Hi! I'm new to Bioc, and I'm trying to install some packages. I'm having this error whith the limma package:
> biocLite('limma')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.25.3), R 3.4.0 (2017-04-21).
Installing package(s) ‘limma’
There is a binary version available but the source version is later:
binary source needs_compilation
limma 3.31.21 3.31.22 FALSE
installing the source package ‘limma’
probando la URL 'https://bioconductor.org/packages/3.5/bioc/src/contrib/limma_3.31.22.tar.gz'
Content type 'application/x-gzip' length 1470528 bytes (1.4 MB)
==================================================
downloaded 1.4 MB
* installing *source* package ‘limma’ ...
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘limma’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/limma’
The downloaded source packages are in
‘/private/var/folders/bl/p0xt2jfj7tndyzj3d1sjygb80000gn/T/Rtmpnc0O8l/downloaded_packages’
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package ‘limma’ had non-zero exit status
Is there anything I can do to fix this?
How can I do it? I've just followed the install instructions from Bioconductor website.
Usually you would be prompted if you wanted to install packages from source. I guess
biocLitemay have skipped the prompt if it thinks that limma doesn't need compilation (which it actually does). Your best bet is to just wait until the updated binary becomes available - probably tomorrow, which would coincide with the next Bioconductor release. If it's urgent, you could download the binary from https://bioconductor.org/packages/release/bioc/html/limma.html and install it manually, but that's a bad habit to get into. You'll have to do a big update for the next release anyway, so you might as well wait.When installing on Windows, if there is a source version that is newer than the binary, you are asked if you want to use the source version:
> biocLite("limma") BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.25.3), R 3.4.0 (2017-04-21). Installing package(s) 'limma' There is a binary version available but the source version is later: binary source needs_compilation limma 3.31.21 3.31.22 TRUE Do you want to install from sources the package which needs compilation? y/n:If you aren't set up to compile C or Fortran code (and the package actually contains C or Fortran code), then you should select 'n'. For things like annotation packages (which these days are only source), you should select 'y'.
But do note that the reason for the discrepancy is likely that today is supposed to be the release of Bioconductor 3.5. For most users, waiting until the actual release before installing anything to the R-3.4.0 library dir is probably the way to go, because you will need to re-install in just a little bit anyway.