[BioC] SomaticSignatures

Dan Tenenbaum dtenenba at fhcrc.org
Tue Apr 1 00:19:43 CEST 2014 

In addition to what Martin says, you'll need to "install" gmake, which on most linux systems is just a matter of creating a symbolic link called 'gmake' which points to make.

sudo ln -s /usr/bin/make /usr/bin/gmake

Dan


----- Original Message -----
> From: "Martin Morgan" <mtmorgan at fhcrc.org>
> To: "Huma Asif" <humaasif79 at yahoo.com>, "Steve Lianoglou" <lianoglou.steve at gene.com>, "Dan Tenenbaum"
> <dtenenba at fhcrc.org>
> Cc: "bioconductor at r-project.org list" <bioconductor at r-project.org>
> Sent: Monday, March 31, 2014 2:43:18 PM
> Subject: Re: [BioC] SomaticSignatures
> 
> 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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> > Bioconductor at r-project.org
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> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> 
> 
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