapply() arguments without success
Here is my environment.
R version 3.5.1 (2018-07-02)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Amazon Linux 2
Matrix products: default
BLAS/LAPACK: /anaconda3/envs/r35p27/lib/R/lib/libRblas.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] rlist_0.4.6.1 stringi_1.4.3
[3] stringr_1.3.1 seqinr_3.4-5
[5] rBLAST_0.99.2 ShortRead_1.40.0
[7] GenomicAlignments_1.18.1 SummarizedExperiment_1.12.0
[9] DelayedArray_0.8.0 matrixStats_0.54.0
[11] Biobase_2.42.0 Rsamtools_1.34.0
[13] GenomicRanges_1.34.0 GenomeInfoDb_1.18.1
[15] Biostrings_2.50.2 XVector_0.22.0
[17] IRanges_2.16.0 S4Vectors_0.20.1
[19] BiocParallel_1.16.6 BiocGenerics_0.28.0
[21] aws.s3_0.3.12 jsonlite_1.5
[23] configr_0.3.3 optparse_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 RColorBrewer_1.1-2 compiler_3.5.1
[4] base64enc_0.1-3 bitops_1.0-6 tools_3.5.1
[7] zlibbioc_1.28.0 digest_0.6.20 lattice_0.20-35
[10] Matrix_1.2-14 yaml_2.2.0 GenomeInfoDbData_1.2.1
[13] hwriter_1.3.2 httr_1.3.1 xml2_1.2.0
[16] ade4_1.7-13 grid_3.5.1 getopt_1.20.2
[19] data.table_1.12.2 glue_1.3.1 R6_2.2.2
[22] latticeExtra_0.6-28 magrittr_1.5 MASS_7.3-51.4
[25] aws.signature_0.5.0 ini_0.3.1 RCurl_1.95-4.12
[28] RcppTOML_0.1.6
Although this is a "Warning message" mclapply quits
Warning messages:
1: In mclapply(1:dim(this.split)[1], BLAST.loop, mc.preschedule = TRUE) :
all scheduled cores encountered errors in user code
