Question: CummeRbund problem when creating gene sets: Error in sqliteSendQuery: rsqlite_query_send: could not execute1: cannot start a transaction within a transaction
0
gravatar for Wet&DryImmunology
3.4 years ago by
Japan
Wet&DryImmunology200 wrote:

Hi, I was following the manual of CummeRbund.

I was trying to creat a gene set, 

> data(sampleData)
> myGeneIds<-sampleIDs
> myGeneIds
 [1] "XLOC_001363" "XLOC_001297" "XLOC_001339" "XLOC_000132" "XLOC_001265" "XLOC_000151"
 [7] "XLOC_001359" "XLOC_000069" "XLOC_000170" "XLOC_000105" "XLOC_001262" "XLOC_001348"
[13] "XLOC_001411" "XLOC_001369" "XLOC_000158" "XLOC_001370" "XLOC_001263" "XLOC_000115"
[19] "XLOC_000089" "XLOC_001240"
> myGenes<-getGenes(cuff,myGeneIds)

then I got an error: 

Error in sqliteSendQuery(conn, statement) : 
  rsqlite_query_send: could not execute1: cannot start a transaction within a transaction


R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

Could anyone have any idea what went wrong? 

Thank you very much .

Here is my sessionInfo

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

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] grid      stats4    parallel  stats     graphics  grDevices
 [7] utils     datasets  methods   base     

other attached packages:
 [1] cummeRbund_2.10.0    Gviz_1.12.1          rtracklayer_1.28.10 
 [4] GenomicRanges_1.20.8 GenomeInfoDb_1.4.3   IRanges_2.2.9       
 [7] S4Vectors_0.6.6      fastcluster_1.1.16   reshape2_1.4.1      
[10] ggplot2_1.0.1        RSQLite_1.0.0        DBI_0.3.1           
[13] BiocGenerics_0.14.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.1               RColorBrewer_1.1-2       
 [3] futile.logger_1.4.1       plyr_1.8.3               
 [5] XVector_0.8.0             GenomicFeatures_1.20.6   
 [7] bitops_1.0-6              futile.options_1.0.0     
 [9] tools_3.2.2               zlibbioc_1.14.0          
[11] rpart_4.1-10              biomaRt_2.24.1           
[13] digest_0.6.8              BSgenome_1.36.3          
[15] biovizBase_1.16.0         lattice_0.20-33          
[17] gtable_0.1.2              proto_0.3-10             
[19] gridExtra_2.0.0           cluster_2.0.3            
[21] stringr_1.0.0             Biostrings_2.36.4        
[23] nnet_7.3-11               Biobase_2.28.0           
[25] AnnotationDbi_1.30.1      survival_2.38-3          
[27] XML_3.98-1.3              BiocParallel_1.2.22      
[29] foreign_0.8-66            Formula_1.2-1            
[31] latticeExtra_0.6-26       lambda.r_1.1.7           
[33] magrittr_1.5              splines_3.2.2            
[35] Hmisc_3.17-0              matrixStats_0.14.2       
[37] scales_0.3.0              Rsamtools_1.20.5         
[39] MASS_7.3-44               GenomicAlignments_1.4.2  
[41] dichromat_2.0-0           colorspace_1.2-6         
[43] stringi_0.5-5             acepack_1.3-3.3          
[45] RCurl_1.95-4.7            munsell_0.4.2            
[47] VariantAnnotation_1.14.13

ADD COMMENTlink modified 2.6 years ago by Satyajeet Khare1.3k • written 3.4 years ago by Wet&DryImmunology200
0
gravatar for juafonso_bio
2.6 years ago by
juafonso_bio40
juafonso_bio40 wrote:

Hi. Did you solve this problem? I am having the same problem and do not know how to solve it.

ADD COMMENTlink written 2.6 years ago by juafonso_bio40

By any chance are you running a shiny app?

ADD REPLYlink written 2.6 years ago by YaGalbi1.4k

@juafonso_bio, you need to shift your post to comment section.

ADD REPLYlink written 2.6 years ago by Satyajeet Khare1.3k
0
gravatar for Satyajeet Khare
2.6 years ago by
Satyajeet Khare1.3k
Pune, India
Satyajeet Khare1.3k wrote:

Try recreating the cuff database. I got this error when connection to cuff was lost. I am assuming that cuff database WAS created earlier. Don't see it in session info.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Satyajeet Khare1.3k
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