issue with hgu95acdf package
1
0
Entering edit mode
@alisherjannyyev-22314
Last seen 5.0 years ago

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 • 1.0k views
ADD COMMENT
3
Entering edit mode
@martin-morgan-1513
Last seen 4 months ago
United States

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

BiocManager::install("hgu95acdf", INSTALL_opts = "--no-multiarch")
ADD COMMENT
0
Entering edit mode

Thank you very very much, Morgan! It worked!

ADD REPLY

Login before adding your answer.

Traffic: 700 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6