Question: Issue with 'Could not obtain CDF environment' after attempting to extract information out of an AffyBatch object
0
gravatar for maxime.vanhaeverbeke
14 months ago by
maxime.vanhaeverbeke0 wrote:

I have no issues with reading the .CEL file  :

 > test_affy  <- ReadAffy('GSM631755.CEL')       

But when trying work with  any one of the raw .CEL files in https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-25724/samples/

for example when I try

geneNames(test)

the following (error) messages appear : 

 

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


* installing *source* package 'hgu133acdf' ...

** R

** data

** preparing package for lazy loading

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 

  there is no package called 'digest'

ERROR: lazy loading failed for package 'hgu133acdf'

* removing 'C:/Users/maxim/OneDrive/Documents/R/win-library/3.3/hgu133acdf'


The downloaded source packages are in

‘C:\Users\maxim\AppData\Local\Temp\RtmpQjmeq5\downloaded_packages’

Error in getCdfInfo(object) : 

  Could not obtain CDF environment, problems encountered:

Specified environment does not contain HG-U133A

Library - package hgu133acdf not installed

Library - package hgu133acdf not installed

In addition: Warning messages:

1: running command '"C:/PROGRA~1/R/R-33~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\maxim\OneDrive\Documents\R\win-library\3.3" C:\Users\maxim\AppData\Local\Temp\RtmpQjmeq5/downloaded_packages/hgu133acdf_2.18.0.tar.gz' had status 1 

2: In install.packages(cdfname, lib = lib, repos = biocinstallRepos(),  :

  installation of package ‘hgu133acdf’ had non-zero exit status


Does anyone happen to know how to solve this problem? Solutions are much appreciated,

Kind regards,

Maxime

 

cdf affy .cel • 346 views
ADD COMMENTlink modified 14 months ago by James W. MacDonald50k • written 14 months ago by maxime.vanhaeverbeke0
Answer: Issue with 'Could not obtain CDF environment' after attempting to extract inform
2
gravatar for James W. MacDonald
14 months ago by
United States
James W. MacDonald50k wrote:

The error message should be instructive:

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 

  there is no package called 'digest'

So try 

biocLite(c("digest","hgu133acdf"))

 

ADD COMMENTlink written 14 months ago by James W. MacDonald50k

This indeed solves the problem , thanks for helping a new user out!

ADD REPLYlink written 14 months ago by maxime.vanhaeverbeke0
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