Visualizzazione post con etichetta upgrade. Mostra tutti i post
Visualizzazione post con etichetta upgrade. Mostra tutti i post
mercoledì 3 aprile 2013
lunedì 31 ottobre 2011
R 2.14.0 is released!
The new R 2.14.0 is out! Get the source code from here.
Take a look at these posts for some miscellaneous advices to make the upgrade easier.
Also this thread on stackoverflow and this post contributed by Tal Galili can be of some value to make the procedure less painful.
Feel free to contribute with suggestions about how to upgrade your R installation.
venerdì 24 giugno 2011
Installing Multiple Version of R in parallel on the same machine - Mac OS X
In a few days I'm going to attend a Bioconductor Course; I was requested to install on my MacBook (Mac OS X 10.5.8) a developer version of R (plus ad hoc Bioconductor packages). In order to keep my old R installation ((2.13) along side the new one (2.14) I decided to use the RSwitch app (you can download from here) and the instructions you can read here.
In practical term, you type the following commands in Terminal:
You install the alternative version of R (for example, following the procedure depicted here) and then you can switch between the different version using the RSwitch GUI (see the below screenshot). So easy!
In practical term, you type the following commands in Terminal:
sudo pkgutil --forget org.r-project.R.Leopard.fw.pkg
sudo pkgutil --forget org.r-project.R.Leopard.GUI.pkg
sudo pkgutil --forget org.r-project.R.Leopard.GUI64.pkgYou install the alternative version of R (for example, following the procedure depicted here) and then you can switch between the different version using the RSwitch GUI (see the below screenshot). So easy!
giovedì 14 aprile 2011
R 2.13.0 is released!
The new R 2.13.0 is out! Get the source code from here.
Take a look at these posts for some miscellaneous advices to make the upgrade easier.
Also this thread on stackoverflow and this post contributed by Tal Galili can be of some value to make the procedure less painful.
Feel free to contribute with suggestions about how to upgrade your R installation.
venerdì 15 ottobre 2010
R 2.12.0 is released!
giovedì 22 aprile 2010
R 2.11.0 is released!
giovedì 29 ottobre 2009
Bioconductor 2.5 is out
For all bioinformaticians and R users out there: the Bioconductor project for the analysis and comprehension of genomic data is out! A lot of interesting new stuff! See the full announcement here.
lunedì 26 ottobre 2009
R 2.10.0 is Out!
giovedì 23 ottobre 2008
R Upgrade on Mac Os X 10.5.5 (Leopard)
To reinstall packages from an old version of R to a new one.
In the old version type:
Install the most recent version of R:
Download the most recent version of R from The Comprehensive R Archive Network (CRAN)
Build from source new R version (see this FAQ).
From inside the decompressed R-?.?.? directory type:
Install BioConductor packages using the biocLite.R installation script.
In an R command window, type the following:
If you have other Bioconductor packages missing from the old installation:
Re-install the missing packages from CRAN:
If you use some package created by Henrik Bengtsson:
If you find your X11 broken after the installation procedure (it happens every time to me, at least on Leopard) install the XQuartz App from here.
Update: If you need to install a recent version of R on old hardware (Power PC G4) and OS (Mac OS X 10.4 here) this post can be useful.
In the old version type:
tmp <- installed.packages()
installedpkgs <- as.vector(tmp[is.na(tmp[,"Priority"]), 1])
save(installedpkgs, file="installed_old.rda")Install the most recent version of R:
Download the most recent version of R from The Comprehensive R Archive Network (CRAN)
# To wipe the old R version
rm -rf /Library/Frameworks/R.framework /Applications/R.app
rm -rf /Library/Receipts/R-*Build from source new R version (see this FAQ).
From inside the decompressed R-?.?.? directory type:
# See Section 2.2 of RMacOSX FAQ for the flag description
./configure --with-blas='-framework vecLib' --enable-BLAS-shlib
make
sudo make installInstall BioConductor packages using the biocLite.R installation script.
In an R command window, type the following:
source("http://bioconductor.org/biocLite.R")
chooseBioCmirror()
biocLite()If you have other Bioconductor packages missing from the old installation:
load("installed_old.rda")
tmp <- installed.packages()
installedpkgs.new <- as.vector(tmp[is.na(tmp[,"Priority"]), 1])
missing <- setdiff(installedpkgs, installedpkgs.new)
for (i in 1:length(missing)) biocLite(missing[i])Re-install the missing packages from CRAN:
load("installed_old.rda")
tmp <- installed.packages()
installedpkgs.new <- as.vector(tmp[is.na(tmp[,"Priority"]), 1])
missing <- setdiff(installedpkgs, installedpkgs.new)
install.packages(missing)
update.packages()If you use some package created by Henrik Bengtsson:
source("http://www.braju.com/R/hbLite.R")
hbLite()If you find your X11 broken after the installation procedure (it happens every time to me, at least on Leopard) install the XQuartz App from here.
Update: If you need to install a recent version of R on old hardware (Power PC G4) and OS (Mac OS X 10.4 here) this post can be useful.
mercoledì 16 aprile 2008
R installing on Unix/Linux - no root access
Thanks and credit to Joern Toedling for this useful and clear how-to!
From The Bioconductor Digest, Vol 62, Issue 14:
You do not need to have root access to a machine to install your own
versions of R and your favourite packages there. This is how to do it:
1. downloaded the tar.gz of the development version of R from
ftp://ftp.stat.math.ethz.ch/Software/R/
2. uncompress it to a directory you have write access to, say ~/local/R
3. change into the uncompressed directory, ~/local/R/R-devel
4. run "./configure"
5. run "make"
Afterwards you can start R by executing ~/local/R/R-devel/bin/R;
to simplify that either add the bin directory to your path or create an alias for R
You do not need to run "make install" to work with R.
For packages,
1. create a directory in which you want the packages installed, e.g. ~/local/rpacks
2. create an evironment variable R_LIBS that holds the path to that directory, e.g. "setenv R_LIBS=${HOME}/local/rpacks" with that directory and a C-shell (use export with a Bash shell)
This environment variable tells R where to look first for installed packages and where to install packages when using "install.packages" or "biocLite".
R_LIBS is safe to use, since it only extends the path to look for packages and does not replace the default R library path.
I would recommend to add the alias for starting R and the R_LIBS
definition to your shell startup file (~/.cshrc or ~/.bashrc).
From The Bioconductor Digest, Vol 62, Issue 14:
You do not need to have root access to a machine to install your own
versions of R and your favourite packages there. This is how to do it:
1. downloaded the tar.gz of the development version of R from
ftp://ftp.stat.math.ethz.ch/Software/R/
2. uncompress it to a directory you have write access to, say ~/local/R
3. change into the uncompressed directory, ~/local/R/R-devel
4. run "./configure"
5. run "make"
Afterwards you can start R by executing ~/local/R/R-devel/bin/R;
to simplify that either add the bin directory to your path or create an alias for R
You do not need to run "make install" to work with R.
For packages,
1. create a directory in which you want the packages installed, e.g. ~/local/rpacks
2. create an evironment variable R_LIBS that holds the path to that directory, e.g. "setenv R_LIBS=${HOME}/local/rpacks" with that directory and a C-shell (use export with a Bash shell)
This environment variable tells R where to look first for installed packages and where to install packages when using "install.packages" or "biocLite".
R_LIBS is safe to use, since it only extends the path to look for packages and does not replace the default R library path.
I would recommend to add the alias for starting R and the R_LIBS
definition to your shell startup file (~/.cshrc or ~/.bashrc).
giovedì 9 agosto 2007
R package installation and administration
A short list of basic but useful commands for managing
the packages in R:
the packages in R:
# install a package
install.packages("ROCR")
# visualize package version
package_version("pamr")
# update a package
update.packages("Cairo")
# remove a package
remove.packages("RGtk2")lunedì 16 luglio 2007
R upgrading on Windows© revisited
From the list:
When I update R the following has worked for me (Windows XP)
1. Install the new version to a new directory (say C:\Program Files\R\R-2.5.1).
2. Rename the new library subdirectory to library2.
3. Copy the entire contents of the old library subdirectory (say
C:\Program Files\R\R-2.4.0\library\ to the new R root to create
C:\Program Files\R\R-2.5.1\library\ .
4. Copy the contents of library2 to library to update your basic library.
5. Now start your new version of R and update packages from the GUI or
from the R console. (You may need to firs check Rprofile .site to
ensure that no packages have been loaded)
6. On occasion I have got warning messages when I tried to load
packages after this procedure. This has been cleared by running
update.packages(checkBuilt = TRUE)
This checks that your packages have been built with the latest
version. When I do this I agree to install all available updates.
7. You may wish to copy various autoloads etc from your old
Rprofile.site to your new Rprofile.site. I understand that there are
some compatibility problems with 2.5.1 and SciViews so be careful.
When I update R the following has worked for me (Windows XP)
1. Install the new version to a new directory (say C:\Program Files\R\R-2.5.1).
2. Rename the new library subdirectory to library2.
3. Copy the entire contents of the old library subdirectory (say
C:\Program Files\R\R-2.4.0\library\ to the new R root to create
C:\Program Files\R\R-2.5.1\library\ .
4. Copy the contents of library2 to library to update your basic library.
5. Now start your new version of R and update packages from the GUI or
from the R console. (You may need to firs check Rprofile .site to
ensure that no packages have been loaded)
6. On occasion I have got warning messages when I tried to load
packages after this procedure. This has been cleared by running
update.packages(checkBuilt = TRUE)
This checks that your packages have been built with the latest
version. When I do this I agree to install all available updates.
7. You may wish to copy various autoloads etc from your old
Rprofile.site to your new Rprofile.site. I understand that there are
some compatibility problems with 2.5.1 and SciViews so be careful.
venerdì 27 aprile 2007
What's the best way to upgrade R on Windows©?
Copied and pasted from R for Windows FAQ - Version for R-2.5.0 - FAQ 2.8:
That's a matter of taste. For most people the best thing to do is to uninstall R (see the previous Q), install the new version, copy any installed packages to the library folder in the new installation, run update.packages() in the new R (`Update packages...' from the Packages menu, if you prefer) and then delete anything left of the old installation. Different versions of R are quite deliberately installed in parallel folders so you can keep old versions around if you wish.
Upgrading from R 1.x.y to R 2.x.y is special as all the packages need to be reinstalled. Rather than copy them across, make a note of their names and re-install them from CRAN.
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