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Question: problem with cummeRbund using latest R version
0
gravatar for mmateos
22 days ago by
mmateos0
mmateos0 wrote:

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

ADD COMMENTlink modified 7 days ago by loyalgoff20 • written 22 days ago by mmateos0
1
gravatar for loyalgoff
7 days ago by
loyalgoff20
United States
loyalgoff20 wrote:

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

ADD COMMENTlink written 7 days ago by loyalgoff20

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').

ADD REPLYlink modified 6 days ago • written 6 days ago by Martin Morgan ♦♦ 20k
1
gravatar for loyalgoff
7 days ago by
loyalgoff20
United States
loyalgoff20 wrote:

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

 

ADD COMMENTlink written 7 days ago by loyalgoff20

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):
 undefined exports: readCufflinks, JSdist, JSdistVec, JSdistFromP, shannon.entropy, makeprobs, makeprobsvec, csClusterPlot

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

Many thanks!

Paul

 

 

 

 

ADD REPLYlink written 2 days ago by wormdoktor0

Sorry - should also add platform info:

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

OSX 10.11.6

ADD REPLYlink written 2 days ago by wormdoktor0
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