[Bioc-devel] error during multiple platform build/check

[Wong, Chao-Jen]

Hi, Dongjun

The problem might be on our end.  When I commit experiment data packages to the repository, I separate the infrastructure files and data files and put them in different locations (https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs and https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/data_store, respectively). The infrastructure package should not contain the data and inst/extdata subdirectories, however, I forgot to delete them.  I just delete these subdirectories from https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/mosaiscExample and hopefully the package will build correctly tomorrow. I will keep my eyes on it.

Regards,

Chao-Jen

----- Original Message -----
From: "Dongjun Chung" <chungdon at stat.wisc.edu>
To: bioc-devel at r-project.org
Sent: Wednesday, March 16, 2011 2:48:40 PM
Subject: [Bioc-devel] error during multiple platform build/check

Dear developers,

I faced some errors during multiple platform build/check
("http://bioconductor.org/checkResults/2.8/bioc-LATEST/")
that I have never had before.

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

* creating vignettes ... ERROR
Info: reading and preprocessing bin-level data...
Warning in file(file, "rt") :
   file("") only supports open = "w+" and open = "w+b": using the former

Error: processing vignette 'mosaics-example.Rnw' failed with diagnostics:
  chunk 4 (label=ts-readbin)
Error in read.table(chipFileName, header = FALSE, sep = "\t") :
   no lines available in input
Execution halted

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

Briefly, I developed a software package & its experimental data package.
Vignette in the software package read the data (text files in 
inst/extdata/)
from experimental data package and fit models and so on.
This error message seems to say that vignette is not able to read the files
from the experimental data package.

Did anyone have similar experiences like this?
And can somebody help me to solve this problem?

Best,
Dongjun

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

-- 
Chao-Jen Wong 
Program in Computational Biology 
Division of Public Health Sciences 
Fred Hutchinson Cancer Research Center 
1100 Fairview Avenue N., M1-B514 
PO Box 19024 
Seattle, WA 98109 
206.667.4485 
cwon2 at fhcrc.org