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Old 10-30-2014, 03:51 AM   #21
RomaChicken
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In fact, I am also stop at the problem below:
> readCufflinks()
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: CuffData.db Model\n-- Project: cummeRbund\n-- Changed: 2011-08-02 14:03\n-- Created: 2011-05-02 12:52\nPRAGMA foreign_keys = OFF", :
could not find function "sqliteQuickSQL"


I don't know how I can resolve the "sqliteQuickSQL" function problem.


Quote:
Originally Posted by BrianU View Post
I tried your solution of uninstalling both and reinstalling, but it didn't work for me. The only thing that I noticed was odd was trying to upgrade bioconductor...

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Old 10-30-2014, 03:59 AM   #22
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In fact, I haven't met your problem before. Maybe you can check with the weblink here:http://www.bioconductor.org/install
Quote:
Originally Posted by BrianU View Post
I tried your solution of uninstalling both and reinstalling, but it didn't work for me. The only thing that I noticed was odd was trying to upgrade bioconductor...

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Old 10-30-2014, 08:40 AM   #23
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Downloading a previous version of the RSQLite package worked for me, as it actually contains the necessary function. I chose the 0.11.4 version from this archive:
http://cran.r-project.org/src/contrib/Archive/RSQLite/

Last edited by gopher; 10-30-2014 at 08:42 AM. Reason: bad link
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Old 10-30-2014, 09:29 AM   #24
axa9070
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So basically what you're saying is that cummeRbund does not work with the updated RSQLite package.

Probably because (whether by mistake or not) RSQLite 1.0.0 does not have the sqliteQuickSQL function anymore.

So this solution may work but also only for Linux. Does anyone know where to find archived R packages of Windows binaries?
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Old 10-30-2014, 09:39 AM   #25
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Quote:
Originally Posted by axa9070 View Post
So basically what you're saying is that cummeRbund does not work with the updated RSQLite package.

Probably because (whether by mistake or not) RSQLite 1.0.0 does not have the sqliteQuickSQL function anymore.

So this solution may work but also only for Linux. Does anyone know where to find archived R packages of Windows binaries?
Nevermind. This way of finding it was totally janky! (If you look at the packages off of these links you'll know what I mean http://cran.fhcrc.org/bin/windows/contrib/)
But the old windows binaries of RSQLite can be found here.

I do hope cummeRbund is updated soon -___- I'm growing tired of all this R garbage in Bioinformatics as it is.

Last edited by axa9070; 10-30-2014 at 09:53 AM. Reason: Doesn't actually work with latest R =-/
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Old 10-30-2014, 09:53 AM   #26
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Quote:
Originally Posted by gopher View Post
Downloading a previous version of the RSQLite package worked for me, as it actually contains the necessary function. I chose the 0.11.4 version from this archive:
http://cran.r-project.org/src/contrib/Archive/RSQLite/
Thanks gopher, this worked for me. Just incase anyone was confused..

In Linux, I cd into my R directory
> cd /home/<me>/R/.../3.1/
removed the RSQLite folder to delete the package.
> rm -rf RSQLite/ (there is probably a more elegant way to delete libraries, but it worked.)

Downladed the older version of RSQLite from the link gopher posted. Then installed the package through RStudio's Package manager. Reload CummeRbund. Done.
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Old 10-30-2014, 10:36 AM   #27
gopher
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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.

Last edited by gopher; 10-30-2014 at 10:40 AM.
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Old 10-30-2014, 10:51 AM   #28
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Yes, you are right.
I apologize for my previously misleading posts.

I keep forgetting that I need to delete the Cuffdiff database to generate a new one.
Otherwise, the function readCufflinks() works, but that is simply because it is not generating a new database. As soon as I deleted the old database, I got the same error message as everyone else.
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Old 10-30-2014, 10:52 AM   #29
lgoff
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Default Fix is in the works...

Hi Guys,
Apologies for not catching this sooner, but it's been brought to my attention that there was a major overhaul of RSQLite with the release of version 1.0.0. This broke a good deal of functionality in cummeRbund. I'm working on brining the code up to spec so that it's compatible with RSQLite 1.0.0 but I'm not sure when this will be available. In the meantime, if you need to use cummeRbund, you should be able to downgrate to an earlier version of RSQLite (<1.0.0) and preserve compatibility. I'll try to remember to post here, and on the cummeRbund website, when the fix is pushed to BioC. Thanks to a few of you guys for contacting me directly to let me know about this issue.

Cheers,
Loyal
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Old 10-30-2014, 10:52 AM   #30
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Quote:
Originally Posted by gopher View Post
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.
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Old 10-30-2014, 10:54 AM   #31
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Thanks again BrianU...
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Old 10-30-2014, 11:00 AM   #32
blancha
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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.
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Old 10-30-2014, 11:03 AM   #33
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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
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Old 10-30-2014, 11:06 AM   #34
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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
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Old 10-30-2014, 11:16 AM   #35
axa9070
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Default 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)


Last edited by axa9070; 11-01-2014 at 08:21 PM.
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Old 10-30-2014, 11:32 AM   #36
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Great work around! Thanks for the tip.

-Loyal
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Old 10-30-2014, 04:47 PM   #37
homeuser1
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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
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Old 10-30-2014, 05:03 PM   #38
spzhangmit
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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!

Quote:
Originally Posted by lgoff View Post
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
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Old 10-30-2014, 06:42 PM   #39
spzhangmit
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If you don't want to remove and reinstall RSQLite, you can use axa9070's way. It works!

Quote:
Originally Posted by axa9070 View Post
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)

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Old 11-01-2014, 08:18 AM   #40
mahesh.sangrithi
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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
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