I have been able to use JASPAR2014 via TFBSTools.  Upgrading to JASPAR2018 has so far not been so successful.  As a fall-back, I thought I would try to access the JASPAR2018.sqlite file using DBI / RSQLite.  When I do this, I find that most of the tables are empty.

Here is my "HelloJaspar" code:

---------------------------------------------------------

library(DBI)

libDir = .libPaths()[1]
dbDir = '/home/mds59/R/x86_64-pc-linux-gnu-library/3.2/JASPAR2018/extdata'
jaspar = 'JASPAR2018'
dbName = sprintf('%s/%s/extdata/%s.sqlite',libDir,jaspar,jaspar)

con = dbConnect(RSQLite::SQLite(), dbName)

allTables = dbListTables(con)

tables = list()
for(t in allTables)
{
    query = sprintf('select * from %s',t)

    df = dbGetQuery(con,query)
    tables[[t]] = df

    print(sprintf('%s  %d  %d',t,nrow(df),ncol(df)))
}

dbDisconnect(con)

----------------------------------------------

Here is the resulting output:

[1] "MATRIX  0  5"
[1] "MATRIX_ANNOTATION  0  3"
[1] "MATRIX_DATA  0  4"
[1] "MATRIX_PROTEIN  0  2"
[1] "MATRIX_SPECIES  0  2"
[1] "TAX  0  2"
[1] "TAX_EXT  0  2"
[1] "TFFM  133  9"
[1] "sqlite_sequence  0  2"

-----------------------------------------------

And here is the session info:

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

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

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

other attached packages:
[1] DBI_0.7

loaded via a namespace (and not attached):
 [1] bit_1.1-12      compiler_3.4.3  pillar_1.2.1    tibble_1.4.2   
 [5] memoise_1.1.0   Rcpp_0.12.15    bit64_0.9-7     RSQLite_2.0    
 [9] blob_1.1.0      digest_0.6.15   pkgconfig_2.0.1 rlang_0.2.0   

---------------------------------------------------------------

Any insight would be much appreciated.

It seems to work for me:

> library(TFBSTools)
> library(JASPAR2018)
> opts <- list()
opts[["species"]] <- 9606
opts[["name"]] <- "RUNX1"
opts[["type"]] <- "SELEX"
opts[["all_versions"]] <- TRUE
PFMatrixList <- getMatrixSet(JASPAR2018, opts)

> PFMatrixList
PFMatrixList of length 1
names(1): MA0002.1

In addition:

> library(DBI)
> library(RSQLite)
> con <- dbConnect(SQLite(), JASPAR2018@db)

> sapply(dbListTables(con), function(x) dbGetQuery(con, paste("select count(*) from", x, ";")))
$`MATRIX.count(*)`
[1] 2404

$`MATRIX_ANNOTATION.count(*)`
[1] 16485

$`MATRIX_DATA.count(*)`
[1] 122616

$`MATRIX_PROTEIN.count(*)`
[1] 1993

$`MATRIX_SPECIES.count(*)`
[1] 2240

$`TAX.count(*)`
[1] 525711

$`TAX_EXT.count(*)`
[1] 23100

$`TFFM.count(*)`
[1] 133