[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]

Thanks again BrianU...

[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]

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

[blancha]

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.

[gopher]

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.

[BrianU]

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.

[axa9070]

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.

[axa9070]

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?

[gopher]

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/

[RomaChicken]

In fact, I haven't met your problem before. Maybe you can check with the weblink here:http://www.bioconductor.org/install

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...

[RomaChicken]

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.

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...

[BrianU]

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.

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...

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> source("http://www.bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help
> biocLite("BiocUpgrade")
Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0
> biocLite("cummeRbund")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.1.
Installing package(s) 'cummeRbund'
also installing the dependency ‘RSQLite’

[sbcn]

I have finally completely uninstalled and re-installed RSQLite as suggested, and it solved the problem!
Although it was loaded in the session previously and it is the same version of the package, now reading in data with "readCufflinks" works...

When I first tried to re-install it, I faced that error message:
"
ERROR: failed to lock directory ‘/nfs/users/test/R/x86_64-redhat-linux-gnu-library/3.1’ for modifying
Try removing ‘/nfs/users/test/R/x86_64-redhat-linux-gnu-library/3.1/00LOCK-RSQLite’

The downloaded source packages are in
‘/tmp/Rtmp7rm8UF/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘RSQLite’ had non-zero exit status
"

which is simply solved by removing the "locked" folder, in case you face the same issue:
rm -r /nfs/users/test/R/x86_64-redhat-linux-gnu-library/3.1/00LOCK-RSQLite/

I opened a fresh R session and simply re-installed RSQLite using biocLite:
source("http://www.bioconductor.org/biocLite.R")
biocLite("RSQLite")

Still don't really understand the issue, but well, it works :-)

[RomaChicken]

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.