Error in getPLP when using Redshift

[rfherrera]

Describe the bug When running getPLP, I am getting the following error java.sql.SQLException: Amazon Invalid operation: Value out of range for 4 bytes. Details: ----------------------------------------------- error: Value out of range for 4 bytes. code: 8001 context: Input:21605144410. query: 26832412 location: numeric_bound.cpp:61 process: query1_302_26832412 [pid=11450]

Set up (please run in R "sessionInfo()" and copy the output here): R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04 LTS

Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
[7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 LC_ADDRESS=en_US.UTF-8
[10] LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] PheValuator_2.1.5 FeatureExtraction_3.2.0 Andromeda_0.6.0
[4] dplyr_1.0.9 DatabaseConnector_5.0.2

loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 pillar_1.7.0 compiler_4.0.3
[4] tools_4.0.3 bit_4.0.4 jsonlite_1.8.0
[7] lattice_0.20-41 RSQLite_2.2.12 memoise_2.0.1
[10] lifecycle_1.0.1 tibble_3.1.6 pkgconfig_2.0.3
[13] rlang_1.0.2 Matrix_1.3-2 rstudioapi_0.13
[16] DBI_1.1.2 cli_3.3.0 PatientLevelPrediction_5.0.5 [19] fastmap_1.1.0 rJava_1.0-6 generics_0.1.2
[22] vctrs_0.4.1 hms_1.1.1 grid_4.0.3
[25] triebeard_0.3.0 bit64_4.0.5 xgboost_1.2.0.1
[28] tidyselect_1.1.2 data.table_1.14.2 glue_1.6.2
[31] R6_2.5.1 fansi_1.0.3 purrr_0.3.4
[34] ParallelLogger_2.0.2 SqlRender_1.9.0 blob_1.2.3
[37] magrittr_2.0.3 urltools_1.7.3 ellipsis_0.3.2
[40] assertthat_0.2.1 utf8_1.2.2 stringi_1.7.6
[43] cachem_1.0.6 crayon_1.5.1

[jreps]

Hi Ron,

That error seems to suggest for some reason there is a large number somewhere (either in the database or being created). What features are you extracting? My guess is that this error is most likely coming from FeatureExtraction. There is code in getPlp for sampling that is casting to BigInt that is the only place I can see in PatientLevelPrediction potentially being responsible, are you sampling any patients?

Best wishes, Jenna