expired SQLiteConnection in GoSemSim package.
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@anupambtech2007-7589
Last seen 6.4 years ago
United States

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

 

gene ontology GOSemsim • 2.1k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 7 months ago
China/Guangzhou/Southern Medical Univer…

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

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> library(org.Hs.eg.db)
> library(GO.db)
> library(GOSemSim)
>
> temp <- geneSim("5921", "9046", ont = "BP", organism = "human", measure = "Wang", combine = "max")
Error in sqliteSendQuery(con, statement, bind.data) :
  expired SQLiteConnection
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_IN       LC_NUMERIC=C         LC_TIME=en_IN       
 [4] LC_COLLATE=en_IN     LC_MONETARY=en_IN    LC_MESSAGES=en_IN   
 [7] LC_PAPER=en_IN       LC_NAME=C            LC_ADDRESS=C        
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_IN LC_IDENTIFICATION=C

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

other attached packages:
 [1] BiocInstaller_1.16.2 GOSemSim_1.24.1      GO.db_3.0.0         
 [4] org.Hs.eg.db_3.0.0   AnnotationDbi_1.28.2 GenomeInfoDb_1.2.5  
 [7] IRanges_2.0.1        S4Vectors_0.4.0      Biobase_2.26.0      
[10] BiocGenerics_0.12.1  RSQLite_1.0.0        DBI_0.3.1           

loaded via a namespace (and not attached):
 [1] bitops_1.0-6   digest_0.6.8   httr_0.6.1     Rcpp_0.11.5    RCurl_1.95-4.5
 [6] stringr_0.6.2  swirl_2.2.21   testthat_0.9.1 tools_3.1.2    yaml_2.1.13   
>

 

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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 7 months ago
China/Guangzhou/Southern Medical Univer…

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?

 

 

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@anupambtech2007-7589
Last seen 6.4 years ago
United States

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")

 

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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 7 months ago
China/Guangzhou/Southern Medical Univer…

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

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@paulson-ariel-6239
Last seen 3.6 years ago
United States

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.

 

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If the issue is due to reloading old saved session, then it is not an issue.

File connection can't be restored in another R session.

> x=file("x.txt", "w")
> x
description       class        mode        text      opened    can read
    "x.txt"      "file"         "w"      "text"    "opened"        "no"
  can write
      "yes"
> save(x, file="x.rda")

If you start another R session and load the x.rda, you will find that x is expired.

> load("x.rda")
> x
Error in summary.connection(x) : invalid connection

 

 

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how to delete the following cache objects in the environment: "GOSemSimEnv", "SemSimCache", "DOSEEnv  ???

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You can use for example rm(GOSemSimEnv) to delete GOSemSimEnv, but you really don't need to delete them. 

 

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