problem with cummeRbund using latest R version
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mmateos • 0
@mmateos-13598
Last seen 4.3 years ago

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)

Creating database multiple_test_T2/cuffData.db

Writing runInfo Table

Writing replicates Table

Writing varModel Table

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

cummeRbund • 2.6k views
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loyalgoff ▴ 20
@loyalgoff-6786
Last seen 4.3 years ago
United States

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

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Hi Loyal -- is your address in the DESCRIPTION file current? We tried to contact you through various means several weeks ago. Also, you can 'subscribe' to the 'cummerbund' tag and get notifications when questions are posted about packages of interest to you (click on your user, edit your profile and add 'my tags').

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loyalgoff ▴ 20
@loyalgoff-6786
Last seen 4.3 years ago
United States

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

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Hi Loya,

I was getting the same error message described by Mariana, so have tried to update my cummeRbund.  For an R newbie, can you please advise how to correctly update my cummeRbund library?  I have cloned the repository from github, then replaced the old files/folders in cummerBund with the new versions.  I'm now getting the following error:

> library(cummeRbund)
Error: package or namespace load failed for 'cummeRbund' in namespaceExport(ns, exports):

I'm running R version 3.4.1 (2017-06-30) -- "Single Candle"

Many thanks!

Paul

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Sorry - should also add platform info:

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

OSX 10.11.6

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@serenaspartano-14008
Last seen 4.2 years ago

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.

Good luck!

Serena