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

[Dongjun Chung]

Hi Chao-Jen,

Thank you very much for taking care of this issue!

Best,
Dongjun

On 3/16/2011 5:35 PM, Wong, Chao-Jen wrote:
> 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
>
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