Rstan fails now when library(rstan) is called simultaneously from a computer cluster.
I run 30 independent jobs that need library(rstan), and a minimal reproducible example
library(rstan)
Will cause failure. Can this depend on some change made in the web link that rstan does? (I also reinstalled rstan but problem persists). Does rstan does some web query at the time of library(rstan)?
Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ COAD.tcga.harmonized.counts.allgenes.rds failed with exit code 1
rule 5 failed, moving any outputs to makeflow.failed.5
2021/03/05 10:19:05.60 makeflow[21278] notice: will retry failed job Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ COAD.tcga.harmonized.counts.allgenes.rds
submitting job: Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ COAD.tcga.harmonized.counts.allgenes.rds
submitted job 1276679
job 1276674 completed
Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ CHOL.tcga.harmonized.counts.allgenes.rds failed with exit code 1
rule 4 failed, moving any outputs to makeflow.failed.4
2021/03/05 10:19:05.63 makeflow[21278] notice: will retry failed job Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ CHOL.tcga.harmonized.counts.allgenes.rds
submitting job: Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ CHOL.tcga.harmonized.counts.allgenes.rds
submitted job 1276680
job 1276675 completed
Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ CESC.tcga.harmonized.counts.allgenes.rds failed with exit code 1
rule 3 failed, moving any outputs to makeflow.failed.3
2021/03/05 10:19:05.65 makeflow[21278] notice: will retry failed job Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ CESC.tcga.harmonized.counts.allgenes.rds
submitting job: Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ CESC.tcga.harmonized.counts.allgenes.rds
submitted job 1276681
job 1276676 completed
Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ BRCA.tcga.harmonized.counts.allgenes.rds failed with exit code 1
rule 2 failed, moving any outputs to makeflow.failed.2
2021/03/05 10:19:05.67 makeflow[21278] notice: will retry failed job Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ BRCA.tcga.harmonized.counts.allgenes.rds
submitting job: Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ BRCA.tcga.harmonized.counts.allgenes.rds
submitted job 1276682
job 1276677 completed
Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ BLCA.tcga.harmonized.counts.allgenes.rds failed with exit code 1
rule 1 failed, moving any outputs to makeflow.failed.1
2021/03/05 10:19:05.69 makeflow[21278] notice: will retry failed job Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ BLCA.tcga.harmonized.counts.allgenes.rds
submitting job: Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ BLCA.tcga.harmonized.counts.allgenes.rds
submitted job 1276683
job 1276678 completed
Rscript dev/TCGA_makeflow_pipeline/create_input.R ~/PhD/deconvolution/ ACC.tcga.harmonized.counts.allgenes.rds failed with exit code 1