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
