Hi,

I am trying to create a cdf package to analyise a set of Affy HTA2.0
arrays, which don't have one yet. I have followed the documentation, but I
get this message:

Creating package in C:/Matthew/Sen vs. non-Sen/HTA
data/HTA-2_0.r1.Psrs_mps Error in copySubstitute(dir(originDir,
full.names = TRUE), pkgdir, symbolValues,  :
  'symbolValues' must only contain characters.

I'm not sure where to go next. I'm not sure how to fix this as this
function is called by biobase, which is called by make.cdf.package
function. All I need is this package to move forward in the analysis.

Here are the details of my session. R3.0.2 in RStudio



##################

library(limma)library(gcrma)


Loading required package: affy Loading required package: BiocGenerics Loading
required package: parallel Attaching package: 'BiocGenerics' The following
objects are masked from 'package:parallel': clusterApply, clusterApplyLB,
clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply,
parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following
object is masked from 'package:limma': plotMA The following object is
masked from 'package:stats': xtabs The following objects are masked from
'package:base': anyDuplicated, append, as.data.frame, as.vector, cbind,
colnames, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unlist Loading required
package: Biobase Welcome to Bioconductor Vignettes contain introductory
material; view with 'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'. >
setwd("C:/Matthew/Sen
vs. non-Sen/HTA data") > targets <- readTargets("targets.txt") > View(targets)
> ab <- ReadAffy(filenames=targets$FileName) > eset <- gcrma(ab) Error in
getCdfInfo(object) : Could not obtain CDF environment, problems
encountered: Specified environment does not contain HTA-2_0 Library -
package hta20cdf not installed Bioconductor - hta20cdf not available



##Trying to create cdf package
## Contacted Affymetrix and downloaded their CDF file for these arrays

source("http://bioconductor.org/biocLite.R")Bioconductor version 2.13
(BiocInstaller 1.12.0), ?biocLite for
helpbiocLite("makecdfenv")BioC_mirror: http://bioconductor.orgUsing
Bioconductor version 2.13 (BiocInstaller 1.12.0), R version
3.0.2.Installing package(s) 'makecdfenv'trying URL
'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/makecdfenv_1.38.0.zip'Content
type 'application/zip' length 3373763 bytes (3.2 Mb)opened
URLdownloaded 3.2 Mb
package 'makecdfenv' successfully unpacked and MD5 sums checked



make.cdf.package("HTA-2_0.r1.Psrs_mps.cdf",+
packagename = "HTA-2_0.r1.Psrs_mps",+                  cdf.path =
getwd(),+                  package.path = getwd(),+
compress = FALSE,+                  author = "The Bioconductor
Project",+                  maintainer = "Biocore Data Team
<biocannotation@lists.fhcrc.org>",+                  version =
packageDescription("makecdfenv", fields ="1.0"),+
species = "Homo_sapiens",+                  unlink = TRUE,+
      verbose = TRUE)Reading CDF file.
Creating CDF environment
Wait for about 681
dots..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
Creating package in C:/Matthew/Sen vs. non-Sen/HTA
data/HTA-2_0.r1.Psrs_mps Error in copySubstitute(dir(originDir,
full.names = TRUE), pkgdir, symbolValues,  :
  'symbolValues' must only contain characters.


Thanks,
Matthew

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