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Old 11-03-2014, 01:31 PM   #41
Location: Cambridge, MA

Join Date: Feb 2008
Posts: 82

Hi all,
I think i've patched cummeRbund for RSQLite 1.0.0 compatibility. It now builds and runs on my machine. I pushed it up to BioC, but it may take a few days to get through the nightly build system.

If you would like to try and build it yourself, you can find the patched version (and the current development version) here:

You will have to:
1) clone the repository
2) R CMD BUILD cummeRbund
3) R CMD INSTALL cummeRbund

Please make sure that you have all the required dependencies installed (including RSQLite 1.0.0). The BioC installer checks this for you, but if you build yourself, it will fail if you do not have all the dependencies installed.

Also, please let me know if you continue to have errors. I don't check seqanswers all that often anymore due to time constraints, but I'll try to keep up on this specific thread.

lgoff is offline   Reply With Quote
Old 11-03-2014, 01:35 PM   #42
Location: Rochester, NY

Join Date: Oct 2014
Posts: 11

Thanks Loyal!

We appreciate your time and hard work!

axa9070 is offline   Reply With Quote
Old 11-04-2014, 05:18 AM   #43
Location: Ithaca, NY

Join Date: Mar 2013
Posts: 78

Hi All,

is not working for me either. is other way to fix this other than uninstalling and reinstalling?

> cuff_data <-readCufflinks()
Creating database /Users/gonzalovillarino/Desktop/05Cuffdiff_novelgenes/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"
> cuff_data <-readCufflinks()
> cuff_data
Error in sqliteSendQuery(con, statement, :
error in statement: no such table: genes
Gonza is offline   Reply With Quote
Old 11-04-2014, 05:34 AM   #44
Location: Freiburg

Join Date: Oct 2012
Posts: 56

Thanks a lot for the help, guys! Working here again.
DonDolowy is offline   Reply With Quote
Old 11-04-2014, 03:06 PM   #45
Junior Member
Location: alabama

Join Date: Oct 2014
Posts: 3

Hi, any update regarding the cummerbund error? Thanks
homeuser1 is offline   Reply With Quote
Old 11-05-2014, 09:18 AM   #46
Location: Cambridge, MA

Join Date: Feb 2008
Posts: 82

Hi All,
Quick update. The patched version of cummeRbund (release 2.8.2) is now up at bioconductor and passes all builds and checks:

So you should be able to update to this version using the bioconductor installer:

I have verified that most of the problems discussed in this thread have been handled, at least as far as I can test. There may be other functionality that has been broken that I have not come across yet. If you are still having problems, and you are certain that it pertains to the RSQLite compatibility, please let me know directly by email and I will try to work with you to get it resolved quickly.

Future development of cummeRbund will be done on Github:

So feel free to open an issue there or submit any pull requests you may have.

Thanks again for bearing with me, and apologies for not catching this change sooner!

lgoff is offline   Reply With Quote
Old 01-22-2015, 04:13 PM   #47
Junior Member
Location: China

Join Date: Apr 2012
Posts: 1

Thanks! I met the same problem and this solution works!

Originally Posted by RomaChicken View Post
I think I may have solved problem. And you can try my steps。
First, upgrade biocLite:

Then, install "cummeRbund"

Last, install or reinstall "RSQLite"

I hope it works for you.
qgong is offline   Reply With Quote

cummerbund, rna-seq

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