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Question: Trouble installing BiocInstaller
gravatar for 2299639P
9 months ago by
2299639P10 wrote:

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("")
Installing package into ‘\\ Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository
  cannot open URL ''
Warning: unable to access index for repository
  cannot open URL ''
'biocLite.R' failed to install 'BiocInstaller', use
  repos="")' or
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.




biocinstaller • 273 views
ADD COMMENTlink modified 9 months ago by Martin Morgan ♦♦ 22k • written 9 months ago by 2299639P10
Answer: Trouble installing BiocInstaller
gravatar for Martin Morgan
9 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Does this link work in a browser? If not, then you are perhaps behind a proxy; see the "Setting proxies" file in ?download.file.

ADD COMMENTlink written 9 months ago by Martin Morgan ♦♦ 22k

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

ADD REPLYlink written 9 months ago by 2299639P10

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 = ""
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 \\ 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 REPLYlink modified 9 months ago • written 9 months ago by Martin Morgan ♦♦ 22k
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