Question

Help with Affymetrix Human Genome U95A 2.0

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pablo.giraudi • 0

@pablogiraudi-22047

Last seen 4.6 years ago

I am attemting to analyse microarrays data with the following tutorial Using Bioconductor for Microarray Analysis but I am not able to install the following package:

with the Affymetrix Human Genome U95A 2.0

BiocManager::install("hgu95av2cdf")

In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : installation of package ‘hgu95av2.db’ had non-zero exit status

Can anyone help me to solve the issue?

Many thanks in advance,

Pablo

microarray • 437 views

ADD COMMENT • link 4.6 years ago pablo.giraudi • 0

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Be sure to include the full output of the installation. If the problem is that an underlying package cannot be installed, try installing it first

BiocManager::install("hgu95av2.db")

Remember to include the output of sessionInfo(). Here's mine

> sessionInfo()
R version 3.6.1 Patched (2019-08-19 r77045)
Platform: x86_64-apple-darwin17.7.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /Users/ma38727/bin/R-3-6-branch/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-3-6-branch/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_3.6.1

ADD REPLY • link 4.6 years ago Martin Morgan 25k

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Many thanks Martin,

unfortunately , I continue to have the same answer.

The downloaded binary packages are in
        C:\Users\Public\Documents\Wondershare\CreatorTemp\RtmpieLVR0\downloaded_packages
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘hgu95av2.db’ had non-zero exit status

>  sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252    LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C                   LC_TIME=Italian_Italy.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.6.0     tools_3.6.0

Thanks, P

ADD REPLY • link updated 4.6 years ago by Martin Morgan 25k • written 4.6 years ago by pablo.giraudi • 0

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Martin asked you to show the full output of the installation, and you instead show just the last bit? Is there a particular reason for not showing everything?

ADD REPLY • link 4.6 years ago James W. MacDonald 65k