[qgong]

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

I think I may have solved problem. And you can try my steps。
First, upgrade biocLite:
>source("http://www.bioconductor.org/biocLite.R")
>biocLite("BiocUpgrade")

Then, install "cummeRbund"
>biocLite("cummeRbund")

Last, install or reinstall "RSQLite"
>biocLite("RSQLite")

I hope it works for you.

[lgoff]

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

http://www.bioconductor.org/checkResults/3.0/bioc-LATEST/cummeRbund/

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

source('http://www.bioconductor.org/biocLite.R')
biocLite('cummeRbund')

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:

http://github.com/gofflab/cummeRbund

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!

Cheers,
Loyal

[homeuser1]

Hi, any update regarding the cummerbund error? Thanks

[DonDolowy]

Thanks a lot for the help, guys! Working here again.

[Gonza]

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, bind.data) :
error in statement: no such table: genes

[axa9070]

Thanks Loyal!

We appreciate your time and hard work!

^_^

[lgoff]

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:

https://github.com/gofflab/cummeRbund

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.

Cheers,
Loyal

[mahesh.sangrithi]

Hi,

I'm having the same problem described here. This started after I'd upgraded to MacOSX Yosemite. I've also updated R to v3.1.2, and I've removed and re-installed RSQLite as well as cummeRbund as suggested, and the error still persists when executing readCufflinks(...).

I've emailed Loyal Goff, who might be able to suggest a solution...

Best,
Mahesh

[spzhangmit]

If you don't want to remove and reinstall RSQLite, you can use axa9070's way. It works!

You CAN have your cake and eat it too!

The latest RSQLite has deprecated the sqliteQuickSQL function! However, has been essentially renamed to dbGetQuery! So by simply loading the cummeRbund library, then assiging that function you're good to go!

library(cummeRbund)

sqliteQuickSQL<-dbGetQuery

cuff<-readCufflinks(gtfFile="/blah/blah/blah.gtf", rebuild=T)

[spzhangmit]

lgoff, thanks a lot! We are expecting your good work to fix it.

Also, thanks a lot for all the guys who responded to this problem. Now I can work with cummeRbund!

Confirmed...and yes..the cummeRbund developers (me and ONLY me) are working on it. It's not just the sqliteQuickSQL method however, there were a number of major changes in RSQLite that have implications for how the cummeRbund backend database is built, but also how it's queried, which is at the heart of how cummeRbund works. So it may take a bit to get cummeRbund working with the new version. I will keep you guys posted.

-Loyal

[homeuser1]

Hi, I also faced the similar problem.

> library(cummeRbund)
Loading required package: RSQLite
Error: package ‘RSQLite’ was built before R 3.0.0: please re-install it
In addition: Warning message:
package ‘cummeRbund’ was built under R version 3.1.1

any tips to solve it? RSQlite 0.11.4 not working too - not compatible with R >=3.0

Thanks

[lgoff]

Great work around! Thanks for the tip.

-Loyal

[axa9070]

Solution

You CAN have your cake and eat it too!

The latest RSQLite has deprecated the sqliteQuickSQL function! However, has been essentially renamed to dbGetQuery! So by simply loading the cummeRbund library, then assiging that function you're good to go!

library(cummeRbund)

sqliteQuickSQL<-dbGetQuery

dbBeginTransaction<-dbBegin

cuff<-readCufflinks(gtfFile="/blah/blah/blah.gtf", rebuild=T)

[lgoff]

Ooo! Also a good time to point out that the cummeRbund code is now on github (http://www.github.com/gofflab/cummeRbund), should anyone be interested in taking a peek or patching it themselves. I'm happy to take pull requests.

Cheers,
Loyal

[lgoff]

Confirmed...and yes..the cummeRbund developers (me and ONLY me) are working on it. It's not just the sqliteQuickSQL method however, there were a number of major changes in RSQLite that have implications for how the cummeRbund backend database is built, but also how it's queried, which is at the heart of how cummeRbund works. So it may take a bit to get cummeRbund working with the new version. I will keep you guys posted.

-Loyal