having searched all forum and still no solution about my cummeRbund problem. Pls help

[spzhangmit]

Yes, is there anyone know how to fix it?

[axa9070]

I'm having the exact same problem =[

Error in FUN(c("\n-- Creator: MySQL Workbench 5.2.33/ExportSQLite plugin 2009.12.02\n-- Author: Loyal Goff\n-- Caption: New Model\n-- Project: Name of the project\n-- Changed: 2012-04-30 22:21\n-- Created: 2011-05-02 12:52\nPRAGMA foreign_keys = OFF", :
could not find function "sqliteQuickSQL"



sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[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 stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] cummeRbund_2.8.0 Gviz_1.10.1 rtracklayer_1.26.1 GenomicRanges_1.18.1 GenomeInfoDb_1.2.2
[6] IRanges_2.0.0 S4Vectors_0.4.0 fastcluster_1.1.13 reshape2_1.4 ggplot2_1.0.0
[11] RSQLite_1.0.0 DBI_0.3.1 BiocGenerics_0.12.0

loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 AnnotationDbi_1.28.0 base64enc_0.1-2 BatchJobs_1.4
[5] BBmisc_1.7 Biobase_2.26.0 BiocParallel_1.0.0 biomaRt_2.22.0
[9] Biostrings_2.34.0 biovizBase_1.14.0 bitops_1.0-6 brew_1.0-6
[13] BSgenome_1.34.0 checkmate_1.5.0 cluster_1.15.3 codetools_0.2-9
[17] colorspace_1.2-4 dichromat_2.0-0 digest_0.6.4 fail_1.2
[21] foreach_1.4.2 foreign_0.8-61 Formula_1.1-2 GenomicAlignments_1.2.0
[25] GenomicFeatures_1.18.1 gtable_0.1.2 Hmisc_3.14-5 iterators_1.0.7
[29] lattice_0.20-29 latticeExtra_0.6-26 MASS_7.3-35 matrixStats_0.10.3
[33] munsell_0.4.2 nnet_7.3-8 plyr_1.8.1 proto_0.3-10
[37] R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.3 RCurl_1.95-4.3
[41] rpart_4.1-8 Rsamtools_1.18.1 scales_0.2.4 sendmailR_1.2-1
[45] splines_3.1.1 stringr_0.6.2 survival_2.37-7 tools_3.1.1
[49] VariantAnnotation_1.12.2 XML_3.98-1.1 XVector_0.6.0 zlibbioc_1.12.0
>

[spzhangmit]

Hey guys,

My problem is that I can load cummeRbund, but cann't create the database (cuffData.db was 0bytes). No matter what package I installed, such as RSQLite, DBI, splite3... , or using other output data from cuffdiff downloaded from GEO, still didn't work.

> cuff<-readCufflinks("diff_out")
Creating database diff_out/cuffData.db
Error in FUN(c("\n-- Creator: MySQL Workbench 5.2.33/ExportSQLite plugin 2009.12.02\n-- Author: Loyal Goff\n-- Caption: New Model\n-- Project: Name of the project\n-- Changed: 2012-04-30 22:21\n-- Created: 2011-05-02 12:52\nPRAGMA foreign_keys = OFF", :
could not find function "sqliteQuickSQL"


I am running ubuntu 14.04 LTS. And I think the environment for R and cummeRbund is okay.
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] cummeRbund_2.8.0 Gviz_1.10.1 rtracklayer_1.26.1
[4] GenomicRanges_1.18.1 GenomeInfoDb_1.2.2 IRanges_2.0.0
[7] S4Vectors_0.4.0 fastcluster_1.1.13 reshape2_1.4
[10] ggplot2_1.0.0 RSQLite_1.0.0 DBI_0.3.1
[13] BiocGenerics_0.12.0

loaded via a namespace (and not attached):
[1] acepack_1.3-3.3 AnnotationDbi_1.28.0 base64enc_0.1-2
[4] BatchJobs_1.4 BBmisc_1.7 Biobase_2.26.0
[7] BiocParallel_1.0.0 biomaRt_2.22.0 Biostrings_2.34.0
[10] biovizBase_1.14.0 bitops_1.0-6 brew_1.0-6
[13] BSgenome_1.34.0 checkmate_1.5.0 cluster_1.15.3
[16] codetools_0.2-9 colorspace_1.2-4 dichromat_2.0-0
[19] digest_0.6.4 fail_1.2 foreach_1.4.2
[22] foreign_0.8-61 Formula_1.1-2 GenomicAlignments_1.2.0
[25] GenomicFeatures_1.18.1 gtable_0.1.2 Hmisc_3.14-5
[28] iterators_1.0.7 lattice_0.20-29 latticeExtra_0.6-26
[31] MASS_7.3-35 matrixStats_0.10.3 munsell_0.4.2
[34] nnet_7.3-8 plyr_1.8.1 proto_0.3-10
[37] RColorBrewer_1.0-5 Rcpp_0.11.3 RCurl_1.95-4.3
[40] R.methodsS3_1.6.1 rpart_4.1-8 Rsamtools_1.18.1
[43] scales_0.2.4 sendmailR_1.2-1 splines_3.1.1
[46] stringr_0.6.2 survival_2.37-7 tools_3.1.1
[49] VariantAnnotation_1.12.2 XML_3.98-1.1 XVector_0.6.0
[52] zlibbioc_1.12.0

Please help me! I have spent all this weekends but didn't get anything.

Thank you guys in advance!