[rxjing]

i've got the same problem, just can not readcufflinks() correctly, and i wonder whether u solve the issue or not?

[[email protected]]

Sorry，I haven't already solved the problems in cummeRbund packages. If there is any other way can address, please reply for me.
Thanks a lot.

[Oskar]

Same issue: can't create the database using readCufflinks

> cuff_data <- readCufflinks("diff_out_R", rebuild = TRUE)
Creating database diff_out_R/cuffData.db
Reading Run Info File diff_out_R/run.info
Writing runInfo Table
Reading Read Group Info  diff_out_R/read_groups.info
Writing replicates Table
Reading Var Model Info  diff_out_R/var_model.info
Writing varModel Table
Reading diff_out_R/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)

I think this is something to do with the updated version, since it worked when I used the same files with a previous version, but with this version they don't work anymore.

[jkofsky]

Does anyone have a good solution for these errors? Mine looks like this:

Creating database /cuffData.db
Error in rsqlite_connect(dbname, loadable.extensions, flags, vfs) :
Could not connect to database:
unable to open database file

or

50+ of these:

1: In rsqlite_fetch(res@ptr, n = n) :
Don't need to call dbFetch() for statements, only for queries

depending on how I submit it

From what I've read people have solved these issues by altering with the input (no symbols in the table) or by correcting the working directory. I have tried these and everything else I can think of. I have tried a cuffdiff output from a previous version and experiment and it runs in cummerbund fine...

I'm stuck. does anyone have a suggestion?

[Oskar]

Hi jkofsky -

We are just having the same discussion in biocinductor - and we came across with some alternatives since seems to be a bug in the new version of bioconductor/cummeRbund. Here you are the link.

https://support.bioconductor.org/p/97561/#97888

Hope it helps.

[jkofsky]

Hi jkofsky -

We are just having the same discussion in biocinductor - and we came across with some alternatives since seems to be a bug in the new version of bioconductor/cummeRbund. Here you are the link.

https://support.bioconductor.org/p/97561/#97888

Hope it helps.

Thanks, I will follow the thread.

I'm a little hesitant to assume its a bug considering data from cuffdiff (that was produced a year ago) is working fine ....