[BrianU]

Yeah the most recent package must no longer have that function. Hope that helped, and thank y'all for further clarifying the download process.

Also Brian, the Bioconductor 3.0 version is the current one, no? It at least appears so on the website. So I think your inability to update just means you have the latest version available, the R output just phrases it like an error.

You're right about the weird error output. I am up to date.

By the way, I just got a reply about the error from the guys working on CummeRbund. Apparently RSQLite just had a huge overhaul to v1.0 last Saturday the 25th. It explains why the SQL function is missing. They are on it.

[lgoff]

Thanks again BrianU...

[blancha]

So, just to confirm what has already been posted.

RSQLite was updated to version 1.0.0 on October 25th, 2014.
This version of the package no longer contains the function used by cummeRbund, "sqliteQuickSQL".

Downgrading to the previous version of RSQLite, 0.11.4 immediately fixes the problem.

So either the cummeRbund or the RSQLite maintainers should fix this problem, whichever one is at fault.

In the meantime, downgrading the package is a quick and easy fix.

[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

[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

[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]

Great work around! Thanks for the tip.

-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

[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

[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)

[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

[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

[axa9070]

Thanks Loyal!

We appreciate your time and hard work!

^_^

[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

[DonDolowy]

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