Question

Trouble installing BiocInstaller

1

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2299639P ▴ 10

@2299639p-15822

Last seen 6.6 years ago

I'm trying to install a package on FlowJo (FlowClean), and as far as I understand it, I need to install the packages on R. To fetch the packages on R, however, I need to have BiocInstaller. However, when I copy and paste the given script for R, it brings up the following:

> source("http://bioconductor.org/biocLite.R")
Installing package into ‘\\cfsk16.campus.gla.ac.uk/SSD_Home_Data_V/2299639P/My Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository https://bioconductor.org/packages/3.7/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5:
  cannot open URL 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/PACKAGES'
'biocLite.R' failed to install 'BiocInstaller', use
  'install.packages("BiocInstaller",
  repos="https://bioconductor.org/packages/3.7/bioc")' or
  'install.packages("BiocInstaller",
  repos="http://bioconductor.org/packages/3.7/bioc")'
Warning message:
package ‘BiocInstaller’ is not available (for R version 3.5.0)

Do I need to install an older version of R for this to work? If so, how do I do that, as I can't seem to find older version on R's website.

Thanks!

Narissa

biocinstaller • 1.6k views

ADD COMMENT • link updated 6.6 years ago by Martin Morgan 25k • written 6.6 years ago by 2299639P ▴ 10

score 0 · Answer 1 · 2018-05-15

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Martin Morgan 25k

@martin-morgan-1513

Last seen 5 months ago

United States

Does this link https://bioconductor.org/packages/3.7/bioc/src/contrib/PACKAGES work in a browser? If not, then you are perhaps behind a proxy; see the "Setting proxies" file in ?download.file.

ADD COMMENT • link 6.6 years ago Martin Morgan 25k

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When I click the link, I can see lines of text - does that mean it works?

ADD REPLY • link 6.6 years ago 2299639P ▴ 10

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Yes, text like

Package: a4
Version: 1.28.0
Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting
Suggests: MLP, nlcv, ALL, Cairo
License: GPL-3
MD5sum: 44fdfaae597a79d4d57e833b0d9d045a
NeedsCompilation: no

Package: a4Base
Version: 1.28.0
...

means that it is working in the browser. The code being evaluated is

url = "https://bioconductor.org/packages/3.7/bioc/src/contrib/PACKAGES"
destfile = tempfile()
method = getOption("download.file.method")
download.file(url = url, destfile = destfile, method = method, mode = "wb")

Does this work for you? If not, try changing method = to other methods documented on ?download.file; some will definitely fail depending on your system.

Also I notice that your file system is on a a network share \\cfsk16.campus.gla.ac.uk/SSD_HOME. Try mapping this to a network drive (google for your specific OS; you'll want to be able to access your files with something like W://SSD_HOME...). This might also involve editing the shortcut you use to start R.

ADD REPLY • link 6.6 years ago Martin Morgan 25k