Uploading file to synapse fails due to Cstack uasage hitting the upper limit

Description

Upload to Synapse continuously fails while hitting the Cstack usage limit.

R Traceback

Memory Info

Environment

sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.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] parallel grid stats graphics grDevices utils datasets methods base

other attached packages:
[1] bindrcpp_0.2.2 doParallel_1.0.10 ComplexHeatmap_1.12.0 GA_3.0.2 iterators_1.0.9 foreach_1.4.4
[7] caret_6.0-78 lattice_0.20-35 MatchIt_3.0.1 Boruta_5.2.0 ROCR_1.0-7 gplots_3.0.1
[13] ranger_0.8.0 lubridate_1.7.4 parsedate_1.1.1 githubr_0.2 knitr_1.20 forcats_0.2.0
[19] stringr_1.3.1 dplyr_0.7.5 purrr_0.2.5 readr_1.1.1 tidyr_0.8.1 tibble_1.4.2
[25] ggplot2_2.2.1 tidyverse_1.2.1 plyr_1.8.4 data.table_1.11.4 CovariateAnalysis_0.1.0 synapser_0.2.38
[31] knit2synapse_2.0.1

loaded via a namespace (and not attached):
[1] colorspace_1.2-6 rjson_0.2.15 class_7.3-14 modeltools_0.2-21 rprojroot_1.2 mclust_5.2.2 circlize_0.3.9
[8] GlobalOptions_0.0.10 rstudioapi_0.7 ggpubr_0.1.6 DRR_0.0.3 flexmix_2.3-13 mvtnorm_1.0-5 prodlim_1.6.1
[15] xml2_1.1.1 codetools_0.2-15 splines_3.4.3 mnormt_1.5-5 robustbase_0.92-7 RcppRoll_0.2.2 jsonlite_1.5
[22] broom_0.4.2 ddalpha_1.3.1 cluster_2.0.6 kernlab_0.9-25 sfsmisc_1.1-1 compiler_3.4.3 httr_1.3.1
[29] backports_1.0.5 assertthat_0.2.0 Matrix_1.2-11 lazyeval_0.2.1 cli_1.0.0 htmltools_0.3.5 tools_3.4.3
[36] gtable_0.2.0 glue_1.2.0 reshape2_1.4.3 Rcpp_0.12.16 trimcluster_0.1-2 cellranger_1.1.0 gdata_2.17.0
[43] nlme_3.1-131 pack_0.1-1 fpc_2.1-10 psych_1.7.3.21 timeDate_3042.101 gower_0.1.2 testthat_1.0.2
[50] rvest_0.3.2 PythonEmbedInR_0.2.24 gtools_3.5.0 dendextend_1.4.0 DEoptimR_1.0-8 MASS_7.3-47 scales_0.4.1
[57] ipred_0.9-6 hms_0.3 RColorBrewer_1.1-2 yaml_2.1.18 gridExtra_2.2.1 rpart_4.1-11 stringi_1.2.3
[64] highr_0.6 caTools_1.17.1 lava_1.5.1 shape_1.4.2 rlang_0.2.1 pkgconfig_2.0.1 prabclus_2.2-6
[71] bitops_1.0-6 evaluate_0.10.1 bindr_0.1.1 labeling_0.3 recipes_0.1.1 cowplot_0.8.0 CVST_0.2-1
[78] tidyselect_0.2.4 magrittr_1.5 R6_2.2.2 dimRed_0.1.0 pillar_1.2.1 haven_1.1.1 whisker_0.3-2
[85] foreign_0.8-69 withr_2.1.1 survival_2.40-1 RCurl_1.95-4.10 nnet_7.3-12 modelr_0.1.2 crayon_1.3.4
[92] KernSmooth_2.23-15 rmarkdown_1.6 viridis_0.3.4 GetoptLong_0.1.5 readxl_1.1.0 ModelMetrics_1.1.0 digest_0.6.12
[99] diptest_0.75-7 stats4_3.4.3 munsell_0.4.3

Status

Assignee

Kimyen Truong

Reporter

Thanneer Perumal

Labels

None

Validator

Thanneer Perumal

Release Version History

None

Components

Fix versions

Affects versions

Priority

Blocker
Configure