Error: C stack usage 7953880 is too close to the limit

[ShihanL]

Hey Alexander. Very interesting tool! I'm getting this error consistently when calling SPANTCR where the inputted data all has the same alpha gene usage:

I suspect its some recursive function being called?

[alexandermxu]

Hi Shihan,Hmm it’s an odd error message, is the data set very large? I have to admit I haven’t stress tested it super hard. I don’t believe there are any loops over alpha genes but it’s possible. Can you provide a bit more information?AlexSent from my iPhoneOn Jul 12, 2024, at 12:02 AM, Shihan Li @.***> wrote: Hey Alexander. Very interesting tool! I'm getting this error consistently when calling SPANTCR where the inputted data all has the same alpha gene usage: Screenshot.2024-07-12.at.5.00.31.PM.png (view on web) I suspect its some recursive function being called?

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[ShihanL]

Hi Alexander,

I get the same error with a dataframe of 5 rows: I've worked out the reason for the error actually, it's to do with the lengths of the CDR3s, if they are all the same length the error occurs. Might be something to do with the sliding window?

FAILS:

  specificity    id     Jgene   gene         CDR3 score      Vgene
        <char> <int>    <char> <char>       <char> <num>     <char>
1:       5opru    27 TRAJ20*01    TRA CAVLSGDYKLSF     1 TRAV1-2*01
2:       5opru     2 TRAJ33*01    TRA CAAMDSNYQLIW     1 TRAV1-2*01
3:       5opru    15 TRAJ33*01    TRA CAVKDSNYQLIW     1 TRAV1-2*01
4:       5opru    69 TRAJ33*01    TRA CAVTDSNYQLIW     1 TRAV1-2*01
5:       5opru    36 TRAJ33*01    TRA CAVMDSNYQLIW     1 TRAV1-2*01

WORKS(change CAAMDSNYQLIW to CAAMDSNYQLI):

  specificity    id     Jgene   gene         CDR3 score      Vgene
        <char> <int>    <char> <char>       <char> <num>     <char>
1:       5opru    27 TRAJ20*01    TRA CAVLSGDYKLSF     1 TRAV1-2*01
2:       5opru     2 TRAJ33*01    TRA CAAMDSNYQLI     1 TRAV1-2*01
3:       5opru    15 TRAJ33*01    TRA CAVKDSNYQLIW     1 TRAV1-2*01
4:       5opru    69 TRAJ33*01    TRA CAVTDSNYQLIW     1 TRAV1-2*01
5:       5opru    36 TRAJ33*01    TRA CAVMDSNYQLIW     1 TRAV1-2*01

z <- SPANTCR(test, "VDJDBCMVAlpha","TRA","Mass", 100,
        2, 0.03, ScoreFunctionExponential5, WeightFunctionLinear)

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Australia/Melbourne
tzcode source: internal

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

other attached packages:
 [1] data.table_1.15.4  SPANTCR_0.0.0.9000 lubridate_1.9.2   
 [4] forcats_1.0.0      stringr_1.5.0      dplyr_1.1.4       
 [7] purrr_1.0.2        readr_2.1.4        tidyr_1.3.0       
[10] tibble_3.2.1       ggplot2_3.5.1      tidyverse_2.0.0   

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       cli_3.6.3         rlang_1.1.4      
 [4] stringi_1.7.12    generics_0.1.3    labeling_0.4.3   
 [7] glue_1.7.0        colorspace_2.1-0  hms_1.1.3        
[10] scales_1.3.0      fansi_1.0.6       grid_4.3.1       
[13] munsell_0.5.1     tzdb_0.4.0        lifecycle_1.0.4  
[16] compiler_4.3.1    timechange_0.2.0  pkgconfig_2.0.3  
[19] rstudioapi_0.15.0 farver_2.1.2      R6_2.5.1         
[22] tidyselect_1.2.1  utf8_1.2.4        pillar_1.9.0     
[25] magrittr_2.0.3    tools_4.3.1       withr_3.0.0      
[28] gtable_0.3.5