Invoking the mirna2mrna() function from affycoretools generates two warnings:

Warning messages:
1: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().
2: In result_fetch(res@ptr, n = n) :
  SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().

The result, however, seems to be OK. It would be nice, if the code in mirna2mrna() could to be changed according to the text in the warnings.

A working example follows below:

  library(affycoretools)
  library(org.Dm.eg.db)
  library(drosophila2.db)

  sigmrna.f <- c("1622906_at", "1628369_at", "1629539_s_at", "1641237_a_at")
  sigmirna.f <- c("dme-miR-14-3p_st", "dme-miR-279-3p_st", "dme-miR-286-3p_st")

  mirna.targets <- data.frame(
                     miRTarBase.ID = c("MIRT001879", "MIRT001888", "MIRT001889", "MIRT002356"),
                     miRNA = c("dme-miR-312-3p", "dme-miR-286-3p", "dme-miR-279-3p", "dme-miR-14-3p"),
                     target.gene = c("CrebA", "boss", "SP555", "EcR"), 
                     Entrez.ID = c(39682L, 43146L, 53471L, 35540L), 
                     ENST = c("FBtr0075557", "FBtr0084949", "FBtr0333534", "FBtr0086009")
                   )
  aname <- "dme_targets.tsv"
  write.table(mirna.targets, aname, sep = "\t", col.names=FALSE, row.names=FALSE, quote=FALSE)

  imap <- mirna2mrna(miRNAids=sigmirna.f, miRNAannot=aname, mRNAids=sigmrna.f, 
                     orgPkg="org.Dm.eg.db", chipPkg="drosophila2.db",
                     sanger=FALSE, miRNAcol=2, mRNAcol=5, transType="ensembl")
  print(imap)
  # $`dme-miR-279-3p`
  # [1] "1629539_s_at" "1641237_a_at"

  # $`dme-miR-286-3p`
  # [1] "1628369_at"

The R and Bioconductor environment is

R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] drosophila2.db_3.13.0 org.Dm.eg.db_3.14.0   AnnotationDbi_1.56.1  IRanges_2.28.0       
[5] S4Vectors_0.32.1      affycoretools_1.66.0  Biobase_2.54.0        BiocGenerics_0.40.0

Thanks for pointing that out. It's not an error, just a warning that RSQLite doesn't like you to use dbGetQuery for calls to the DB that don't return values. I've switched it to use dbExecute in devel.