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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!

  • --prefix=$HOME/Programme and -L/$HOME/Programme/zlib-1.2.11/lib look like two different things, where is zlib actually? (And does it ship with a *.pc file so you can use pkg-config?) – thrig Feb 8 '17 at 14:49
  • @thrig, sorry, I did not put my configure information correctly, I have edited it so as to make it exactly like what I have done. – Jun Feb 8 '17 at 14:58
  • 2
    For the "not found" shared libraries a quick hack would be to set LD_LIBRARY_PATH to include the necessary lib directories. – thrig Feb 8 '17 at 17:00
  • If it were me, I'd try installing the dependencies with a common prefix such as --prefix=/opt (rather than separate subdirectories --prefix=/opt/zlib-1.2.11 and so on), and then setting an appropriate search path for pkg-config e.g. export PKG_CONFIG_PATH=/opt/lib/pkgconfig:$PKG_CONFIG_PATH before configuring R – steeldriver Feb 8 '17 at 17:46
  • @thrig. TKS! it worked! – Jun Feb 9 '17 at 2:39
5

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.

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