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llply is equivalent to lapply except that it will preserve labels and can display a progress bar.
llply is equivalent to lapply except that it will preserve labels and can display a progress bar.


=== mclapply() is a mult-core version of lapply() ===
=== mclapply() from paralle package is a mult-core version of lapply() ===
But Windows OS can not take advantage of it.
But Windows OS can not take advantage of it.

Revision as of 15:29, 31 December 2012

Install Rtools for Windows users

See File:Rtools installation.pdf

Install R using binary package

Redhat el6

It should be pretty easy to install via the EPEL: http://fedoraproject.org/wiki/EPEL

Just follow the instructions to enable the EPEL and then from the CLI as root: 

yum install R

or via sudo: 

sudo yum install R

Install R from source (ix86, x86_64 and arm platforms, Linux system)

Debian system (with arm architecture)

Simplest configuration

On my debian system in Pogoplug (armv5), I can compile R. See R's admin manual. If I don't need x11, I just need to install 2 required packages.

  • install gfortran: apt-get install gfortran
  • install readline library: apt-get install libreadline5-dev

Note: if I need x11, I should install

  • libx11 and libx11-devel, libXt, libXt-devel (for fedora)
  • xorg-dev (for debian)

I also run apt-get install readline-common. I don't know if this is necessary. Since I don't need x11, I use the option in configure command. After running 

./configure --with-x=no --enable-R-shlib

I got 

R is now configured for armv5tel-unknown-linux-gnueabi

  Source directory:          .
  Installation directory:    /usr/local

  C compiler:                gcc -std=gnu99  -g -O2
  Fortran 77 compiler:       gfortran  -g -O2

  C++ compiler:              g++  -g -O2
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:

  Interfaces supported:
  External libraries:        readline
  Additional capabilities:   NLS
  Options enabled:           shared R library, shared BLAS, R profiling

  Recommended packages:      yes

configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help pages
configure: WARNING: I could not determine a browser
configure: WARNING: I could not determine a PDF viewer

However, make gave errors for recommanded packages like KernSmooth, MASS, boot, class, cluster, codetools, foreign, lattice, mgcv, nlme, nnet, rpart, spatial, and survival. The error stems from gcc: SHLIB_LIBADD: No such file or directory. Note that I can get this error message even I try install.packages("MASS", type="source"). 

make[1]: Entering directory `/mnt/usb/R-2.15.2/src/library/Recommended'
make[2]: Entering directory `/mnt/usb/R-2.15.2/src/library/Recommended'
begin installing recommended package MASS
* installing *source* package 'MASS' ...
** libs
make[3]: Entering directory `/tmp/Rtmp4caBfg/R.INSTALL1d1244924c77/MASS/src'
gcc -std=gnu99 -I/mnt/usb/R-2.15.2/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c MASS.c -o MASS.o
gcc -std=gnu99 -I/mnt/usb/R-2.15.2/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c lqs.c -o lqs.o
gcc -std=gnu99 -shared -L/usr/local/lib -o MASSSHLIB_EXT MASS.o lqs.o SHLIB_LIBADD -L/mnt/usb/R-2.15.2/lib -lR
gcc: SHLIB_LIBADD: No such file or directory
make[3]: *** [MASSSHLIB_EXT] Error 1
make[3]: Leaving directory `/tmp/Rtmp4caBfg/R.INSTALL1d1244924c77/MASS/src'
ERROR: compilation failed for package 'MASS'
* removing '/mnt/usb/R-2.15.2/library/MASS'
make[2]: *** [MASS.ts] Error 1
make[2]: Leaving directory `/mnt/usb/R-2.15.2/src/library/Recommended'
make[1]: *** [recommended-packages] Error 2
make[1]: Leaving directory `/mnt/usb/R-2.15.2/src/library/Recommended'
make: *** [stamp-recommended] Error 2
root@debian:/mnt/usb/R-2.15.2#
root@debian:/mnt/usb/R-2.15.2# bin/R

R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: armv5tel-unknown-linux-gnueabi (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.

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.

> library(MASS)
Error in library(MASS) : there is no package called 'MASS'
> library()
Packages in library '/mnt/usb/R-2.15.2/library':

base                    The R Base Package
compiler                The R Compiler Package
datasets                The R Datasets Package
grDevices               The R Graphics Devices and Support for Colours
                        and Fonts
graphics                The R Graphics Package
grid                    The Grid Graphics Package
methods                 Formal Methods and Classes
parallel                Support for Parallel computation in R
splines                 Regression Spline Functions and Classes
stats                   The R Stats Package
stats4                  Statistical Functions using S4 Classes
tcltk                   Tcl/Tk Interface
tools                   Tools for Package Development
utils                   The R Utils Package
> Sys.info()["machine"]
   machine
"armv5tel"
> gc()
         used (Mb) gc trigger (Mb) max used (Mb)
Ncells 170369  4.6     350000  9.4   350000  9.4
Vcells 163228  1.3     905753  7.0   784148  6.0

See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=679180

Full configuration

  Interfaces supported:      X11, tcltk
  External libraries:        readline
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo
  Options enabled:           shared R library, shared BLAS, R profiling, Java

Install r-base and r-base-dev

In fact, if we want to take a short cut, it seems OK to run the following statement to install r-base and all required components for building r-base and extra packages. Notice that for readline package, it installs 'libreadline6-dev' instead of 'libreadline5-dev' as I just did.

Note that I did not touch /etc/apt/sources.list file so I don't know what version of R will be installed by this method. 

root@debian:/mnt/usb/R-2.15.2# apt-get install r-base-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following package was automatically installed and is no longer required:
  libreadline5
Use 'apt-get autoremove' to remove them.
The following extra packages will be installed:
  defoma dpatch file fontconfig libblas-dev libblas3gf libbz2-dev libcairo2 libdatrie1
  libjpeg62-dev liblapack-dev liblapack3gf libnewt0.52 libpango1.0-0 libpango1.0-common
  libpaper-utils libpaper1 libpcre3-dev libpcrecpp0 libpixman-1-0 libpng12-dev libreadline-dev
  libreadline6-dev libthai-data libthai0 libxcb-render-util0 libxcb-render0 r-base-core unzip
  whiptail xdg-utils zip zlib1g-dev
Suggested packages:
  defoma-doc psfontmgr x-ttcidfont-conf dfontmgr curl ttf-japanese-gothic ttf-japanese-mincho
  ttf-thryomanes ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp
  ttf-arphic-bkai00mp ess r-doc-info r-doc-pdf r-mathlib r-base-html cdbs debhelper gvfs-bin
Recommended packages:
  libfont-freetype-perl fakeroot patchutils libfribidi0 r-recommended r-doc-html iceweasel
  www-browser x11-utils x11-xserver-utils shared-mime-info
The following packages will be REMOVED:
  libreadline5-dev
The following NEW packages will be installed:
  defoma dpatch file fontconfig libblas-dev libblas3gf libbz2-dev libcairo2 libdatrie1
  libjpeg62-dev liblapack-dev liblapack3gf libnewt0.52 libpango1.0-0 libpango1.0-common
  libpaper-utils libpaper1 libpcre3-dev libpcrecpp0 libpixman-1-0 libpng12-dev libreadline-dev
  libreadline6-dev libthai-data libthai0 libxcb-render-util0 libxcb-render0 r-base-core
  r-base-dev unzip whiptail xdg-utils zip zlib1g-dev
0 upgraded, 34 newly installed, 1 to remove and 0 not upgraded.
Need to get 22.9 MB of archives.
After this operation, 58.2 MB of additional disk space will be used.
Do you want to continue [Y/n]? n

Install all dependencies for building R

This is a comprehensive list. This list is even larger than r-base-dev. 

root@debian:/mnt/usb/R-2.15.2# apt-get build-dep r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
  libreadline5-dev
The following NEW packages will be installed:
  bison ca-certificates ca-certificates-java debhelper defoma ed file fontconfig gettext
  gettext-base html2text intltool-debian java-common libaccess-bridge-java
  libaccess-bridge-java-jni libasound2 libasyncns0 libatk1.0-0 libaudit0 libavahi-client3
  libavahi-common-data libavahi-common3 libblas-dev libblas3gf libbz2-dev libcairo2
  libcairo2-dev libcroco3 libcups2 libdatrie1 libdbus-1-3 libexpat1-dev libflac8
  libfontconfig1-dev libfontenc1 libfreetype6-dev libgif4 libglib2.0-dev libgtk2.0-0
  libgtk2.0-common libice-dev libjpeg62-dev libkpathsea5 liblapack-dev liblapack3gf libnewt0.52
  libnspr4-0d libnss3-1d libogg0 libopenjpeg2 libpango1.0-0 libpango1.0-common libpango1.0-dev
  libpcre3-dev libpcrecpp0 libpixman-1-0 libpixman-1-dev libpng12-dev libpoppler5 libpulse0
  libreadline-dev libreadline6-dev libsm-dev libsndfile1 libthai-data libthai0 libtiff4-dev
  libtiffxx0c2 libunistring0 libvorbis0a libvorbisenc2 libxaw7 libxcb-render-util0
  libxcb-render-util0-dev libxcb-render0 libxcb-render0-dev libxcomposite1 libxcursor1
  libxdamage1 libxext-dev libxfixes3 libxfont1 libxft-dev libxi6 libxinerama1 libxkbfile1
  libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender-dev libxss-dev libxt-dev libxtst6 luatex m4
  openjdk-6-jdk openjdk-6-jre openjdk-6-jre-headless openjdk-6-jre-lib openssl pkg-config
  po-debconf preview-latex-style shared-mime-info tcl8.5-dev tex-common texi2html texinfo
  texlive-base texlive-binaries texlive-common texlive-doc-base texlive-extra-utils
  texlive-fonts-recommended texlive-generic-recommended texlive-latex-base texlive-latex-extra
  texlive-latex-recommended texlive-pictures tk8.5-dev tzdata-java whiptail x11-xkb-utils
  x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev xauth xdg-utils xfonts-base
  xfonts-encodings xfonts-utils xkb-data xserver-common xvfb zlib1g-dev
0 upgraded, 136 newly installed, 1 to remove and 0 not upgraded.
Need to get 139 MB of archives.
After this operation, 410 MB of additional disk space will be used.
Do you want to continue [Y/n]?

Web Applications

HTTP protocol

shiny

The following is what we see on a browser after we run an example from shiny package. See http://rstudio.github.com/shiny/tutorial/#hello-shiny. Note that the R session needs to be on; i.e. R command prompt will not be returned unless we press Ctrl+C or ESC.

ShinyHello.png Shinympg.png ShinyReactivity.png ShinyTabsets.png ShinyUpload.png

shiny depends on websockets, caTools, bitops, digest packages.

Q & A:

  • Q: If we run runExample('01_hello') in Rserve from an R client, we can continue our work in R client without losing the functionality of the GUI from shiny. Question: how do we kill the job?
  • If I run the example "01_hello", the browser only shows the control but not graph on Firefox? A: Use Chrome or Opera as the default browser.
  • If I run the example "01_hello" on RHEL the first time, it works fine. But if I click 'Ctrl + C' to stop it and run it again, I got a message
Warning in .SOCK_SERVE(port) : R-Websockets(tcpserv): bind() failed. 
Error in createContext(port, webpage, is.binary = is.binary) : 
  Unable to bind socket on port 8100; is it realsy in use?

A simple solution is to close R and open it again.

  • Q: Deployment on web. A: Not ready yet. Shiny server platform is still under beta testing. Shiny apps are hosted using the R websockets package which acts more like a tcp server than a web server, and that architecture just doesn't fit with rApache, or even apache for that matter.
  • Q: How difficult to put the code in Gist:github? A: Just create an account. Do not even need to create a repository. Just go to http://gist.github.com and create a new gist. The new gist can be secret or public. A secret gist can not be edited again after it is created although it works fine when it was used in runGist() function.

RApache

gWidgetsWWW

Rook

Since R 2.13, the internal web server was exposed.

Tutorual from useR2012 and Jeffrey Horner

Here is another one from http://www.rinfinance.com.

Rook is also supported by [rApache too. See http://rapache.net/manual.html.

Google group. https://groups.google.com/forum/?fromgroups#!forum/rrook

Advantage

  • the web applications are created on desktop, whether it is Windows, Mac or Linux.
  • No Apache is needed.
  • create multiple applications at the same time. This complements the limit of rApache.

4 lines of code example. 

library(Rook)
s <- Rhttpd$new()
s$start(quiet=TRUE)
s$print()
s$browse(1)  # OR s$browse("RookTest")

Notice that after s$browse() command, the cursor will return to R because the command just a shortcut to open the web page http://127.0.0.1:10215/custom/RookTest.

Rook.png Rook2.png Rookapprnorm.png

We can add Rook application to the server; see ?Rhttpd. 

s$add(
    app=system.file('exampleApps/helloworld.R',package='Rook'),name='hello'
)
s$add(
    app=system.file('exampleApps/helloworldref.R',package='Rook'),name='helloref'
)
s$add(
    app=system.file('exampleApps/summary.R',package='Rook'),name='summary'
)

s$print()

#Server started on 127.0.0.1:10221
#[1] RookTest http://127.0.0.1:10221/custom/RookTest
#[2] helloref http://127.0.0.1:10221/custom/helloref
#[3] summary  http://127.0.0.1:10221/custom/summary
#[4] hello    http://127.0.0.1:10221/custom/hello

#  Stops the server but doesn't uninstall the app
## Not run: 
s$stop()

## End(Not run)
s$remove(all=TRUE)
rm(s)

For example, the interface and the source code of summary app are given below

Rookappsummary.png 

app <- function(env) {
    req <- Rook::Request$new(env)
    res <- Rook::Response$new()
    res$write('Choose a CSV file:\n')
    res$write('<form method="POST" enctype="multipart/form-data">\n')
    res$write('<input type="file" name="data">\n')
    res$write('<input type="submit" name="Upload">\n</form>\n<br>')

    if (!is.null(req$POST())){
	data <- req$POST()[['data']]
	res$write("<h3>Summary of Data</h3>");
	res$write("<pre>")
	res$write(paste(capture.output(summary(read.csv(data$tempfile,stringsAsFactors=FALSE)),file=NULL),collapse='\n'))
	res$write("</pre>")
	res$write("<h3>First few lines (head())</h3>");
	res$write("<pre>")
	res$write(paste(capture.output(head(read.csv(data$tempfile,stringsAsFactors=FALSE)),file=NULL),collapse='\n'))
	res$write("</pre>") 
    }
    res$finish()
}

More example:

Stockplot

FastRWeb

Rwui

CGHWithR (removed from CRAN)

But it is still working with old version of R.

Creating local repository for CRAN and Bioconductor

How to set up a package repository

Guide: http://cran.r-project.org/doc/manuals/R-admin.html#Setting-up-a-package-repository

NOTE

  • If the binary package was built on R 2.15.1, then it cannot be installed on R 2.15.2. But vice is OK.

To create CRAN repository

Before creating a local repository please give a dry run first. You don't want to be surprised how long will it take to mirror a directory.

Dry run (-n option). Pipe out the process to a text file for an examination. 

rsync -avn cran.r-project.org::CRAN > crandryrun.txt

To mirror only partial repository, it is necessary to create directories before running rsync command. 

mkdir /media/WD640/CRAN
mkdir /media/WD640/CRAN/bin
mkdir /media/WD640/CRAN/bin/windows
mkdir /media/WD640/CRAN/bin/windows/contrib
mkdir /media/WD640/CRAN/bin/windows/contrib/2.15
rsync -rtlzv --delete cran.r-project.org::CRAN/bin/windows/contrib/2.15/ /media/WD640/CRAN/bin/windows/contrib/2.15
(one line with space before /media)
rsync -rtlzv --delete cran.r-project.org::CRAN/src/ /media/WD640/CRAN/src/

And optionally 

library(tools)
write_PACKAGES("/var/www/CRAN/bin/windows/contrib/2.15", type="win.binary")

We can use du -h to check the folder size.

To create Bioconductor repository

Dry run 

rsync -avn bioconductor.org::2.11 > biocdryrun.txt

Then creates directories before running rsync.

The software part (aka bioc directory) installation: 

mkdir ~/Bioc/packages/2.11/bioc
mkdir ~/Bioc/packages/2.11/bioc/bin
mkdir ~/Bioc/packages/2.11/bioc/bin/windows
mkdir ~/Bioc/packages/2.11/bioc/src
rsync -zrtlv  --delete bioconductor.org::2.11/bioc/bin/windows/ ~/Bioc/packages/2.11/bioc/bin/windows
rsync -zrtlv  --delete bioconductor.org::2.11/bioc/src/ ~/Bioc/packages/2.11/bioc/src

and annotation (aka data directory) part: 

mkdir ~/Bioc/packages/2.11/data
mkdir ~/Bioc/packages/2.11/data/annotation
mkdir ~/Bioc/packages/2.11/data/annotation/bin
mkdir ~/Bioc/packages/2.11/data/annotation/bin/windows
mkdir ~/Bioc/packages/2.11/data/annotation/src
rsync -zrtlv --delete bioconductor.org::2.11/data/annotation/bin/windows/ ~/Bioc/packages/2.11/data/annotation/bin/windows
rsync -zrtlv --delete bioconductor.org::2.11/data/annotation/src/ ~/Bioc/packages/2.11/data/annotation/src

To test local repository

To test CRAN

r <- getOption("repos"); r["CRAN"] <- "http://arraytools.no-ip.org/CRAN"
options(repos=r)
install.packages("pamr")

We can test if the backup server is working or not by installing a package which was removed from the CRAN. For example, 'ForImp' was removed from CRAN in 11/8/2012, but I still a local copy built on R 2.15.2 (run rsync on 11/6/2012). 

r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"
r <- c(r, BRB='http://arraytools.no-ip.org/CRAN')
#                        CRAN                            CRANextra                                  BRB 
# "http://cran.r-project.org" "http://www.stats.ox.ac.uk/pub/RWin"   "http://arraytools.no-ip.org/CRAN"
options(repos=r)
install.packages('ForImp')

Note by default, CRAN mirror is selected interactively. 

> getOption("repos")
                                CRAN                            CRANextra 
                            "@CRAN@" "http://www.stats.ox.ac.uk/pub/RWin"

To test Bioconductor

options("BioC_mirror" = "http://arraytools.no-ip.org/Bioc")
source("http://bioconductor.org/biocLite.R")
# This source biocLite.R line can be placed either before or after the previous 2 lines
biocLite("aCGH")

If there is a connection problem, check folder attributes. 

chmod -R 755 ~/CRAN/bin
  • Note that if a binary package was created for R 2.15.1, then it can be installed under R 2.15.1 but not R 2.15.2. The R console will show package xxx is not available (for R version 2.15.2).
  • For binary installs, the function also checks for the availability of a source package on the same repository, and reports if the source package has a later version, or is available but no binary version is.

So for example, if the mirror does not have contents under src directory, we need to run the following line in order to successfully run install.packages() function. 

options(install.packages.check.source = "no")
  • If we only mirror the essential directories, we can run biocLite() successfully. However, the R console will give some warning
> biocLite("aCGH")
BioC_mirror: http://arraytools.no-ip.org/Bioc
Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
Installing package(s) 'aCGH'
Warning: unable to access index for repository http://arraytools.no-ip.org/Bioc/packages/2.11/data/experiment/src/contrib
Warning: unable to access index for repository http://arraytools.no-ip.org/Bioc/packages/2.11/extra/src/contrib
Warning: unable to access index for repository http://arraytools.no-ip.org/Bioc/packages/2.11/data/experiment/bin/windows/contrib/2.15
Warning: unable to access index for repository http://arraytools.no-ip.org/Bioc/packages/2.11/extra/bin/windows/contrib/2.15
trying URL 'http://arraytools.no-ip.org/Bioc/packages/2.11/bioc/bin/windows/contrib/2.15/aCGH_1.36.0.zip'
Content type 'application/zip' length 2431158 bytes (2.3 Mb)
opened URL
downloaded 2.3 Mb

package ‘aCGH’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\limingc\AppData\Local\Temp\Rtmp8IGGyG\downloaded_packages
Warning: unable to access index for repository http://arraytools.no-ip.org/Bioc/packages/2.11/data/experiment/bin/windows/contrib/2.15
Warning: unable to access index for repository http://arraytools.no-ip.org/Bioc/packages/2.11/extra/bin/windows/contrib/2.15
> library()

CRAN repository directory structure

The information below is specific to R 2.15.2. There are linux and macosx subdirecotries whenever there are windows subdirectory. 

bin/winows/contrib/2.15
src/contrib
   /contrib/2.15.2
   /contrib/Archive
web/checks
   /dcmeta
   /packages
   /views

Bioconductor repository directory structure

The information below is specific to Bioc 2.11. There are linux and macosx subdirecotries whenever there are windows subdirectory. 

bioc/bin/windows/contrib/2.15
    /html
    /install
    /license
    /manuals 
    /news
    /src
    /vignettes
data/annotation/bin/windows/contrib/2.15
               /html
               /licenses
               /manuals
               /src
               /vignettes
     /experiment/bin/windows/contrib/2.15
                /html
                /manuals
                /src/contrib
                /vignettes
extra/bin/windows/contrib
     /html
     /src
     /vignettes

List all R packages from CRAN/Bioconductor

First copy sorttable.js to the desired www location (~/Dropbox/test/ in this example). 

$ rsync -avn bioconductor.org::2.11/data/annotation/bin/windows/contrib/2.15 > annotation
$ R

createPackagehtml <- function(input, jsLoc, output, text1) {
  require(xtable)
  x <- readLines(input)
  ind <- grep("zip", x)
  npac <- length(ind)
  y <- read.table(input, header=F, skip=ind[1]-1, nrows=npac, as.is=T)
  psize <- y[, 2]/2^20
  pname <- basename(y[, 5])
  packdf <- data.frame(size=psize, date=y[, 3], name=pname)
  # Show total number of packages
  text2 <- paste("<H3>Number of total packages:", npac, "</H3>")
  # Add header and include js file
  text3 <- print(xtable(packdf), type="html")
  # insert class='sorttable' in TABLE 
  text3 <- gsub('border=1', "border=1 class='sortable'", text3)
  writeLines(c(text1, text2, text3), output)
}

input <- "annotation"
jsLoc <- "/test/sorttable.js" # relative to /var/www
output <- "~/Dropbox/test/annotation.html"    # absolute path
text1 <- paste("<H2> Bioc/annotation package</H2>\n<script src='",
               jsLoc, "'></script>\n", sep="")
createPackagehtml(input, jsLoc, output, text1)

Similarly for CRAN and other Bioconductor directories 

$ rsync -avn bioconductor.org::2.11/bioc/bin/windows/contrib/2.15 > bioc
$ R

input <- "bioc"
jsLoc <- "/test/sorttable.js" # relative to /var/www
output <- "~/Dropbox/test/bioc.html"    # absolute path
text1 <- paste("<H2> Bioc/software packages</H2>\n<script src='",
               jsLoc, "'></script>\n", sep="")
createPackagehtml(input, jsLoc, output, text1)


$ rsync -avn bioconductor.org::2.11/data/experiment/bin/windows/contrib/2.15 > experiment
$ R

input <- "experiment"
jsLoc <- "/test/sorttable.js" # relative to /var/www
output <- "~/Dropbox/test/experiment.html"    # absolute path
text1 <- paste("<H2> Bioc/experiment packages</H2>\n<script src='",
               jsLoc, "'></script>\n", sep="")
createPackagehtml(input, jsLoc, output, text1)


$ rsync -avn cran.r-project.org::CRAN/bin/windows/contrib/2.15 > cran
$ R

input <- "cran"
jsLoc <- "/test/sorttable.js" # relative to /var/www
output <- "~/Dropbox/test/cran.html"    # absolute path
text1 <- paste("<H2> CRAN packages</H2>\n<script src='",
               jsLoc, "'></script>\n", sep="")
createPackagehtml(input, jsLoc, output, text1)

The end result is shown on

  1. CRAN
  2. Bioc software
  3. Bioc annotation
  4. Bioc experiment

Others

What is the best place to save Rconsole on Windows platform

Put it in C:/Users/USERNAME/Documents folder so no matter how R was upgraded/downgraded, it always find my preference.

Web scraping

http://www.slideshare.net/schamber/web-data-from-r#btnNext

Launch Rstudio

If multiple versions of R was detected, Rstudio can not be launched successfully. A java-like clock will be spinning without a stop. The trick is to click Ctrl key and click the Rstudio at the same time. After done that, it will show up a selection of R to choose from.

RStudio.jpg

List files using regular expression

  • Extension
list.files(pattern = "\\.txt$")
  • Start with
list.files(pattern = "^Something")

Hidden tool: rsync in Rtools

c:\Rtools\bin>rsync -avz "/cygdrive/c/users/limingc/Downloads/a.exe" "/cygdrive/c/users/limingc/Documents/"
sending incremental file list
a.exe

sent 323142 bytes  received 31 bytes  646346.00 bytes/sec
total size is 1198416  speedup is 3.71

c:\Rtools\bin>

And rsync works best when we need to sync folder. 

c:\Rtools\bin>rsync -avz "/cygdrive/c/users/limingc/Downloads/binary" "/cygdrive/c/users/limingc/Documents/"
sending incremental file list
binary/
binary/Eula.txt
binary/cherrytree.lnk
binary/depends64.chm
binary/depends64.dll
binary/depends64.exe
binary/mtputty.exe
binary/procexp.chm
binary/procexp.exe
binary/pscp.exe
binary/putty.exe
binary/sqlite3.exe
binary/wget.exe

sent 4115294 bytes  received 244 bytes  1175868.00 bytes/sec
total size is 8036311  speedup is 1.95

c:\Rtools\bin>rm c:\users\limingc\Documents\binary\procexp.exe
cygwin warning:
  MS-DOS style path detected: c:\users\limingc\Documents\binary\procexp.exe
  Preferred POSIX equivalent is: /cygdrive/c/users/limingc/Documents/binary/procexp.exe
  CYGWIN environment variable option "nodosfilewarning" turns off this warning.
  Consult the user's guide for more details about POSIX paths:
    http://cygwin.com/cygwin-ug-net/using.html#using-pathnames

c:\Rtools\bin>rsync -avz "/cygdrive/c/users/limingc/Downloads/binary" "/cygdrive/c/users/limingc/Documents/"
sending incremental file list
binary/
binary/procexp.exe

sent 1767277 bytes  received 35 bytes  3534624.00 bytes/sec
total size is 8036311  speedup is 4.55

c:\Rtools\bin>

Unforunately, if the destination is a network drive, I could get a permission denied (13) error. See also http://superuser.com/questions/69620/rsync-file-permissions-on-windows

Install rgdal package on ubuntu

sudo apt-get install libgdal1-dev libproj-dev
R
> install.packages("rgdal")

Embedding R

First make sure before 'make' R, R is configured with 

./configure --enable-R-shlib

Reference http://bioconductor.org/help/course-materials/2012/Seattle-Oct-2012/AdvancedR.pdf 

mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ export R_HOME=/home/mli/Downloads/R-2.15.2
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/mli/Downloads/R-2.15.2/lib
mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ g++ embed.c -I/home/mli/Downloads/R-2.15.2/include -L/home/mli/Downloads/R-2.15.2/lib -lR

mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ R CMD ./a.out
WARNING: ignoring environment value of R_HOME

R version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-linux-gnu (64-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.


ns> require(stats); require(graphics)

ns> ns(women$height, df = 5)
                 1            2           3          4             5
 [1,] 0.000000e+00 0.000000e+00  0.00000000 0.00000000  0.0000000000
 [2,] 7.592323e-03 0.000000e+00 -0.08670223 0.26010669 -0.1734044626
 [3,] 6.073858e-02 0.000000e+00 -0.15030440 0.45091320 -0.3006088020
 [4,] 2.047498e-01 6.073858e-05 -0.16778345 0.50335034 -0.3355668952
 [5,] 4.334305e-01 1.311953e-02 -0.13244035 0.39732106 -0.2648807067
 [6,] 6.256681e-01 8.084305e-02 -0.07399720 0.22199159 -0.1479943948
 [7,] 6.477162e-01 2.468416e-01 -0.02616007 0.07993794 -0.0532919575
 [8,] 4.791667e-01 4.791667e-01  0.01406302 0.02031093 -0.0135406187
 [9,] 2.468416e-01 6.477162e-01  0.09733619 0.02286023 -0.0152401533
[10,] 8.084305e-02 6.256681e-01  0.27076826 0.06324188 -0.0405213106
[11,] 1.311953e-02 4.334305e-01  0.48059836 0.12526031 -0.0524087186
[12,] 6.073858e-05 2.047498e-01  0.59541597 0.19899261  0.0007809246
[13,] 0.000000e+00 6.073858e-02  0.50097182 0.27551020  0.1627793975
[14,] 0.000000e+00 7.592323e-03  0.22461127 0.35204082  0.4157555879
[15,] 0.000000e+00 0.000000e+00 -0.14285714 0.42857143  0.7142857143
attr(,"degree")
[1] 3
attr(,"knots")
 20%  40%  60%  80%
60.8 63.6 66.4 69.2
attr(,"Boundary.knots")
[1] 58 72
attr(,"intercept")
[1] FALSE
attr(,"class")
[1] "ns"     "basis"  "matrix"

ns> summary(fm1 <- lm(weight ~ ns(height, df = 5), data = women))

Call:
lm(formula = weight ~ ns(height, df = 5), data = women)

Residuals:
     Min       1Q   Median       3Q      Max
-0.38333 -0.12585  0.07083  0.15401  0.30426

Coefficients:
                    Estimate Std. Error t value Pr(>|t|)
(Intercept)         114.7447     0.2338  490.88  < 2e-16 ***
ns(height, df = 5)1  15.9474     0.3699   43.12 9.69e-12 ***
ns(height, df = 5)2  25.1695     0.4323   58.23 6.55e-13 ***
ns(height, df = 5)3  33.2582     0.3541   93.93 8.91e-15 ***
ns(height, df = 5)4  50.7894     0.6062   83.78 2.49e-14 ***
ns(height, df = 5)5  45.0363     0.2784  161.75  < 2e-16 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.2645 on 9 degrees of freedom
Multiple R-squared: 0.9998,     Adjusted R-squared: 0.9997
F-statistic:  9609 on 5 and 9 DF,  p-value: < 2.2e-16


ns> ## example of safe prediction
ns> plot(women, xlab = "Height (in)", ylab = "Weight (lb)")

ns> ht <- seq(57, 73, length.out = 200)

ns> lines(ht, predict(fm1, data.frame(height=ht)))

ns> ## Don't show:
ns> ## Consistency:
ns> x <- c(1:3,5:6)

ns> stopifnot(identical(ns(x), ns(x, df = 1)),
ns+           identical(ns(x, df=2), ns(x, df=2, knots=NULL)),# not true till 2.15.2
ns+           !is.null(kk <- attr(ns(x), "knots")),# not true till 1.5.1
ns+           length(kk) == 0)

ns> ## End Don't show
ns>
ns>
ns>

The above result can be compared with running

mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ R WARNING: ignoring environment value of R_HOME

R version 2.15.2 (2012-10-26) -- "Trick or Treat" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-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.

> library(splines) > example("ns")

ns> require(stats); require(graphics)

ns> ns(women$height, df = 5) 

                1            2           3          4             5
[1,] 0.000000e+00 0.000000e+00  0.00000000 0.00000000  0.0000000000
[2,] 7.592323e-03 0.000000e+00 -0.08670223 0.26010669 -0.1734044626
[3,] 6.073858e-02 0.000000e+00 -0.15030440 0.45091320 -0.3006088020
[4,] 2.047498e-01 6.073858e-05 -0.16778345 0.50335034 -0.3355668952
[5,] 4.334305e-01 1.311953e-02 -0.13244035 0.39732106 -0.2648807067
[6,] 6.256681e-01 8.084305e-02 -0.07399720 0.22199159 -0.1479943948
[7,] 6.477162e-01 2.468416e-01 -0.02616007 0.07993794 -0.0532919575
[8,] 4.791667e-01 4.791667e-01  0.01406302 0.02031093 -0.0135406187
[9,] 2.468416e-01 6.477162e-01  0.09733619 0.02286023 -0.0152401533

[10,] 8.084305e-02 6.256681e-01 0.27076826 0.06324188 -0.0405213106 [11,] 1.311953e-02 4.334305e-01 0.48059836 0.12526031 -0.0524087186 [12,] 6.073858e-05 2.047498e-01 0.59541597 0.19899261 0.0007809246 [13,] 0.000000e+00 6.073858e-02 0.50097182 0.27551020 0.1627793975 [14,] 0.000000e+00 7.592323e-03 0.22461127 0.35204082 0.4157555879 [15,] 0.000000e+00 0.000000e+00 -0.14285714 0.42857143 0.7142857143 attr(,"degree") [1] 3 attr(,"knots") 

20%  40%  60%  80%

60.8 63.6 66.4 69.2 attr(,"Boundary.knots") [1] 58 72 attr(,"intercept") [1] FALSE attr(,"class") [1] "ns" "basis" "matrix"

ns> summary(fm1 <- lm(weight ~ ns(height, df = 5), data = women))

Call: lm(formula = weight ~ ns(height, df = 5), data = women)

Residuals: 

    Min       1Q   Median       3Q      Max

-0.38333 -0.12585 0.07083 0.15401 0.30426

Coefficients: 

                   Estimate Std. Error t value Pr(>|t|)

(Intercept) 114.7447 0.2338 490.88 < 2e-16 *** ns(height, df = 5)1 15.9474 0.3699 43.12 9.69e-12 *** ns(height, df = 5)2 25.1695 0.4323 58.23 6.55e-13 *** ns(height, df = 5)3 33.2582 0.3541 93.93 8.91e-15 *** ns(height, df = 5)4 50.7894 0.6062 83.78 2.49e-14 *** ns(height, df = 5)5 45.0363 0.2784 161.75 < 2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.2645 on 9 degrees of freedom Multiple R-squared: 0.9998, Adjusted R-squared: 0.9997 F-statistic: 9609 on 5 and 9 DF, p-value: < 2.2e-16


ns> ## example of safe prediction ns> plot(women, xlab = "Height (in)", ylab = "Weight (lb)")

ns> ht <- seq(57, 73, length.out = 200)

ns> lines(ht, predict(fm1, data.frame(height=ht)))

ns> ## Don't show: ns> ## Consistency: ns> x <- c(1:3,5:6)

ns> stopifnot(identical(ns(x), ns(x, df = 1)), ns+ identical(ns(x, df=2), ns(x, df=2, knots=NULL)),# not true till 2.15.2 ns+ !is.null(kk <- attr(ns(x), "knots")),# not true till 1.5.1 ns+ length(kk) == 0)

ns> ## End Don't show ns> ns> ns>

Note that if I follow the instruction to put embed.c at the end of g++ command, I will get an error. 

mli@PhenomIIx6:~/Downloads/R-2.15.2/library/AdvancedR/embedding$ g++ -I/home/mli/Downloads/R-2.15.2/include -L/home/mli/Downloads/R-2.15.2/lib -lR embed.c
/tmp/cc7Vum5j.o: In function `main':
embed.c:(.text+0x1c): undefined reference to `Rf_initEmbeddedR'
embed.c:(.text+0x2b): undefined reference to `Rf_endEmbeddedR'
/tmp/cc7Vum5j.o: In function `doSplinesExample()':
embed.c:(.text+0x45): undefined reference to `Rf_mkString'
embed.c:(.text+0x52): undefined reference to `Rf_install'
embed.c:(.text+0x5d): undefined reference to `Rf_lang2'
embed.c:(.text+0x6d): undefined reference to `Rf_protect'
embed.c:(.text+0x74): undefined reference to `R_GlobalEnv'
embed.c:(.text+0x87): undefined reference to `R_tryEval'
embed.c:(.text+0x91): undefined reference to `Rf_unprotect'
embed.c:(.text+0x9b): undefined reference to `Rf_ScalarLogical'
embed.c:(.text+0xa8): undefined reference to `Rf_install'
embed.c:(.text+0xb3): undefined reference to `Rf_lang2'
embed.c:(.text+0xc3): undefined reference to `Rf_protect'
embed.c:(.text+0xcd): undefined reference to `Rf_install'
embed.c:(.text+0xdc): undefined reference to `CDR'
embed.c:(.text+0xe7): undefined reference to `SET_TAG'
embed.c:(.text+0xee): undefined reference to `R_GlobalEnv'
embed.c:(.text+0x102): undefined reference to `R_tryEval'
embed.c:(.text+0x10c): undefined reference to `Rf_unprotect'
embed.c:(.text+0x116): undefined reference to `Rf_mkString'
embed.c:(.text+0x123): undefined reference to `Rf_install'
embed.c:(.text+0x12e): undefined reference to `Rf_lang2'
embed.c:(.text+0x13e): undefined reference to `Rf_protect'
embed.c:(.text+0x145): undefined reference to `R_GlobalEnv'
embed.c:(.text+0x158): undefined reference to `R_tryEval'
embed.c:(.text+0x162): undefined reference to `Rf_unprotect'
collect2: ld returned 1 exit status

Set up Emacs on Windows

Edit the file C:\Program Files\GNU Emacs 23.2\site-lisp\site-start.el with something like 

(setq-default inferior-R-program-name
              "c:/program files/r/r-2.15.2/bin/i386/rterm.exe")

Database

RMySQL

RSQLite

Not suitable for client/server architecture. The limit is quite large; see here.

Github

R source (read only)

https://github.com/wch/r-source/

github

https://github.com/languages/R

My collection

Tricks

llply() from plyr package

llply is equivalent to lapply except that it will preserve labels and can display a progress bar.

mclapply() from paralle package is a mult-core version of lapply()

But Windows OS can not take advantage of it.

Retrieved from "https://wiki.taichimd.us/index.php?title=R&oldid=789"