[BioC] missing example data from cghMCR package

[Burak Kutlu]

Hi Martin
Strange, I think the issue is related to my installation.
Because when I made a fresh installation on a separate machine, I
could see the files with no problem.
Thanks for looking into this
-burak

On Wed, Feb 24, 2010 at 12:45 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> Hi Burak --
>
> On 02/21/2010 09:43 PM, Burak Kutlu wrote:
>> Hi
>> I am trying to replicate the example in the vignette of cghMCR package.
>> I am afraid the data is not bundled in the package, I verified that
>> they do not exist in the ~/lib/R/cghMCR/data directory.
>> -burak
>>
>>> arrayFiles  <- list.files(system.file("sampleData", package = "cghMCR"),
>> +      full.names = TRUE, pattern = "TCGA")
>> Warning message:
>> In list.files(system.file("sampleData", package = "cghMCR"),
>> full.names = TRUE,  :
>>   list.files: '' is not a readable directory
>>> arrayFiles
>> character(0)
>>>
>>>
>>> system.file("sampleData", package = "cghMCR")
>> [1] ""
>
> What does
>
>  library(cghMCR)
>  system.file(package="cghMCR")
>
> say? The files should _not_ be in a directory called 'data', but in a
> directory called 'sampleData'. Here's what I see
>
>> list.files(system.file(package="cghMCR"))
> [1] "data"        "DESCRIPTION" "doc"         "help"        "html"
> [6] "INDEX"       "Meta"        "NAMESPACE"   "R"           "sampleData"
>
>> list.files(system.file("sampleData", package="cghMCR"))
> [1] "TCGA-06-0881-01A-02D-0387-02-short.txt"
> [2] "TCGA-12-0818-01A-01D-0387-02-short.txt"
> [3] "TCGA-12-0827-01A-01D-0387-02-short.txt"
>
> The output of .libPaths() might also be helpful; you did install cghMCR
> with biocLite(), right?
>
> Martin
>
>> sessionInfo()
> R version 2.10.1 Patched (2010-02-23 r51168)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] cghMCR_1.4.0      limma_3.2.1       CNTools_1.2.0     genefilter_1.28.2
> [5] DNAcopy_1.20.0
>
> loaded via a namespace (and not attached):
> [1] annotate_1.24.0     AnnotationDbi_1.8.1 Biobase_2.6.1
> [4] DBI_0.2-4           RSQLite_0.7-3       splines_2.10.1
> [7] survival_2.35-8     tools_2.10.1        xtable_1.5-6
>
>
>
>>>
>>> sessionInfo()
>> R version 2.10.1 (2009-12-14)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8      LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8      LC_NAME=C
>> [9] LC_ADDRESS=C              LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] grid      stats    graphics  grDevices datasets  utils    methods
>> [8] base
>>
>> other attached packages:
>> [1] cghMCR_1.14.0      arrayQuality_1.24.0 RColorBrewer_1.0-2
>> [4] gridBase_0.4-3      hexbin_1.20.0      lattice_0.17-26
>> [7] convert_1.22.0      marray_1.24.0      DNAcopy_1.18.0
>> [10] limma_3.2.1        org.Hs.eg.db_2.3.6  GSEABase_1.8.0
>> [13] annotate_1.24.0    RMySQL_0.7-4        Biostrings_2.14.8
>> [16] IRanges_1.4.9      RUnit_0.4.25        GOstats_2.12.0
>> [19] graph_1.24.2        Category_2.12.0    GO.db_2.3.5
>> [22] org.Mm.eg.db_2.3.6  RSQLite_0.8-1      DBI_0.2-5
>> [25] AnnotationDbi_1.8.1 Biobase_2.6.1
>>
>> loaded via a namespace (and not attached):
>> [1] genefilter_1.28.2 RBGL_1.22.0      splines_2.10.1    survival_2.35-7
>> [5] tools_2.10.1      XML_2.6-0        xtable_1.5-6
>>>
>>
>>
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>



-- 
Burak Kutlu, PhD.
Research Scientist
Hood Lab
Institute for Systems Biology