[BioC] SomaticSignatures
Martin Morgan
mtmorgan at fhcrc.org
Mon Mar 31 23:43:18 CEST 2014
On 03/31/2014 12:16 PM, Huma Asif wrote:
> Hi every one,
> here is the new summary of what i did. sorry in advance for if it bothers u much.
> first
> R
> R version 3.1.0 alpha (2014-03-25 r65283)
> Copyright (C) 2014 The R Foundation for Statistical Computing
> Platform: i686-pc-linux-gnu (32-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> Then > source("http://bioconductor.org/biocLite.R")
> Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) :
> 'lib = "/usr/local/lib/R/library"' is not writable
> Would you like to use a personal library instead? (y/n) y
> Would you like to create a personal library
> ~/R/i686-pc-linux-gnu-library/3.1
> to install packages into? (y/n) y
> trying URL 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstaller_1.13.3.tar.gz'
> Content type 'application/x-gzip' length 14183 bytes (13 Kb)
> opened URL
> ==================================================
> downloaded 13 Kb
>
> * installing *source* package ‘BiocInstaller’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help
> * DONE (BiocInstaller)
>
> The downloaded source packages are in
> ‘/tmp/RtmpM1d0B0/downloaded_packages’
> Bioconductor version 2.14 (BiocInstaller 1.13.3), ?biocLite for help
>> library(tools)
>> library(utils)
>> library(BiocInstaller)
At this point, to install SomaticSignatures with internet access, you just want to
biocLite("SomaticSignatures")
If that accomplishes what you want, then stop reading. If this is what you want
to do, but there is an error, then please copy and paste the commands you used
and the error that occurred.
If you want to install SomaticSignatures from your own repository, then continue
to read below
>> pdb <- available.packages(contrib.url(biocinstallRepos()))
>> pkgs <- unlist(unname(package_dependencies("SomaticSignatures",
> + db=pdb, recursive=TRUE)))
>> pkgs <- c("SomaticSignatures", pkgs)
>> download.packages(pkgs, '.', repos=biocinstallRepos(), type="source")
> trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/SomaticSignatures_0.99.0.tar.gz'
> Content type 'application/x-gzip' length 1270216 bytes (1.2 Mb)
> opened URL
SNIP! This info WAS useful in the original email
> ==================================================
> downloaded 10 Kb
>
> trying URL 'http://cran.fhcrc.org/src/contrib/base64enc_0.1-1.tar.gz'
> Content type 'application/x-gzip' length 6296 bytes
> opened URL
> ==================================================
> downloaded 6296 bytes
>
> [,1] [,2]
> [1,] "SomaticSignatures" "./SomaticSignatures_0.99.0.tar.gz"
> [2,] "GenomicRanges" "./GenomicRanges_1.15.41.tar.gz"
SNIP
> [64,] "fail" "./fail_1.2.tar.gz"
> [65,] "base64enc" "./base64enc_0.1-1.tar.gz"
>
>
> install.packages(dir('.', pattern=".tar.gz$"),
> repos=NULL, type="source")
Your command says to install the packages as given, with no information about
relation between packages. It fails on the first one (AnnotationDbi) because it
has not yet installed dependencies.
If you want a one-time, off-line installation, then
1. create a directory, e.g., /tmp/R3.1_Bioc2.14/src/contrib/
2. download files into that directory
3. create a PACKAGES file to index the repository
4. install packages from your repository
Here's what I did, entirely in R:
## 1. create repository
repos <- "file:///tmp/R3.1_Bioc2.14"
dest <- "/tmp/R3.1_Bioc2.14/src/contrib/"
dir.create(dest, recursive=TRUE)
## 2. populate with relevant packages
pdb <- available.packages(contrib.url(biocinstallRepos()))
deps <- tools::package_dependencies("SomaticSignatures", db=pdb,
recursive=TRUE)
pkgs <- c("SomaticSignatures", deps$SomaticSignatures)
download.packages(pkgs, dest, repos=biocinstallRepos(), type="source")
## 3. create a PACKAGES file
tools::write_PACKAGES(dest)
## 4. install from repository
install.packages("SomaticSignatures", repos=repos)
However, it will usually be better to maintain a proper mirror of the
Bioconductor repository, as outlined at
http://bioconductor.org/about/mirrors/mirror-how-to/
For instance, to mirror the software only portion of the Bioconductor devel branch
/tmp$ mkdir -p 2.14/bioc/src/contrib
/tmp$ rsync -zrtlv --delete master.bioconductor.org::2.14/bioc/src/contrib
/tmp/2.14/bioc/src/
Likely you would also mirror CRAN http://cran.r-project.org/mirror-howto.html
following a similar scenario. You'd update these repositories regularly using
the rsync linux command (which just downloads the changes, not the entire
repository), and would install packages from them using
install.packages("SomaticSignatures", repos="file:///tmp/2.14/bioc")
Perhaps you would make your repositories available via a local http server.
There are instructions in the 'R-admin' document
http://cran.r-project.org/doc/manuals/R-admin.html#Setting-up-a-package-repository
>
> now the summary of warning after this command i attached please see
> Regards
> Huma
>
>
>
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