I installed the latest version of R (R version 3.4.1 (2017-06-30) -- "Single Candle"), Bioconductor, and cummeRbund

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Mac OS X 10.11.6

I've seen posts of similar problems in the last few days.  Is it possible that there cummeRbund is incompatible with updated R or Bioconductor?  Could it be that my sqlite3 version is too old? SQLite version 3.8.10.2 2015-05-20 18:17:19  If so, I can't seem to find a way to replace with with a newer one.  If I compile the newest one, it still calls the old one when I type sqlite3 at the Terminal window.

We have ruled out the input folder (cuffdiff output); it works on prior version.  Below I post the warning messages I receive when running cuff_data.

I would appreciate any prompt help with this.

Thanks,

Mariana

---------------------------------

> library(cummeRbund)

> cuff_data = readCufflinks('multiple_test_T2')

Creating database multiple_test_T2/cuffData.db

Reading Run Info File multiple_test_T2/run.info

Writing runInfo Table

Reading Read Group Info  multiple_test_T2/read_groups.info

Writing replicates Table

Reading Var Model Info  multiple_test_T2/var_model.info

Writing varModel Table

Reading multiple_test_T2/genes.fpkm_tracking

Checking samples table...

Populating samples table...

Error: Column name mismatch.

In addition: There were 50 or more warnings (use warnings() to see the first 50)

> warnings()

Warning messages:

1: In rsqlite_fetch(res@ptr, n = n) :

  Don't need to call dbFetch() for statements, only for queries

2: In rsqlite_fetch(res@ptr, n = n) :

  Don't need to call dbFetch() for statements, only for queries

3: In rsqlite_fetch(res@ptr, n = n) :

  Don't need to call dbFetch() for statements, only for queries

Hi Mariana,

Apparently RSQLite has changed a bit recently, and I'm only now becoming aware of this.  I will try to put together a fix in the next few days and push it up to devel.  Thanks.

-Loyal

Hi Mariana,

I just pushed a (hopefully) corrected version up to BioC devel.  If you would like to try and install it before it gets auto-built, you can find it here:

https://github.com/Bioconductor-mirror/cummeRbund/tree/master

Please let me know if you have any other issues getting cummeRbund up and running.

Cheers,

Loya

Hi Paul,

I'm a newbie too but I've just discovered that is not sufficient to replace files after cloning a repo.

You have to build and install it.

You can build the repo using devtools, i've done that in this way:

install.packages("devtools")
library(devtools)
build("~/put/the/package/path/here")

 a tar.gz will be developed and you can install it in R(i've solved with R studio.

CummeRbund perfectly works with this repo, without column mismatches. Now I'm fighting with some troubles on annotate XLOC but I think it depends on GTF reference....I'm trying to repeat cuffmerge with an IGenome GTF.

Hoping this could help you a bit .....

Good luck!

Serena