problem of GOSemSim R package operation geneSim()
2
0
Entering edit mode
@bnembarekmarwa-10593
Last seen 5.4 years ago

Hi All, I have installed and loaded GOSemSim, tried the functions implemented in the package using the examples. All the functions work fine, except clusterSim() and  geneSim().  it throws and error as below. Please, advise ...

gosemsim • 708 views
ADD COMMENT
0
Entering edit mode

Did you mean to include more text?

ADD REPLY
0
Entering edit mode

> geneSim("241", "251", ont="MF", organism="human", measure="Wang", combine="BMA")
Error in sqliteSendQuery(con, statement, bind.data) :
  expired SQLiteConnection
> sessionInfo()
R version 3.2.4 Revised (2016-03-16 r70336)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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

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

other attached packages:
 [1] BiocInstaller_1.20.1 GO.db_3.2.2          org.Hs.eg.db_3.2.3  
 [4] AnnotationDbi_1.32.3 Biobase_2.30.0       Rcpp_0.12.4         
 [7] IRanges_2.4.8        S4Vectors_0.8.11     BiocGenerics_0.16.1
[10] GOSemSim_1.28.2      RSQLite_1.0.0        DBI_0.3.1           

loaded via a namespace (and not attached):
[1] tools_3.2.4

 

ADD REPLY
0
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 7 months ago
China/Guangzhou/Southern Medical Univer…

see the discussion in expired SQLiteConnection in GoSemSim package.

ADD COMMENT
0
Entering edit mode
@bnembarekmarwa-10593
Last seen 5.4 years ago

I run the same exemple puplished and  I have the same error 'Error in sqliteSendQuery(con, statement, bind.data) :
  expired SQLiteConnection
' , have u some advise

 

ADD COMMENT

Login before adding your answer.

Traffic: 244 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6