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I have some Affymetrix data that I would like to open using the read.affybatch() command in affy. I have downloaded the biocLite and affy packages with no issues, but as soon as I try and read my .CEL files using the read command it comes up with the following problem:

Library - package hgu133acdf not installed
Library - package hgu133acdf not installed
In addition: Warning messages:
1: In read.affybatch(filenames = "MonoHypo_U133A_04_12_03.CEL", "MonoC_U133A_04_12_03.CEL",  :
  Incompatible phenoData object. Created a new one.

2: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.2\library" C:\windows\TEMP\RtmpKKBTXV/downloaded_packages/hgu133acdf_2.18.0.tar.gz' had status 1 
3: In install.packages(cdfname, lib = lib, repos = biocinstallRepos(),  :
  installation of package ‘hgu133acdf’ had non-zero exit status
4: missing cdf environment! in show(AffyBatch) 
5: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.2\library" C:\windows\TEMP\RtmpKKBTXV/downloaded_packages/hgu133acdf_2.18.0.tar.gz' had status 1 
6: In install.packages(cdfname, lib = lib, repos = biocinstallRepos(),  :
  installation of package ‘hgu133acdf’ had non-zero exit status

So, the issue seems to be this hgu133acdf package, but using the command from BioConductor to install this package I get the following error:

biocLite("hgu133acdf")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘hgu133acdf’
installing the source package ‘hgu133acdf’

trying URL 'https://bioconductor.org/packages/3.4/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1732200 bytes (1.7 MB)
downloaded 1.7 MB

'\\filestore.soton.ac.uk\users\rl1e15\mydocuments\PhD\PhD Year 1 2016-2017\Analysis\In Silico\R\Hypoxia and Normoxia Monocytes'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported.  Defaulting to Windows directory.
ERROR: unable to create 'C:/Program Files/R/R-3.3.2/library/hgu133acdf'

The downloaded source packages are in
    ‘C:\Windows\Temp\RtmpKKBTXV\downloaded_packages’
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Program Files\R\R-3.3.2\library" C:\windows\TEMP\RtmpKKBTXV/downloaded_packages/hgu133acdf_2.18.0.tar.gz' had status 1 
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘hgu133acdf’ had non-zero exit status

I have tried installing hgu133acdf to my local drive using biocLite("hgu133acdf", lib="C:/Program Files/R/R-3.3.2/library") but the same non-zero exit status comes up. Sometimes it tells me I need to update nlme so I try that but the nlme_3.1-130 is not compatible with R-3-3-2 or when I update the package it still doesn't work.

user2100721
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RLiu
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1 Answers1

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So if anybody was curious, after hours of playing around with R I finally found the solution. As I have a work laptop, administrative rights are not automatically permitted, so I set the security of the directory all my packages download to to allow everything. I ran R as an administrator, installed all the necessary packages that kept flagging up when I tried the read.affybatch() command, and it worked!

RLiu
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