Question: Error trying to install GenomicRanges
0
gravatar for Kevin
3.0 years ago by
Kevin0
Kevin0 wrote:

Hi all,

I recently updated R to version 3.2.1 as I am running OSX 10.7.5. I tried to install the cummeRbund library but keep getting an error saying GenomicRanges is not installed. Therefore I tried installing Genomic ranges but get an error (see below). It seems like there are packages that are missing but I can't figure out how to get the packages that I need. Any help would appreciated.

Thanks!

Kevin

> library(cummeRbund)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply,
    parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval,
    evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
    rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist, unsplit

Loading required package: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster

Attaching package: ‘fastcluster’

The following object is masked from ‘package:stats’:

    hclust

Loading required package: rtracklayer
Error: package ‘GenomicRanges’ required by ‘rtracklayer’ could not be found
In addition: Warning messages:
1: package ‘cummeRbund’ was built under R version 3.2.2 
2: package ‘rtracklayer’ was built under R version 3.2.2 
> warnings()
Warning messages:
1: package ‘cummeRbund’ was built under R version 3.2.2
2: package ‘rtracklayer’ was built under R version 3.2.2
> library(cummeRbund)
Loading required package: rtracklayer
Error: package ‘GenomicRanges’ required by ‘rtracklayer’ could not be found
In addition: Warning messages:
1: package ‘cummeRbund’ was built under R version 3.2.2 
2: package ‘rtracklayer’ was built under R version 3.2.2 
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
> biocLite("GenomicRanges")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.1 (2015-06-18).
Installing package(s) ‘GenomicRanges’
also installing the dependencies ‘S4Vectors’, ‘IRanges’


  There are binary versions available but the source versions are later:
              binary source needs_compilation
S4Vectors      0.8.1  0.8.7             FALSE
IRanges        2.4.1  2.4.6             FALSE
GenomicRanges 1.22.1 1.22.3             FALSE

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

trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/S4Vectors_0.8.7.tar.gz'
Content type 'application/x-gzip' length 203508 bytes (198 KB)
==================================================
downloaded 198 KB

trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/IRanges_2.4.6.tar.gz'
Content type 'application/x-gzip' length 496858 bytes (485 KB)
==================================================
downloaded 485 KB

trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/GenomicRanges_1.22.3.tar.gz'
Content type 'application/x-gzip' length 932826 bytes (910 KB)
==================================================
downloaded 910 KB

* 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 ‘GenomicRanges’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/GenomicRanges’

The downloaded source packages are in
    ‘/private/var/folders/ck/08smx42s6375blmy1cmmj1th0000gn/T/RtmpxlyHOd/downloaded_packages’
Old packages: 'manipulate', 'nlme', 'XML'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
       binary   source needs_compilation
nlme  3.1-123  3.1-124              TRUE
XML  3.98-1.2 3.98-1.3              TRUE

  Binaries will be installed
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/contrib/3.2/manipulate_1.0.1.tgz'
Content type 'application/x-gzip' length 33315 bytes (32 KB)
==================================================
downloaded 32 KB

trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/contrib/3.2/nlme_3.1-123.tgz'
Content type 'application/x-gzip' length 2134610 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/contrib/3.2/XML_3.98-1.2.tgz'
Content type 'application/x-gzip' length 1874790 bytes (1.8 MB)
==================================================
downloaded 1.8 MB


The downloaded binary packages are in
    /var/folders/ck/08smx42s6375blmy1cmmj1th0000gn/T//RtmpxlyHOd/downloaded_packages
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 ‘GenomicRanges’ had non-zero exit status

ADD COMMENTlink modified 3.0 years ago by Mike Smith3.2k • written 3.0 years ago by Kevin0
Answer: Error trying to install GenomicRanges
1
gravatar for Mike Smith
3.0 years ago by
Mike Smith3.2k
EMBL Heidelberg / de.NBI
Mike Smith3.2k wrote:

It looks like biocLite() is trying to build those three packages from source, but your Mac does not have the appropriate tools available to do this.  It's trying to do this as the Bioconductor build server for OSX versions below 10.9 as had some issues and the pre-built binaries are now a little out of date.  This may even be a deliberate choice since Rcore are phasing out support for OSX below 10.9, I'm not sure.

I think there are a few things you can try:

Hopefully the following code will force biocLite() to install the slightly outdated pre-built version for you.  (I don't have a Mac so I can't test this).

biocLite(pkgs = c("S4Vectors", "IRanges", "GenomicRanges", type = "binary")

Alternatively, you could manually download the Mac OS X 10.6 (Snow Leopard) binary from the package landing pages (e.g. https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html) and then install using install.packages() or the R/Rstudio GUI.

There are presumably reasons why the package code has been updated, so you may want to get the latest versions.  To do this you could install the tools necessary to build from source.  This requires installing Xcode and gfortran.  There's some information here and here, and you can probably find more guides online.

ADD COMMENTlink written 3.0 years ago by Mike Smith3.2k
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