CummeRbund problem when creating gene sets: Error in sqliteSendQuery: rsqlite_query_send: could not execute1: cannot start a transaction within a transaction

Question

[Wet&DryImmunology]

Hi, I was following the manual of CummeRbund.

I was trying to create 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

[juafonso_bio]

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

[BioinfGuru]

By any chance are you running a shiny app?

[Satyajeet Khare]

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

Answer 1

[Satyajeet Khare]

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.

[maperezm.medi]

Hello, did someone can fixed this problem?