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

[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!

[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]

Yes, is there anyone know how to fix it?

[mandar.bobade60]

Please set the Path using setwd("wherever/ur/cuffdiff/result/is") in R
And check once again.
I had got same even though I had mentioned path with:

cuff <- readCufflinks("cuffdiff/output/dir/path")

Since cummerRbund only takes currentpath as input, u need to set that path in R before starting working.

This had resolved my problem.

If this doesn't resolve for you. Then please pardon me.

[DonDolowy]

I have the same problem and the path is correct.

/Update: Thought it was related to Yosemite, as apparently there are some issues with Rstudio and Yosemite getting the path right. Tried to boot up on my old partition with Mavericks. Same problem, and it worked a couple of weeks ago, so it must be related to either the new cummeRbund update or other packages, that have been updated recently.

[austrinas]

Hello,
I had the same problem and trying close, install old/new version of R but didnt change anything. The problem I have updated the packages and something is wrong with new version os sqliteQuickSQL.
So I managed to get cummerbund, DIB and sqliteQuickSQL packages previously downloaded and added in the R packages library. That solved my problems and R works nicely now. Hope that helps
Good Luck

[sbcn]

Same problem here, just updated to the latest version cummeRbund (cummeRbund_2.8.0) and I get an error I didn't get some weeks ago when I last used cuffdiff+cummeRbund:

cuff<-readCufflinks()
Creating database /..../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 have a previous version (cummeRbund_2.6.1) loaded on another terminal, and it works fine reading the same data: did anyone manage to figure that out?

Cheers
S.

sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-redhat-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] BiocInstaller_1.16.0 cummeRbund_2.8.0 Gviz_1.10.1
[4] rtracklayer_1.26.1 GenomicRanges_1.18.1 GenomeInfoDb_1.2.2
[7] IRanges_2.0.0 S4Vectors_0.4.0 fastcluster_1.1.13
[10] reshape2_1.4 ggplot2_1.0.0 RSQLite_1.0.0
[13] 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
[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_1.15.2
[16] codetools_0.2-8 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_1.18.2 gtable_0.1.2 Hmisc_3.14-5
[28] iterators_1.0.7 lattice_0.20-29 latticeExtra_0.6-26
[31] MASS_7.3-33 matrixStats_0.10.3 munsell_0.4.2
[34] 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
[40] RCurl_1.95-4.3 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

[blancha]

Who don't you just install the R package RSQLite?
If it's already installed, uninstall it and reinstall it.

The function "sqliteQuickSQL" is found in RSQLite.

When I load cummeRbund, RSQLite is also loaded.
I don't see the package in any of your sessions.

[blancha]

I now see that in the first post the author specified that he had installed RSQLite. However, I don't see it as being loaded in the session info.

When I load cummeRbund, I get the following message: "Loading required package: RSQLite"

You should post all the messages posted during loading to see if there was an error loading RSQLite.

[jthomas5062]

Having the same problem here. When loading cummeRbund everything seems to be go smoothly and then I get the following message at the end of the load:

Warning message:
package 'RSQLite' was built under R version 3.1.2

Disregarding this, I change my path to where the Cuffdiff output files are and execute the following command:
cuff_data<-readCufflinks()

Error:
Creating database /Users/jamesdthomas/Desktop/Mbnl2RNASeq/Cuffdiff/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"


It seems like the problem is in RSQLite, although after running "sessionInfo()", I can see that RSQLite_1.0.0 is loaded. I've tried to run these same commands on another RNA-Seq experiment and am getting the same error.

Any thoughts?

[blancha]

Try uninstalling RSQLite, reinstalling it, restarting your R session with a new workspace, and reloading cummeRbund.

The warning message about RSQLite shouldn't appear when you reload cummeRbund.

remove.packages("RSQLite")
install.packages("RSQLite")

[jthomas5062]

Getting the following messages . . . sorry, super new to R!

> remove.packages(RSQLite)
Error in remove.packages : object 'RSQLite' not found
> install.packages(RSQLite)
Error in install.packages : object 'RSQLite' not found

[blancha]

My fault. I edited the post above quickly but you executed the code faster.
Just add the quotes.
Also, the session may need to restart if the package is already loaded.
Execute the second line of code once you have the confirmation the package is properly removed.

remove.packages("RSQLite")
install.packages("RSQLite")

[jthomas5062]

This worked:
> remove.packages('RSQLite')
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library’
(as ‘lib’ is unspecified)

> install.packages("RSQLite")
trying URL 'http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.1/RSQLite_1.0.0.tgz'
Content type 'application/x-gzip' length 1920084 bytes (1.8 Mb)
opened URL
==================================================
downloaded 1.8 Mb


But, still no dice on getting the package to work in cummeRbund :/

[blancha]

Well, I tried reinstalling RSQLite on my system just to check my instructions were correct.
I managed to mess up RSQLite.

I got the following error message when trying to load cummeRbund.
Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'

I was however able to get cummeRbund working properly again after updating from from R-3.1.0 to R-3.1.1, and updating all my packages.

So, while I cannot pinpoint the exact source of the problem, the solution appears to simply make sure that you have the latest version of R, and the latest packages. If necessary, reinstall the packages.

You should really post the error messages posted when loading cummeRbund to make the problem easier to diagnose.

Anyway, I'll get back to work and try to waste less time on seqanswers.com.