Question: Problem Installing limma package
0
2.5 years ago by

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)
==================================================

* 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’

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?

modified 2.5 years ago by Gordon Smyth38k • written 2.5 years ago by segador670
1
2.5 years ago by
Aaron Lun25k
Cambridge, United Kingdom
Aaron Lun25k wrote:

It seems like you're downloading the limma source and trying to install it. However, you don't have the necessary tools to compile the native code. Stick with the binary version unless you know what you're doing.

P.S. limma definitely has C code in it, so I don't know why needs_compilation is FALSE.

P.P.S. I suppose it's due to the absence of a NeedsCompilation: Yes in the DESCRIPTION.

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 biocLite may 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.

1

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.

1
2.5 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

Bioconductor hasn't been officially released yet for R 3.4.0 -- that will happen within the next 24 hours (April 25 American time). In the meantime, you're trying to install the developmental version.

The reason why you've run into a problem is probably that there was an error in limma 3.31.21 which was fixed in limma 3.31.22. You tried to install during the brief interval after limma 3.31.22 had been committed to the svn (3 days ago) but before Bioconductor had compiled the new version for your platform.

If you try again now, limma will install without any errors. However, it would be best for you to wait for the official Bioconductor release.