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Question: Issue Downloading GenomicRanges
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gravatar for megan.e.paul.17
16 months ago by
megan.e.paul.170 wrote:

So when I try to download the GenomicRanges package it continuously comes up with this error.  When running from other devices, it seems to download without a problem. Does anyone have any insight? 

> source("http://bioconductor.org/biocLite.R")

Bioconductor version 3.2 (BiocInstaller 1.20.3), ?biocLite for help
A new version of Bioconductor is available after installing the most recent version of R; see
  http://bioconductor.org/install
> biocLite("GenomicRanges")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.1 (2015-06-18).
Installing package(s) ‘GenomicRanges’
also installing the dependencies ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’

  There are binary versions available but the source versions are later:
              binary source needs_compilation
S4Vectors      0.8.1 0.8.11             FALSE
IRanges        2.4.1  2.4.8             FALSE
GenomeInfoDb   1.6.1  1.6.3             FALSE
GenomicRanges 1.22.1 1.22.4             FALSE

installing the source packages ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘GenomicRanges’

...
* installing *source* package ‘S4Vectors’ ...
** libs
sh: make: command not found
ERROR: compilation failed for package ‘S4Vectors’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors’
ERROR: dependency ‘S4Vectors’ is not available for package ‘IRanges’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’ are not available for package ‘GenomeInfoDb’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/GenomeInfoDb’
ERROR: dependencies ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’ are not available for package ‘GenomicRanges’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/GenomicRanges’

The downloaded source packages are in
    ‘/private/var/folders/n9/h_68v4_s0ks305b1z22l8k0h0000gn/T/Rtmptw7rg9/downloaded_packages’
Old packages: 'openssl'
Update all/some/none? [a/s/n]: 
n
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘S4Vectors’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘IRanges’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘GenomicRanges’ had non-zero exit status
ADD COMMENTlink modified 16 months ago by Martin Morgan ♦♦ 20k • written 16 months ago by megan.e.paul.170

It's unusual that the source version is so far ahead of the binary version for a release (3.3 is the current Bioconductor release) that is no longer current. I guess this is because you are using Mac Snow Leopard, and the Snow Leopard builds were terminated part way through the 3.2 release cycle. You are, unfortunately, using an operating system version (snow leopard) that neither R nor Bioconductor support.

It's also unusual that the packages claim not to need compilation, when they clearly do. I don't know what the source of this is.

ADD REPLYlink written 16 months ago by Martin Morgan ♦♦ 20k
0
gravatar for Dan Tenenbaum
16 months ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

R is not giving you a chance to say whether you want to install packages from source, and then it fails when it can't find the tools (such as 'make') needed to install packages from source.

So you have two choices:

1) Tell R to a) either ask you before installing packages from source, or b) to never install packages from source.

For option a) do this before the biocLite() command:

options(install.packages.compile.from.source="interactive")

Then, when biocLite() asks you whether to install packages from source, say (n)o.

For option b) do this before the biocLite() command:

options(install.packages.compile.from.source="never")

For more info see the install.packages.compile.from.source section of ?options. FWIW, this seems like incorrect behavior on the part of R, based on the information in that man page.

 

2) Install the tools needed so that R can build packages from source, by following this link.

ADD COMMENTlink modified 16 months ago • written 16 months ago by Dan Tenenbaum ♦♦ 8.2k
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