Error in db_create(): result would exceed 2^31-1 bytes

[btupper]

Hello,

We are encountering an issue using db_create() that we can't seem to work around. The database creating proceeds until we get the error shown below. We have tried varying values of max_length but so far have not been able to avoid the error.

Do you have any suggestion?

Thanks!

library(restez)
restez_root = tmpdir(check = TRUE)
restez::restez_path_set(restez_root)
restez::db_download(preselection = "1")
restez::db_create(max_length = 1e6)

# Inspecting 2099 file(s) to add to the database ...
# ... 'gbinv1.seq.gz' (1/2099)
# ... 'gbinv10.seq.gz' (2/2099)
# ... 'gbinv100.seq.gz' (3/2099)
# ... 'gbinv1000.seq.gz' (4/2099)
# ... ... No sequences found that meet filters; skipping file.
# ... 'gbinv1001.seq.gz' (5/2099)
# ... ... No sequences found that meet filters; skipping file.
# ... 'gbinv1002.seq.gz' (6/2099)
# ... ... No sequences found that meet filters; skipping file.
# ... 'gbinv1003.seq.gz' (7/2099)
# ... 'gbinv1004.seq.gz' (8/2099)
# ... 'gbinv1005.seq.gz' (9/2099)
# ... ... No sequences found that meet filters; skipping file.
# ... 'gbinv1006.seq.gz' (10/2099)
# ... 'gbinv1007.seq.gz' (11/2099)
# ... ... No sequences found that meet filters; skipping file.
# ... 'gbinv1008.seq.gz' (12/2099)
# ... ... No sequences found that meet filters; skipping file.
# ... 'gbinv1009.seq.gz' (13/2099)
# ... 'gbinv101.seq.gz' (14/2099)
# ... 'gbinv1010.seq.gz' (15/2099)
# ... ... No sequences found that meet filters; skipping file.
# ... 'gbinv1011.seq.gz' (16/2099)
# ... 'gbinv1012.seq.gz' (17/2099)
# ... 'gbinv1013.seq.gz' (18/2099)
# ... 'gbinv1014.seq.gz' (19/2099)
# ... ... No sequences found that meet filters; skipping file.
# ... 'gbinv1015.seq.gz' (20/2099)
# ... ... No sequences found that meet filters; skipping file.
# ... 'gbinv1016.seq.gz' (21/2099)
# ... ... No sequences found that meet filters; skipping file.
# ... 'gbinv1017.seq.gz' (22/2099)
# ... ... No sequences found that meet filters; skipping file.
# ... 'gbinv1018.seq.gz' (23/2099)
# Error in paste0(lines[indexes], collapse = "\n") : 
#   result would exceed 2^31-1 bytes
# Calls: <Anonymous> ... gb_build -> flatfile_read -> lapply -> FUN -> paste0
# In addition: There were 13 warnings (use warnings() to see them)
# Execution halted

Session info follows...

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 8.9 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /mnt/modules/bin/R/4.1.3/lib/libopenblasp-r0.3.20.so

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

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

other attached packages:
[1] restez_2.1.4

loaded via a namespace (and not attached):
[1] compiler_4.1.3 tools_4.1.3   

[joelnitta]

Fixed by #61