How to install R 3.3.1 in the own directory

configurersoftware installation

This is a somewhat duplicate question (see How to set PATH for R installed in my directory ) but I did meet some new problem with new version of R.

I was trying install a new version of R (R 3.3.1) in my own directory.
I followed my previous installation flow

But I met an issue which I did not have before.

./configure --prefix=$HOME/Programme/R-3.3.1 
.......
checking for zlib.h... yes
checking if zlib version >= 1.2.5... no
checking whether zlib support suffices... configure: error: zlib library and headers are required

it seems that the zlib version is too low, so I installed the current version of zlib

tar xvf zlib-1.2.11.tar.gz
cd zlib-1.2.11
 ./configure --prefix=$HOME/Programme/zlib-1.2.11
make && make install

then I tried to do the configure for R again like:

./configure --prefix=$HOME/Programme/R-3.3.1 --enable-R-shlib LDFLAGS="-L/$HOME/Programme/zlib-1.2.11/lib" CPPFLAGS="-I/$HOME/Programme/zlib-1.2.11/include"

still I had the same error:

checking if zlib version >= 1.2.5... no
checking whether zlib support suffices... configure: error: zlib library and headers are required

Then I noticed someone circumvent the problem by modify the configure file of R
I followed that example, solved the zlib error.
but other errors ensued. To put a long story short,
I installed other dependent libraries

tar xvf zlib-1.2.11.tar.gz
cd zlib-1.2.11
./configure --prefix=$HOME$Programme/zlib-1.2.11
make && make install

tar zxvf bzip2-1.0.6.tar.gz
cd bzip2-1.0.6
make -f Makefile-libbz2_so
make clean
# modify the Makefile (original: CC=gcc after modification: CC=gcc -fPIC) as suggested [here][2]
make 
make install PREFIX=/opt/bzip2-1.0.6

tar zxvf xz-5.2.3.tar.gz
cd /root/xz-5.2.3
./configure --prefix=$HOME/Programme/xz-5.2.3
make -j3
make install

tar zxvf pcre-8.40.tar.gz
cd /root/pcre-8.40
./configure  --prefix=$HOME/Programme/pcre-8.40  --enable-utf8
make -j3 && make install

tar zxvf curl-7.52.1.tar.gz
cd /root/curl-7.52.1
./configure  --prefix=$HOME/Programme/curl-7.52.1
make && make install

./configure --prefix=$HOME/Programme/R-3.3.1 --enable-R-shlib LDFLAGS="-L/$HOME/Programme/zlib-1.2.11/lib -L/$HOME/Programme/bzip2-1.0.6/lib -L/$HOME/Programme/xz-5.2.3/lib -L/$HOME/Programme/pcre-8.40/lib -L/$HOME/Programme/curl-7.52.1/lib" CPPFLAGS="-I/$HOME/Programme/zlib-1.2.11/include -I/$HOME/Programme/bzip2-1.0.6/include -I/$HOME/Programme/xz-5.2.3/include -I/$HOME/Programme/pcre-8.40/include -I/$HOME/Programme/curl-7.52.1/include"

The configure seemed to work:

R is now configured for x86_64-pc-linux-gnu

  Source directory:          .
  Installation directory:    $HOME/Programme/R-3.3.1

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

  C++ compiler:              g++  -g -O2
  C++11 compiler:            g++  -std=c++0x -g -O2
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:         

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

  Capabilities skipped:      TIFF
  Options not enabled:       memory profiling
  Recommended packages:      yes

but when I call

make && make install

still "make" could not make it until the end:

...
  gcc -std=gnu99 -Wl,--export-dynamic -fopenmp  -L../../lib -L//HOME/Programme/zlib-1.2.11/lib -L//HOME/Programme/bzip2-1.0.6/lib -L//HOME/Programme/xz-5.2.3/lib -L//HOME/Programme/pcre-8.40/lib -L//HOME/Programme/curl-7.52.1/lib -o R.bin Rmain.o  -lR -lRblas
/usr/bin/ld: warning: libpcre.so.1, needed by ../../lib/libR.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: liblzma.so.5, needed by ../../lib/libR.so, not found (try using -rpath or -rpath-link)
../../lib/libR.so: undefined reference to `pcre_fullinfo'
../../lib/libR.so: undefined reference to `lzma_lzma_preset@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_alone_decoder@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_crc64@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_raw_encoder@XZ_5.0'
../../lib/libR.so: undefined reference to `pcre_config'
../../lib/libR.so: undefined reference to `lzma_code@XZ_5.0'
../../lib/libR.so: undefined reference to `lzma_stream_decoder@XZ_5.0'
../../lib/libR.so: undefined reference to `pcre_free'
../../lib/libR.so: undefined reference to `lzma_raw_decoder@XZ_5.0'
../../lib/libR.so: undefined reference to `pcre_exec'
../../lib/libR.so: undefined reference to `lzma_version_string@XZ_5.0'
../../lib/libR.so: undefined reference to `pcre_maketables'
../../lib/libR.so: undefined reference to `lzma_stream_encoder@XZ_5.0'
../../lib/libR.so: undefined reference to `pcre_compile'
../../lib/libR.so: undefined reference to `pcre_study'
../../lib/libR.so: undefined reference to `pcre_version'
../../lib/libR.so: undefined reference to `lzma_end@XZ_5.0'
collect2: error: ld returned 1 exit status

...
make: *** [R] Error 1

Follow up:
Based on thrig 's suggestion, I added the lines below to my .cshrc file

setenv LD_LIBRARY_PATH $HOME/Programme/pcre-8.40/lib
setenv LD_LIBRARY_PATH $HOME/Programme/xz-5.2.3/lib

and

source .cshrc

problem solved!

Best Answer

This is the solution to the issue mentioned above

Follow the example to modify the configure file of R Then:

tar xvf zlib-1.2.11.tar.gz
cd zlib-1.2.11
./configure --prefix=$HOME/Programme/zlib-1.2.11
make && make install

tar zxvf bzip2-1.0.6.tar.gz
cd bzip2-1.0.6
make -f Makefile-libbz2_so
make clean

modify the Makefile (original: CC=gcc after modification: CC=gcc -fPIC) as suggested here

make 
make install PREFIX=$HOME/Programme/bzip2-1.0.6

tar zxvf xz-5.2.3.tar.gz
cd xz-5.2.3
./configure --prefix=$HOME/Programme/xz-5.2.3
make -j3
make install

tar zxvf pcre-8.40.tar.gz
cd pcre-8.40
./configure  --prefix=$HOME/Programme/pcre-8.40  --enable-utf8
make -j3 && make install

tar zxvf curl-7.52.1.tar.gz
cd curl-7.52.1
./configure  --prefix=$HOME/Programme/curl-7.52.1 --with-ssl
make && make install

./configure --prefix=$HOME/Programme/R-3.3.1 --enable-R-shlib LDFLAGS="-L/$HOME/Programme/zlib-1.2.11/lib -L/$HOME/Programme/bzip2-1.0.6/lib -L/$HOME/Programme/xz-5.2.3/lib -L/$HOME/Programme/pcre-8.40/lib -L/$HOME/Programme/curl-7.52.1/lib" CPPFLAGS="-I/$HOME/Programme/zlib-1.2.11/include -I/$HOME/Programme/bzip2-1.0.6/include -I/$HOME/Programme/xz-5.2.3/include -I/$HOME/Programme/pcre-8.40/include -I/$HOME/Programme/curl-7.52.1/include"

Add the lines below to my .cshrc file

setenv LD_LIBRARY_PATH $HOME/Programme/pcre-8.40/lib
setenv LD_LIBRARY_PATH $HOME/Programme/xz-5.2.3/lib

and

source .cshrc

Now go to R-3.3.1 directory:

make && make install

it should work.

Related Solutions

Install R in the own directory

The easiest way to do this is to install R from source:

$ wget http://cran.rstudio.com/src/base/R-3/R-3.4.1.tar.gz
$ tar xvf R-3.4.1.tar.gz
$ cd R-3.4.1
$ ./configure --prefix=$HOME/R
$ make && make install

The second-to-last step is the critical one. It configures R to be installed into a subdirectory of your own home directory.

To run it on Linux, macOS and similar systems, add $HOME/R/bin to your PATH. Then, shell commands like R and Rscript will work.

On macOS, you have another alternative: build R.app and install it into your user's private Applications folder. You need to have Xcode installed to do this.

You might consider giving --prefix=$HOME instead. That installs R at the top level of your home directory, so that the R and Rscript binaries end up in $HOME/bin, which is likely already in your user's PATH. The downside is that it makes later uninstallation harder, since R would be intermingled among your other $HOME contents.

(If this is the first thing you've installed to $HOME/bin, you might have to log out and back in to get this in your PATH, since it's often added conditionally only if $HOME/bin exists at login time.)

This general pattern applies to a large amount of Unix software you can install from source code. If the software has a configure script, it probably understands the --prefix option, and if not, there is usually some alternative with the same effect.

These features are common for a number of reasons. In decreasing order of likelihood, in my experience:

The safe default (/usr/local) is not the right $prefix in all situations. Circumstances might dictate something else such as /usr, /opt/$PKGNAME, etc.
Binary package building systems (RPM, DEB, PKG, Cygport...) typically build and install the package into a special staging directory, then pack that up in such a way that it expands into the desired installation location.
Your case, where you can't get root to install the software into a typical location, so you install into $HOME instead.

Ubuntu – How to Install R’s devtools and digitize

httr imports the openssl package which needs as system requirement libssl-dev (sudo apt install libssl-dev)

------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
 * deb: libssl-dev (Debian, Ubuntu, etc)
...

The curl package needs as system requirement libcurl4-openssl-dev:

------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
...

So, to install you will need to run:

sudo apt-get install libssl-dev
sudo apt-get install libcurl4-openssl-dev

Then start an R shell with sudo R and:

install.packages('httr')
install.packages('git2r')
install.packages('devtools')
library(devtools)
install_github('tpoisot/digitize')

Best Answer

Related Solutions

Install R in the own directory

Ubuntu – How to Install R’s devtools and digitize

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