When loading a VCF file, one of the records is ignored. The missing record has a 4094 byte record immediately prior to it and any change to the length of that record makes the loading succeed again. Changing the content of the prior record without changing the length also causes the record to fail to load.

Reproduction steps:

names(readVcf("repo.vcf"))

Expected output:

[1] "gridss9_272646b" "gridss9_31852o" 

Actual output:

[1] "gridss9_272646b"

The offending file can be found at https://pastebin.com/qJ0afBAP

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                     
[5] LC_TIME=English_Australia.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] VariantAnnotation_1.28.3    Rsamtools_1.34.0            Biostrings_2.50.1           XVector_0.22.0              SummarizedExperiment_1.12.0
[6] DelayedArray_0.8.0          BiocParallel_1.16.2         matrixStats_0.54.0          Biobase_2.42.0              GenomicRanges_1.34.0      
[11] GenomeInfoDb_1.18.1         IRanges_2.16.0              S4Vectors_0.20.1            BiocGenerics_0.28.0        

loaded via a namespace (and not attached):
[1] Rcpp_1.0.0               compiler_3.5.1           prettyunits_1.0.2        GenomicFeatures_1.34.1   bitops_1.0-6             tools_3.5.1            
[7] zlibbioc_1.28.0          progress_1.2.0           biomaRt_2.38.0           digest_0.6.18            bit_1.1-14               BSgenome_1.50.0        
[13] RSQLite_2.1.1            memoise_1.1.0            lattice_0.20-38          pkgconfig_2.0.2          rlang_0.3.0.1            Matrix_1.2-15          
[19] DBI_1.0.0                rstudioapi_0.8           yaml_2.2.0               GenomeInfoDbData_1.2.0   rtracklayer_1.42.1       httr_1.3.1             
[25] stringr_1.3.1            hms_0.4.2                bit64_0.9-7              grid_3.5.1               R6_2.3.0                 AnnotationDbi_1.44.0   
[31] XML_3.98-1.16            magrittr_1.5             blob_1.1.1               GenomicAlignments_1.18.0 assertthat_0.2.0         stringi_1.2.4          
[37] RCurl_1.95-4.11          crayon_1.3.4