[BioC] regarding GCRMA

[James W. MacDonald]

Hi Sneha,

sneha patil wrote:
> hiii
> 
> please check out this following error...and let me know where am going
> wrong....
> 
> 
> 
>> outdir = "C:/Users/neurooncolab new pc/Documents/R"
>> me <- "Wolfgang Huber <w.huber at dkfz.de>"
>> species <- "Homo_sapiens"
>> species <- "Homo_sapiens"
>> makeProbePackage("HG-U95Av2", datafile = gzfile(filename, open = "r"),
> + outdir = outdir, maintainer = me, species = species, version = "0.0.1",
> + force = TRUE)
> Importing the data.
> Creating package in C:/Users/neurooncolab new pc/Documents/R/hgu95av2probe
> Writing the data.
> Checking the package.
> Error in makeProbePackage("HG-U95Av2", datafile = gzfile(filename, open =
> "r"),  :
>   Expected but did not find the log-file hgu95av2probe.Rcheck/00check.log
> after R CMD check
> In addition: Warning message:
> closing unused connection 3 (C:/Users/neurooncolab new
> pc/Documents/R/win-library/2.10/AnnotationDbi/extdata/HG-U95Av2_probe_tab.gz)

I would add check = FALSE and build = FALSE to your makeProbePackage() 
call. Then just do R CMD build and R CMD check separately.

This makes the assumption that you are set up to build/install packages. 
If not, see here:

http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install-packages-into-libraries-in-this-version_003f


Best,

Jim


> 
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> i386-pc-mingw32
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252
> LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] hgu95av2cdf_2.5.0   affy_1.24.2         matchprobes_1.18.0
> Biostrings_2.14.10
> [5] IRanges_1.4.10      AnnotationDbi_1.8.1 Biobase_2.6.1
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0        DBI_0.2-5            preprocessCore_1.8.0
> RSQLite_0.8-1
> [5] tools_2.10.1
> 
> 
>> traceback()
> 2: stop(paste("Expected but did not find the log-file", logFile,
>        "after R CMD check"))
> 1: makeProbePackage("HG-U95Av2", datafile = gzfile(filename, open = "r"),
>        outdir = outdir, maintainer = me, species = species, version =
> "0.0.1",
>        force = TRUE)
> 
> 	[[alternative HTML version deleted]]
> 
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