Same issue
I am glad I'm not the only one pulling my hair out over this issue. I've tried updating to the latest version of R and CummeRbund in both Windows 7 and Ubuntu 12.04. Reinstalled RSQLite a couple times along with it's dependencies. Am I missing something?
I get no errors loading CummeRbund, only when I try to create an SQLite database using readCufflinks().
I am glad I'm not the only one pulling my hair out over this issue. I've tried updating to the latest version of R and CummeRbund in both Windows 7 and Ubuntu 12.04. Reinstalled RSQLite a couple times along with it's dependencies. Am I missing something?
> library(cummeRbund)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘packagearallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq,
Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unlist, unsplit
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster
Attaching package: ‘fastcluster’
The following object is masked from ‘package:stats’:
hclust
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Attaching package: ‘cummeRbund’
The following object is masked from ‘package:GenomicRanges’:
promoters
The following object is masked from ‘package:IRanges’:
promoters
The following object is masked from ‘package:BiocGenerics’:
conditions
> wd <- "/home/brian/diff_out/"
> setwd(wd)
> gtfFile <- "mm10_genes.gtf"
> cuff <- readCufflinks(dir=getwd(), gtfFile=gtfFile, genome="mm10", rebuild=TRUE)
Creating database /home/brian/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"
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘packagearallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq,
Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unlist, unsplit
Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster
Attaching package: ‘fastcluster’
The following object is masked from ‘package:stats’:
hclust
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Gviz
Loading required package: grid
Attaching package: ‘cummeRbund’
The following object is masked from ‘package:GenomicRanges’:
promoters
The following object is masked from ‘package:IRanges’:
promoters
The following object is masked from ‘package:BiocGenerics’:
conditions
> wd <- "/home/brian/diff_out/"
> setwd(wd)
> gtfFile <- "mm10_genes.gtf"
> cuff <- readCufflinks(dir=getwd(), gtfFile=gtfFile, genome="mm10", rebuild=TRUE)
Creating database /home/brian/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 get no errors loading CummeRbund, only when I try to create an SQLite database using readCufflinks().
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
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_1.28.1 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_1.18.2 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] RColorBrewer_1.0-5 Rcpp_0.11.3 RCurl_1.95-4.3 R.methodsS3_1.6.1
[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
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
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_1.28.1 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_1.18.2 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] RColorBrewer_1.0-5 Rcpp_0.11.3 RCurl_1.95-4.3 R.methodsS3_1.6.1
[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
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