[BioC] CummeRbund getGenes command broken in R?

Zain Alvi [guest] guest at bioconductor.org
Fri Mar 7 02:10:36 CET 2014

Dear Sir or Madam,

I hope this reaches you well. I have been working with R and cummeRbund for the past few months. Everything seemed to be fine with the getGenes command in the manual.

Apparently, today when I was trying to create a heatmap for my genes of interest. I would get the following error no matter what I have do: 

> myGenes <- getGenes(cuff,myGeneIds)
Getting gene information:
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (error in statement: near ")": syntax error)

I am using latest version of cummeRbund with R. Also my Cuffdiff output was done through Cufflinks/Cuffmerge/Cuffdiff 2.0.2.

I checked my old data, which has worked in the past and I received the same error, which is strange.

Also I have reinstalled cummeRbund as well. I've rebuilt the database file as well. No matter, what I do I get this same error.

If you could kindly help me. I would really appreciate it.



 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] cummeRbund_2.4.1     Gviz_1.6.0           rtracklayer_1.22.4   GenomicRanges_1.14.4
 [5] XVector_0.2.0        IRanges_1.20.7       fastcluster_1.1.13   reshape2_1.2.2      
 [9] ggplot2_0.9.3.1      RSQLite_0.11.4       DBI_0.2-7            BiocGenerics_0.8.0  

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.24.0   Biobase_2.22.0         biomaRt_2.18.0         Biostrings_2.30.1     
 [5] biovizBase_1.10.8      bitops_1.0-6           BSgenome_1.30.0        cluster_1.14.4        
 [9] colorspace_1.2-4       dichromat_2.0-0        digest_0.6.4           Formula_1.1-1         
[13] GenomicFeatures_1.14.3 gtable_0.1.2           Hmisc_3.14-3           labeling_0.2          
[17] lattice_0.20-23        latticeExtra_0.6-26    MASS_7.3-29            munsell_0.4.2         
[21] plyr_1.8.1             proto_0.3-10           RColorBrewer_1.0-5     Rcpp_0.11.0           
[25] RCurl_1.95-4.1         Rsamtools_1.14.3       scales_0.2.3           splines_3.0.2         
[29] stats4_3.0.2           stringr_0.6.2          survival_2.37-7        tools_3.0.2           
[33] XML_3.98-1.1           zlibbioc_1.8.0        

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