[BioC] missing example data from cghMCR package

[Martin Morgan]

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