I get warnings from standardChromosomes. I did not have this problem with R-3.4.1.

library(GenomeInfoDb)
library(GenomicRanges)
standardChromosomes(GRanges(seqnames="chr1",IRanges(start=1,end=2)))
[1] "chr1"
Warning messages:
1: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  EOF within quoted string
2: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  EOF within quoted string

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS/LAPACK: /mnt/share/apps/tools/intel-2018_3/compilers_and_libraries_2018.3.222/linux/mkl/lib/intel64_lin/libmkl_rt.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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] GenomicRanges_1.34.0 GenomeInfoDb_1.18.0  IRanges_2.16.0      
[4] S4Vectors_0.20.0     BiocGenerics_0.28.0 

loaded via a namespace (and not attached):
[1] zlibbioc_1.28.0        compiler_3.5.1         XVector_0.22.0        
[4] GenomeInfoDbData_1.2.0 RCurl_1.95-4.11        bitops_1.0-6

Thank you for the clear example. Please check that your installation is current -- BiocManager::valid() -- I believe GenomeInfoDb is at version 1.18.1.