hgu133plus2cdf cant download
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@marionryan-9732
Last seen 4.1 years ago

 

Trying to RMA normalise CEL files using the  commands below (Bold), but it having issues with package ‘hgu133plus2cdf’. does anyone have any idea how to solve this problem, there is either a problem with the directories or the package wont work on R version 3.4.

Any help would be appreciated

Regards

Marion

> Data <-ReadAffy()
> eset <-rma(Data)
installing the source package ‘hgu133plus2cdf’

trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/hgu133plus2cdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 4353300 bytes (4.2 MB)
downloaded 4.2 MB

* installing *source* package 'hgu133plus2cdf' ...
** 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 'Rcpp'
ERROR: lazy loading failed for package 'hgu133plus2cdf'
* removing 'C:/Users/Marion Ryan/Documents/R/win-library/3.4/hgu133plus2cdf'

The downloaded source packages are in
‘C:\Users\Marion Ryan\AppData\Local\Temp\RtmpUTu0M3\downloaded_packages’
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG-U133_Plus_2
Library - package hgu133plus2cdf not installed
Library - package hgu133plus2cdf not installed
In addition: Warning messages:
1: running command '"C:/PROGRA~1/R/R-34~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\Marion Ryan\Documents\R\win-library\3.4" C:\Users\MARION~1\AppData\Local\Temp\RtmpUTu0M3/downloaded_packages/hgu133plus2cdf_2.18.0.tar.gz' had status 1 
2: In install.packages(cdfname, lib = lib, repos = biocinstallRepos(),  :
  installation of package ‘hgu133plus2cdf’ had non-zero exit status
normalization hgu133plus2 • 1.2k views
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@martin-morgan-1513
Last seen 3 months ago
United States

This warning

Warning: unable to access index for repository http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.4:

says that R is trying to access the repository for Bioconductor 3.0, R version 3.4. But Bioconductor version 3.0 was released on R version 3.1 (see the release announcements for mapping between R and Bioconductor versions; parsing the URL above is not meant to be an end-user skill!). It's also different from in your original message, where you were trying to access the Bioconductor 3.5 repository (which is valid for R 3.4), so you've done something (e.g., changed the .libPaths() seen by R) to point to an old installation of R packages, and in particular an old version of the BiocInstaller package.

I'm not sure how best to suggest proceeding. One option is to remove all installations of R and of R packages (e.g., under C:\Users\Marion\.RLibrary) and to start again using

source("https://bioconductor.org/biocLite.R")
biocLite(c("affy", "hgu133plus2cdf"))
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@martin-morgan-1513
Last seen 3 months ago
United States

Work on the first error

Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
 there is no package called 'Rcpp'

Confirming that there is no Rcpp installed on your system

library(Rcpp)               ## fails?

and then installing it before trying to install the annotation package

biocLite("Rcpp")            ## succeeds?
biocLite("hgu133plus2cdf")  ## succeeds?
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@marionryan-9732
Last seen 4.1 years ago

Thank you for your help Martin, unfortunately I am now getting a different set of errors (see below), I have found that as I correct some errors a different set keep emerging. I'll keep going ...

 

 

 

 

> Data <-ReadAffy()
> eset <-rma(Data)
also installing the dependencies ‘IRanges’, ‘GenomeInfoDb’, ‘S4Vectors’, ‘AnnotationDbi’

Warning: unable to access index for repository http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.4:
  cannot open URL 'http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/annotation/bin/windows/contrib/3.4:
  cannot open URL 'http://bioconductor.org/packages/3.0/data/annotation/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/experiment/bin/windows/contrib/3.4:
  cannot open URL 'http://bioconductor.org/packages/3.0/data/experiment/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/extra/bin/windows/contrib/3.4:
  cannot open URL 'http://bioconductor.org/packages/3.0/extra/bin/windows/contrib/3.4/PACKAGES'
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘IRanges’ ‘S4Vectors’
  These will not be installed
installing the source packages ‘GenomeInfoDb’, ‘AnnotationDbi’, ‘hgu133plus2cdf’

trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/GenomeInfoDb_1.2.5.tar.gz'
Content type 'application/x-gzip' length 265460 bytes (259 KB)
downloaded 259 KB

trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/AnnotationDbi_1.28.2.tar.gz'
Content type 'application/x-gzip' length 4254362 bytes (4.1 MB)
downloaded 4.1 MB

trying URL 'http://bioconductor.org/packages/3.0/data/annotation/src/contrib/hgu133plus2cdf_2.15.0.tar.gz'
Content type 'application/x-gzip' length 4353291 bytes (4.2 MB)
downloaded 4.2 MB

ERROR: dependencies 'S4Vectors', 'IRanges' are not available for package 'GenomeInfoDb'
* removing 'C:/Users/Marion/.RLibrary/GenomeInfoDb'
ERROR: dependencies 'GenomeInfoDb', 'S4Vectors' are not available for package 'AnnotationDbi'
* removing 'C:/Users/Marion/.RLibrary/AnnotationDbi'
ERROR: dependency 'AnnotationDbi' is not available for package 'hgu133plus2cdf'
* removing 'C:/Users/Marion/.RLibrary/hgu133plus2cdf'

The downloaded source packages are in
‘C:\Users\Marion\AppData\Local\Temp\RtmpcFpCJp\downloaded_packages’
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG-U133_Plus_2
Library - package hgu133plus2cdf not installed
Library - package hgu133plus2cdf not installed
In addition: Warning messages:
1: running command '"C:/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Marion\.RLibrary" C:\Users\Marion\AppData\Local\Temp\RtmpcFpCJp/downloaded_packages/GenomeInfoDb_1.2.5.tar.gz' had status 1 
2: In install.packages(cdfname, lib = lib, repos = biocinstallRepos(),  :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
3: running command '"C:/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Marion\.RLibrary" C:\Users\Marion\AppData\Local\Temp\RtmpcFpCJp/downloaded_packages/AnnotationDbi_1.28.2.tar.gz' had status 1 
4: In install.packages(cdfname, lib = lib, repos = biocinstallRepos(),  :
  installation of package ‘AnnotationDbi’ had non-zero exit status
5: running command '"C:/R-34~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Marion\.RLibrary" C:\Users\Marion\AppData\Local\Temp\RtmpcFpCJp/downloaded_packages/hgu133plus2cdf_2.15.0.tar.gz' had status 1 
6: In install.packages(cdfname, lib = lib, repos = biocinstallRepos(),  :
  installation of package ‘hgu133plus2cdf’ had non-zero exit status
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@marionryan-9732
Last seen 4.1 years ago

Thanks again Martin, no doubt I've done something..

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