Step-By-step instruction for install R from source.Rmd

#load java and gcc

```{bash}
module load java/1.8.0_60
module load gcc/4.9.3

# add the following settings to $HOME/.bashrc, then source $HOME/.bashrc
export PATH=$HOME/packages/bin:$PATH
export LD_LIBRARY_PATH=$HOME/packages/lib:$LD_LIBRARY_PATH
export CFLAGS="-I$HOME/packages/include"
export LDFLAGS="-L$HOME/packages/lib"
export CPLUS_INCLUDE_PATH="$CPLUS_INCLUDE_PATH:$HOME/packages/include"
```

# Install zlib

```{bash}

mkdir $HOME/src
mkdir $HOME/packages

cd ~/src
wget http://www.zlib.net/zlib-1.2.8.tar.gz
tar -xvzf zlib-1.2.8.tar.gz
cd zlib-1.2.8

./configure –prefix=$HOME/packages

vi Makefile:
  CC= gcc  -fPIC
original：CFLAGS=-I$HOME/packages/include 
revised：CFLAGS=-I$HOME/packages/include -fPIC

make
make install
```


# Install bzlib
```{bash}
cd ~/src
wget http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz
tar xzvf bzip2-1.0.6.tar.gz
cd bzip2-1.0.6

vi Makefile:
  CC=gcc -fPIC  
AR=ar
RANLIB=ranlib
LDFLAGS=
  
BIGFILES=-D_FILE_OFFSET_BITS=64
CFLAGS=-fPIC -Wall -Winline -O2 -g $(BIGFILES)  

make -f Makefile-libbz2_so
make clean
make
make -n install PREFIX=$HOME/packages
```

# Install  liblzma
```{bash}
cd ~/src
wget http://tukaani.org/xz/xz-5.2.2.tar.gz
tar xzvf xz-5.2.2.tar.gz
cd xz-5.2.2
./configure --prefix=$HOME/packages
make -j3
make install
```

# Install pcre
```{bash}
cd ~/src
wget ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.38.tar.gz

tar xzvf pcre-8.38.tar.gz
cd pcre-8.38
./configure --enable-utf8 --prefix=$HOME/packages (UTF-8 support  )
make -j3
make install
```
# Install libcurl
```{bash}
cd ~/src
wget --no-check-certificate https://curl.haxx.se/download/curl-7.47.1.tar.gz
tar xzvf curl-7.47.1.tar.gz
cd curl-7.47.1
./configure --prefix=$HOME/packages
make -j3
make install
```

# install R-devel
```{bash}
mkdir src
cd src
wget –no-check-certificate https://stat.ethz.ch/CRAN/src/base-prerelease/R-devel_2016-12-11_r71774.tar.gz

tar xzvf R-devel_2016-12-11_r71774.tar.gz
cd R-devel

./configure --prefix=$HOME/src/R-devel/ --with-cairo  --with-jpeglib --with-readline --with-tcltk  --with-blas --enable-BLAS-shlib --with-lapack --enable-R-profiling '--enable-R-shlib' '--enable-memory-profiling'

make
make install
```


# When You need install new package, you need specify the library:

```{r}
.libPaths()

# select path
install.packages("parallel",lib=.libPaths()[2])
```
## or
```{bash}
emacs .Renviron
```
##add
```{bash}
R_LIBS_USER=$HOME/R/lib64/R/library to .Renviron
```
## install   R-3.3.1
```{bash}
wget http://cran.r-project.org/src/base/R-3/R-3.3.1.tar.gz
tar -xzf R-3.3.1.tar.gz
cd R-3.3.1
./configure --prefix=$HOME/src/R-3.3.1/ --with-cairo  --with-jpeglib --with-readline --with-x --with-tcltk  --with-blas --enable-BLAS-shlib --with-lapack --enable-R-profiling '--enable-R-shlib' '--enable-memory-profiling' 
 make
 
 #to install R to $HOME, using the following command
  make prefix=$HOME/R install
 
 
 #set path for R
 emacs ~/.bashrc, 
 add line:
 export PATH=$HOME/R/bin/R:PATH
 source ~/.bashrc
 
 #check where is R
 which R
 
```

# Install R development verwsion for windows
```{bash}

https://cran.r-project.org/bin/windows/base/rdevel.html

```

# Some Problems for using gfortran
```{bash}

#Problems:
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lquadmath I had your same problem (in OS X Yosemite), and (unfortunately) painstakingly recreated 

#Solution:
brew uninstall gcc
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /

```
# To install ChipSeq, you need to do on terminal liking this: 
```{bash}
export _JAVA_OPTIONS="-Xss2560k -Xmx2g"
```