I have seen a question that asks how to install MEDIPS on Ubuntu 14.04:
installing BSgenome and problems with XML and RCurl packages
See below. Any ideas?
Ubuntu 14.04 comes with R-3.0.2. These are the results below:
> source('http://bioconductor.org/biocLite.R')
Bioconductor version 2.13 (BiocInstaller 1.12.1), ?biocLite for help
A newer version of Bioconductor is available after installing a new version of
R, ?BiocUpgrade for help
> biocLite(character())
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
> biocLite("BiocUpgrade")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Warning message:
Bioconductor version 2.13 is the latest available for R version 3.0.0
> biocLite('MEDIPS')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2.
Installing package(s) 'MEDIPS'
also installing the dependency ‘GenomicFeatures’
trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/GenomicFeatures_1.14.5.tar.gz'
Content type 'application/x-gzip' length 814511 bytes (795 Kb)
opened URL
==================================================
downloaded 795 Kb
trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/MEDIPS_1.12.0.tar.gz'
Content type 'application/x-gzip' length 287882 bytes (281 Kb)
opened URL
==================================================
downloaded 281 Kb
* installing *source* package ‘GenomicFeatures’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “AsIs” in package ‘DBI’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'
ERROR: lazy loading failed for package ‘GenomicFeatures’
* removing ‘/usr/local/lib/R/site-library/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘MEDIPS’
* removing ‘/usr/local/lib/R/site-library/MEDIPS’
The downloaded source packages are in
‘/tmp/RtmpfX6gPS/downloaded_packages’
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘GenomicFeatures’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘MEDIPS’ had non-zero exit status
I then created an R-3.2.1 folder and changed the $PATH so that it would pick up these binaries first.
Repeating the same as above, also gave the GenomicFeatures error:
> biocLite("BiocUpgrade")
[...]
> biocLite("MEDIPS")
[...]
Note: the specification for S3 class “AsIs” in package ‘DBI’ seems equivalent to one from package ‘BiocGenerics’: not turning on duplicate class definitions for this class.
Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'
ERROR: lazy loading failed for package ‘GenomicFeatures’
* removing ‘/usr/local/lib/R/site-library/GenomicFeatures’
ERROR: dependency ‘GenomicFeatures’ is not available for package ‘MEDIPS’
* removing ‘/usr/local/lib/R/site-library/MEDIPS’
The downloaded source packages are in
‘/tmp/RtmpWv9Ty1/downloaded_packages’
Old packages: 'class'
Update all/some/none? [a/s/n]: a
trying URL 'http://cran.fhcrc.org/src/contrib/class_7.3-14.tar.gz'
Content type 'application/x-gzip' length 19726 bytes (19 Kb)
opened URL
==================================================
downloaded 19 Kb
* installing *source* package ‘class’ ...
** package ‘class’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c class.c -o class.o
gcc -std=gnu99 -shared -o class.so class.o -L/usr/lib/R/lib -lR
installing to /usr/lib/R/library/class/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (class)
The downloaded source packages are in
‘/tmp/RtmpWv9Ty1/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘GenomicFeatures’ had non-zero exit status
2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘MEDIPS’ had non-zero exit status
