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Question: ALL Library and ALL Data Set error
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gravatar for alyssa.ylescu
9 months ago by
alyssa.ylescu0 wrote:

I am trying to access the ALL library and ALL data set. When I enter the following commands, I run into errors. How do I resolve this? 

​> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("ALL")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘ALL’
installing the source package ‘ALL’

trying URL 'https://bioconductor.org/packages/3.4/data/experiment/src/contrib/ALL_1.16.0.tar.gz'
Content type 'application/x-gzip' length 11401988 bytes (10.9 MB)
downloaded 10.9 MB

'D:\Program' is not recognized as an internal or external command,
operable program or batch file.

The downloaded source packages are in
    ‘C:\Users\alyss\AppData\Local\Temp\RtmpOIwH4i\downloaded_packages’
Warning messages:
1: running command '"D:/Program Files/R/R-3.3.2/bin/x64/R" CMD INSTALL -l "D:\Program Files\R\R-3.3.2\library" C:\Users\alyss\AppData\Local\Temp\RtmpOIwH4i/downloaded_packages/ALL_1.16.0.tar.gz' had status 1
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘ALL’ had non-zero exit status

What does the command

strsplit(Sys.getenv("PATH"), ";")

print? Does

install.packages("ALL", repos=BiocInstaller::biocinstallRepos())

work? What is the result of

getOption("pkgType")
ADD REPLYlink written 9 months ago by Martin Morgan ♦♦ 20k
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