Question: issue with hgu95acdf package
0
gravatar for alisher.jannyyev
4 weeks ago by
alisher.jannyyev0 wrote:

Can anyone help me with following issue? My version of R is 3.6.1 and Rtools are installed as well. I tried to manually install "hgu95acdf" package, but it seems that it did not work out well. I am using Windows 7 64bit.

**Loading required package: affy

Loading required package: BiocGenerics
Loading req**uired 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 objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max,
    which.min

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")'.****

> library(affy)
> affy.data <- ReadAffy()
> eset.mas5 = mas5(affy.data)
background correction: mas 
PM/MM correction : mas 
expression values: mas 
background correcting...installing the source package ‘hgu95acdf’

trying URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/hgu95acdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1331364 bytes (1.3 MB)
downloaded 1.3 MB

* installing *source* package 'hgu95acdf' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hgu95acdf'
Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hgu95acdf'
** help
*** installing help indices
  converting help for package 'hgu95acdf'
    finding HTML links ... готово
    geometry                                html  
    hgu95acdf                               html  
    hgu95adim                               html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
Error in system2(if (nzchar(arch)) file.path(R.home(), "bin", arch, "Rterm.exe") else file.path(R.home("bin"),  :
  '"C:/PROGRA~1/R/R-36~1.1/bin/i386/Rterm.exe"' not found
* removing 'C:/Program Files/R/R-3.6.1/library/hgu95acdf'

The downloaded source packages are in
    ‘C:\Users\Lenovo\AppData\Local\Temp\Rtmp8GaBSs\downloaded_packages’
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95A
Library - package hgu95acdf not installed
Library - package hgu95acdf not installed
In addition: Warning message:
In install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘hgu95acdf’ had non-zero exit status
affy • 82 views
ADD COMMENTlink modified 4 weeks ago by Martin Morgan ♦♦ 24k • written 4 weeks ago by alisher.jannyyev0
Answer: issue with hgu95acdf package
3
gravatar for Martin Morgan
4 weeks ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

Did you install just the 64-bit version of R for Windows? You might try

BiocManager::install("hgu95acdf", INSTALL_opts = "--no-multiarch")
ADD COMMENTlink written 4 weeks ago by Martin Morgan ♦♦ 24k

Thank you very very much, Morgan! It worked!

ADD REPLYlink written 4 weeks ago by alisher.jannyyev0
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