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Issue 18: CellHTS2 node not woking / causes Rserve to shutdown
2 people starred this issue and may be notified of changes. Back to list
Status:  Fixed
Owner:  aborgabor
Closed:  May 2009


 
Reported by gbon...@gmail.com, Apr 28, 2009
What steps will reproduce the problem?
1. When launching the sample1 example after mapping all files from the 
svn/plate8 location, when launching the node cellHTS2, the Rserver starts 
working (loading libraries etc), but terminates, without completing.
2.
3.

What is the expected output? What do you see instead?
Not sure yet. It also appears that the screen log provided in the SVN is 
empty, although I am not sure whether it  optional, and what it is exactly 
for.

What version of the product are you using? On what operating system?
R2.9.0, followed installation procedure described in the wiki.
Surprisingly, I get a different output than expected with for the R 
library "cellHTS2":

> library("cellHTS2")
Loading required package: RColorBrewer
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: genefilter
Loading required package: splots
Loading required package: grid
Loading required package: vsn
Loading required package: hwriter
Scalable Robust Estimators with High Breakdown Point (version 0.5-01)


Please provide any additional information below.

Wen installing cellHTS2 in R I get the folwing message which seems to have 
some errors (inparticular with some incompatibilities between bioconductor 
and R2.9.0):
> source("http://bioconductor.org/biocLite.R")
> biocLite("cellHTS2")
Running biocinstall version 2.4.10 with R version 2.9.0 
Your version of R requires version 2.4 of Bioconductor.
Warning: unable to access index for repository 
http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.9
trying 
URL 'http://bioconductor.org/packages/2.4/bioc/bin/windows/contrib/2.9/cell
HTS2_2.8.0.zip'
Content type 'application/zip' length 3702776 bytes (3.5 Mb)
opened URL
downloaded 3.5 Mb

package 'cellHTS2' successfully unpacked and MD5 sums checked

The downloaded packages are in
        C:\Users\ghislain\AppData\Local\Temp\Rtmp4bKnjq\downloaded_packages
updating HTML package descriptions

Apr 29, 2009
Project Member #1 aborgabor
Expected problem. The latest version of cellHTS2 is not yet tried, but changed a lot.
Sorry, this is not yet supported. Expected: the release followed this week's release.
(Somewhen in May 2009.)

You might want to use R 2.8.x, it installs cellHTS2 version 2.6.x. Hope this helps as
a workaround. Sorry for the problems.
Status: Accepted
Labels: -Priority-Medium Priority-Critical Milestone-Release1.0
Apr 29, 2009
Project Member #2 aborgabor
(No comment was entered for this change.)
Summary: CellHTS2 node not woking / causes Rserve to shutdown
Labels: -Milestone-Release1.0 Milestone-Release0.3
May 14, 2009
Project Member #3 aborgabor
Hope the new version (2.8.0), and the previous one (2.6.0) is working well with the
actual version from SVN. Soon (within 2 weeks?) it will be released.
Status: Fixed
Owner: aborgabor
May 14, 2009
#4 gbon...@gmail.com
Great news. I look forward to using this!

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