All issues

Uploading file to synapse fails due to Cstack uasage hitting the upper limit
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Core dump on UCSC CentOS servers
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large file access
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Make R Client follow redirects
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downloadEntity broken
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SYNR-1431
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SYNR-1424
Fix `synSendMessage`
SYNR-1420
Basic table code fails when run from Rscript vs console
SYNR-1414
build R packages for R v. 3.6
SYNR-1411
tableQuery stopped working
SYNR-1404
Deploy R packages to S3 hosted staging-ran and ran
SYNR-1391
synapser fails to populate date columns from file views
SYNR-1380
issue 1 of 1191

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.

1 2 3 4 > obj = synapser::File('ageMatchHealthCodes.html', parentId = CODE$properties$id) > obj = synapser::synStore(obj, activityName = activityName, + activityDescription = activityDescription, + used = all.used.ids, executed = thisFile)

R Traceback

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 Error in value[[3L]](cond) : ################################################## Uploading file to Synapse storage ################################################## Uploading [--------------------]0.00% 0.0bytes/1.1MB ageMatchHealthCodes.html C stack usage 646639505852 is too close to the limit 13. stop(errorToReport) 12. value[[3L]](cond) 11. tryCatchOne(expr, names, parentenv, handlers[[1L]]) 10. tryCatchList(expr, classes, parentenv, handlers) 9. tryCatch({ result <- do.call(callable, args) sink() close(conn) ... 8. cleanUpStackTrace(pyCall, list("gateway.invoke", args = functionAndArgs, kwargs = argsAndKwArgs$kwargs, simplify = F)) 7. .synStore(<environment>, activityName = "Age match case-control", activityDescription = "Age match samples for case-control classification with a random forest model", used = c("syn10676309", "syn11225372", "syn10371840", "syn12178233", "syn12299821", "syn11958147", "syn11958151", "syn11958154", ... 6. do.call(rWrapperName, args = list(...)) 5. synStore(...) 4. eval(mc, env) 3. eval(mc, env) 2. standardGeneric("synStore") 1. synapser::synStore(obj, activityName = activityName, activityDescription = activityDescription, used = all.used.ids, executed = thisFile)

Memory Info

1 2 3 4 5 > memory.profile() NULL symbol pairlist closure environment promise language special builtin char logical integer double 1 40923 1705837 34335 11972 33061 459204 45 671 126028 53813 194930 145729 complex character ... any list expression bytecode externalptr weakref raw S4 50 541354 98 0 101051 20 47733 5887 1443 1442 6119

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

synapser-0.2

Priority

Blocker
Configure