I have just installed GOSeSim package in Biocoundoctor. I tried to run genesim function. for the 1st time it worked. But after that, its giving below error :

Error in sqliteSendQuery(con, statement, bind.data) :
  expired SQLiteConnection

please post your sessionInfo() and also code for me to reproduce your error.

I can't reproduce your error.

> temp <- geneSim("5921", "9046", ont = "BP", organism = "human", measure = "Wang", combine = "max")
> temp
$geneSim
[1] 1

$GO1
 [1] "GO:0000281" "GO:0001570" "GO:0009790" "GO:0043524" "GO:0001953"
 [6] "GO:0007165" "GO:0007162" "GO:0030833" "GO:0048514" "GO:0035556"
[11] "GO:0008360" "GO:0051252" "GO:0032320" "GO:0046580"

$GO2
[1] "GO:0007596" "GO:0007165" "GO:0007166" "GO:0050900"

> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-apple-darwin14.1.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] GOSemSim_1.24.1      GO.db_3.0.0          org.Hs.eg.db_3.0.0
 [4] RSQLite_1.0.0        DBI_0.3.1            AnnotationDbi_1.28.2
 [7] GenomeInfoDb_1.3.13  IRanges_2.1.40       S4Vectors_0.5.21
[10] Biobase_2.27.1       BiocGenerics_0.13.4  roxygen2_4.1.0
[13] devtools_1.7.0       magrittr_1.5         BiocInstaller_1.16.2

loaded via a namespace (and not attached):
[1] fortunes_1.5-2 Rcpp_0.11.5    stringr_0.6.2  tools_3.1.3

Actually, GOSemSim do not use SQLiteConnection directly, it use interface provided by AnnotationDbi package.

Can you post traceback() output after the error shown?

Error in sqliteSendQuery(con, statement, bind.data) :
  expired SQLiteConnection
> temp <- geneSim("5921", "9046", ont = "BP", organism = "human", measure = "Wang", combine = "max")
Error in sqliteSendQuery(con, statement, bind.data) :
  expired SQLiteConnection
> traceback()
26: .Call(rsqlite_query_send, con@Id, as.character(statement), bind.data)
25: sqliteSendQuery(con, statement, bind.data)
24: sqliteGetQuery(conn, statement)
23: .local(conn, statement, ...)
22: dbGetQuery(conn, SQL)
21: dbGetQuery(conn, SQL)
20: dbQuery(conn, SQL)
19: dbSelectFromL2Rchain(dbconn(x), L2Rchain, x@Lkeys, x@Rkeys)
18: getPartialSubmap("BP")
17: eval(expr, envir, enclos)
16: eval(quote(list(...)), env)
15: eval(quote(list(...)), env)
14: standardGeneric("rbind")
13: rbind(getPartialSubmap("BP"), getPartialSubmap("CC"), getPartialSubmap("MF"))
12: .local(x, ...)
11: flatten(x, fromKeys.only = TRUE)
10: flatten(x, fromKeys.only = TRUE)
9: as.list(envir)
8: as.list(envir)
7: mget(i, envir = x, ifnotfound = NA)
6: mget(i, envir = x, ifnotfound = NA)
5: .doubleBracketSub(x, i, j, ...)
4: gomap[[gene]]
3: gomap[[gene]]
2: gene2GO(gene1, organism = organism, ont = ont, dropCodes = drop)
1: geneSim("5921", "9046", ont = "BP", organism = "human", measure = "Wang",
       combine = "max")

Do you still have the problem when updating to Bioconductor 3.1 with R 3.2.0?
 

I had a similar problem after reloading an old saved session.  I deleted the following cache objects in my environment: "GOSemSimEnv", "SemSimCache", "DOSEEnv" and re-ran the function and things worked fine.