Error in rm_tbi() : could not find function "rm_tbi"

[bschilder]

 Solution

A very small but important fix was editing this line in the .Rbuildignore. The syntax was wrong and was ignoring the rm_tbi.R file (not just .tbi files, which i do want to ignore). Therefore echotabix was blind to the rm_tbi function.

.*.tbi --> .*\.tbi$

Reprex

query_dat <- echodata::BST1[seq(1, 50), ] 
locus_dir <- file.path(tempdir(), echodata::locus_dir)  
LD_list <- echoLD::get_LD(
    locus_dir = locus_dir,
    query_dat = query_dat,
    LD_reference = "1KGphase1")

Here is what I got:
LD_reference identified as: 1kg.
Using 1000Genomes as LD reference panel.
Constructing GRanges query using min/max ranges across one or more chromosomes.
+ as_blocks=TRUE: Will query a single range per chromosome that covers all regions requested (plus anything in between).
LD Reference Panel = 1KGphase1
Querying 1KG remote server.
========= echotabix::query =========
query_dat is already a GRanges object. Returning directly.
Explicit format: 'vcf'
Querying VCF tabix file.
Importing existing VCF file: /tmp/RtmpdpQfkr/VCF/RtmpdpQfkr.chr4-14884541-16649679.ALL.chr4.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.bgz

Session info

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.1

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: Europe/London
tzcode source: internal

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

other attached packages:
[1] echotabix_0.99.10

loaded via a namespace (and not attached):
  [1] tidyselect_1.2.0            dplyr_1.1.3                 blob_1.2.4                 
  [4] filelock_1.0.2              R.utils_2.12.2              Biostrings_2.70.1          
  [7] bitops_1.0-7                fastmap_1.1.1               RCurl_1.98-1.13            
 [10] BiocFileCache_2.10.1        VariantAnnotation_1.48.0    GenomicAlignments_1.38.0   
 [13] XML_3.99-0.15               digest_0.6.33               lifecycle_1.0.4            
 [16] KEGGREST_1.42.0             RSQLite_2.3.3               magrittr_2.0.3             
 [19] compiler_4.3.1              rlang_1.1.2                 progress_1.2.2             
 [22] tools_4.3.1                 utf8_1.2.4                  yaml_2.3.7                 
 [25] data.table_1.14.8           rtracklayer_1.62.0          htmlwidgets_1.6.2          
 [28] prettyunits_1.2.0           S4Arrays_1.2.0              bit_4.0.5                  
 [31] curl_5.1.0                  reticulate_1.34.0           DelayedArray_0.28.0        
 [34] xml2_1.3.5                  pkgload_1.3.3               abind_1.4-5                
 [37] BiocParallel_1.36.0         purrr_1.0.2                 BiocGenerics_0.48.1        
 [40] R.oo_1.25.0                 grid_4.3.1                  stats4_4.3.1               
 [43] echoconda_0.99.9            fansi_1.0.5                 biomaRt_2.58.0             
 [46] SummarizedExperiment_1.32.0 cli_3.6.1                   crayon_1.5.2               
 [49] generics_0.1.3              rstudioapi_0.15.0           tzdb_0.4.0                 
 [52] httr_1.4.7                  rjson_0.2.21                piggyback_0.1.5            
 [55] DBI_1.1.3                   cachem_1.0.8                stringr_1.5.1              
 [58] zlibbioc_1.48.0             parallel_4.3.1              AnnotationDbi_1.64.1       
 [61] BiocManager_1.30.22         XVector_0.42.0              restfulr_0.0.15            
 [64] matrixStats_1.1.0           basilisk_1.14.0             vctrs_0.6.4                
 [67] Matrix_1.6-1.1              jsonlite_1.8.7              dir.expiry_1.10.0          
 [70] IRanges_2.36.0              hms_1.1.3                   S4Vectors_0.40.1           
 [73] bit64_4.0.5                 GenomicFeatures_1.54.1      tidyr_1.3.0                
 [76] glue_1.6.2                  codetools_0.2-19            DT_0.30                    
 [79] stringi_1.8.1               GenomeInfoDb_1.38.1         GenomicRanges_1.54.1       
 [82] BiocIO_1.12.0               tibble_3.2.1                pillar_1.9.0               
 [85] htmltools_0.5.7             basilisk.utils_1.14.0       rappdirs_0.3.3             
 [88] GenomeInfoDbData_1.2.11     BSgenome_1.70.1             R6_2.5.1