R 安装报错问题（解决lib的缺少和版本问题）

redhat6 上编译安装R语言：版本：3.3.2

1) 下载：

R-3.3.2.tar.gz（https://mirrors.tuna.tsinghua.edu.cn/CRAN/    点击：R-3.3.2.tar.gz 下载：最新版！）

 

2）安装：

解压：

cd /software

tar -zxvf R-3.3.2.tar.gz

mkdir -p  /home/liyg/software/R

cd R-3.3.2
./configure --prefix=/home/liyg/software/R --enable-R-shlib

3) 报错和解决方法：./configure --prefix=/home/liyg/software/R --enable-R-shlib

a) 报错如下：

configure:5783: result: no
configure:5846: checking for cc
configure:5893: result: no
configure:5949: checking for cl.exe
configure:5979: result: no
configure:6003: error: in `/software/R-3.3.2':
configure:6005: error: no acceptable C compiler found in $PATH
See `config.log' for more details

解决方法：yum install gcc

 

b) 报错如下：

 checking for fc... no
configure: error: No F77 compiler found

解决方法：yum install gcc-gfortran

c)报错如下：

checking how to run the C++ preprocessor... /lib/cpp
configure: error: in `/software/R-3.3.2':
configure: error: C++ preprocessor "/lib/cpp" fails sanity check
See `config.log' for more details

解决方法：yum install gcc gcc-c++

 

d)报错如下：

--with-readline=yes (default) and headers/libs are not available

解决方法：yum install readline-devel

e)报错如下：

 –with-x=yes (default) and X11 headers/libs are not available

解决方法：yum install libXt-devel

f)报错如下：

 checking for rpc/xdr.h... yes
checking for XDR support... yes
checking for inflateInit2_ in -lz... no
checking whether zlib support suffices... configure: error: zlib library and headers are required

解决方法：yum install zlib-devel

                    yum -y install bzip2-devel 

 

g)报错如下：zlib版本太低！

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

解决方法：下载：http://zlib.net/zlib-1.2.8.tar.gz

                    tar xzvf zlib-1.2.8.tar.gz

                    cd zlib-1.2.8

                    ./configure --prefix=$HOME/packages

                  设置环境变量：

          export PATH=/software/packages/bin:$PATH
  export LD_LIBRARY_PATH=/software/packages/lib:$LD_LIBRARY_PATH 
  export CFLAGS="-fPIC -I/software/packages/include" 
 export LDFLAGS="-fPIC -L/software/packages/lib"

h) 报错如下：bzip2 版本太低

checking bzlib.h presence... yes
 checking for bzlib.h... yes
 checking if bzip2 version >= 1.0.6... no
 checking whether bzip2 support suffices... configure: 
error: bzip2 library and headers are required

解决方法：下载：http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz

                   tar -zxvf bzip2-1.0.6.tar.gz

        cd bzip2-1.0.6

                    make

                     make install PREFIX=/software/packages

                      make -f Makefile-libbz2_so   //建立共享library,可能会报错！后面有解决方法！

i) 报错如下：

checking for lzma_version_number in -llzma... no
configure: error: "liblzma library and headers are required"

解决方法：yum -y install xz-devel.x86_64

j）报错如下：版本太低

checking if lzma version >= 5.0.3... no
configure: error: "liblzma library and headers are required"

解决方法：下载：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=/software/packages

make -j3
make install

k)报错如下：版本太低

checking if PCRE version >= 8.10, < 10.0 and has UTF-8 support... no
checking whether PCRE support suffices... configure: error: pcre >= 8.10 library and headers are required

解决方法：下载：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 --prefix=/software/packages
  make -j3
  make install

l)报错如下：编码不对

checking if PCRE version >= 8.10, < 10.0 and has UTF-8 support... no
checking whether PCRE support suffices... configure: error: pcre >= 8.10 library and headers are required

解决方法：    cd pcre-8.38

./configure --enable-utf8 --prefix=/software/packages
make 
make install

m）错误如下：

checking for curl-config... no
checking curl/curl.h usability... no
checking curl/curl.h presence... no
checking for curl/curl.h... no
configure: error: libcurl >= 7.28.0 library and headers are required with support for https

解决办法：下载： https://curl.haxx.se/download/curl-7.47.1.tar.gz

           ./configure --prefix=/software/packages
   make -j3
   make install

n)错误如下：https是安全的需要安装：openssl

checking if libcurl is version 7 and >= 7.28.0... yes
checking if libcurl supports https... no
configure: error: libcurl >= 7.28.0 library and headers are required with support for https

解决方法：下载：openssl-1.0.1u.tar.gz

          tar -xzvf openssl-1.0.1u.tar.gz
cd openssl-1.0.1u
./config -fPIC --prefix=/usr/local/openssl enable-shared
./config -t
make && make install

       设置环境变量： export OPENSSL=/usr/local/openssl/bin
                 export PATH=$OPENSSL:$PATH:$HOME/bin 

       重新安装curl:指定openssl

        ./configure --prefix=/software/packages --with-openssl-include=/usr/local/openssl/include/ --with-openssl-lib=/usr/local/openssl/lib

   make -j3

make install

4）重新编译：

cd R-3.3.2
./configure --prefix=/home/liyg/software/R --enable-R-shlib

编译成功：结果如下：

Source directory:          .
  Installation directory:    /home/liyg/software/R


  C compiler:                gcc -std=gnu99  -I/software/packages/include
  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
  External libraries:        readline, curl
  Additional capabilities:   NLS
  Options enabled:           shared R library, shared BLAS, R profiling


  Capabilities skipped:      PNG, JPEG, TIFF, cairo, ICU
  Options not enabled:       memory 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

5）执行编译： make

报错如下：

gcc -std=gnu99 -shared -fopenmp -L/software/packages/lib  -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o   `ls ../unix/*.o ../appl/*.o ../nmath/*.o` ../extra/tre/libtre.a    -L../../lib -lRblas -lgfortran -lm   -lreadline  -lpcre -llzma -lbz2 -lz -lrt -ldl -lm  
/usr/bin/ld: /software/packages/lib/libbz2.a(bzlib.o): relocation R_X86_64_32S against `.text' can not be used when making a shared object; recompile with -fPIC
/software/packages/lib/libbz2.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libR.so] Error 1
make[3]: Leaving directory `/software/R-3.3.2/src/main'
make[2]: *** [R] Error 2
make[2]: Leaving directory `/software/R-3.3.2/src/main'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/software/R-3.3.2/src'
make: *** [R] Error 1
-fPIC --prefix=/usr/local/openssl enable-shared

解决方法：重新编译安装libbz2！并指定 -fPIC！！！共享library

步骤：

第一：设置环境变量：注意：CFLAGS和LDFLAGS 加上 -fPIC  如下：

export PATH=/software/packages/bin:$PATH
  export LD_LIBRARY_PATH=/software/packages/lib:$LD_LIBRARY_PATH 
  export CFLAGS="-fPIC -I/software/packages/include" 
  export LDFLAGS="-fPIC  -L/software/packages/lib" 

第二：指定-fPIC编译：重新编译步骤：h)

                    cd bzip2-1.0.6

 

                    make CC='gcc -fPIC'   

                    make install PREFIX=/software/packages

                    make -f Makefile-libbz2_so   //建立共享library,不会报错说明正确

第三：重新编译R: 

           cd /software/R-3.3.2

     ./configure --prefix=/home/liyg/software/R --enable-R-shlib

               make  //需要等比较长时间

  结果：终于编译成功！！！！！太不容易了！！

                结果信息如下：

trying to compile and link a JNI program 
detected JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
make[2]: Entering directory `/tmp/Rjavareconf.BzLkuk'
gcc -std=gnu99 -I/software/R-3.3.2/include -DNDEBUG -I/usr/java/jdk1.7.0_67-cloudera/include -I/usr/java/jdk1.7.0_67-cloudera/include/linux -I/usr/local/include    -fpic  -fPIC -I/software/packages/include  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/software/R-3.3.2/lib -fPIC -L/software/packages/lib -o conftest.so conftest.o -L/usr/java/jdk1.7.0_67-cloudera/jre/lib/amd64/server -ljvm -L/software/R-3.3.2/lib -lR
make[2]: Leaving directory `/tmp/Rjavareconf.BzLkuk'
JAVA_HOME        : /usr/java/jdk1.7.0_67-cloudera
Java library path: $(JAVA_HOME)/jre/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
Updating Java configuration in /software/R-3.3.2
Done.
make[1]: Leaving directory `/software/R-3.3.2'

6） 执行make install 即可：

结果如下：

make[3]: Leaving directory `/software/R-3.3.2/src/modules/internet'
make[3]: Entering directory `/software/R-3.3.2/src/modules/lapack'
make[3]: Leaving directory `/software/R-3.3.2/src/modules/lapack'
make[3]: Entering directory `/software/R-3.3.2/src/modules/X11'
make[3]: Leaving directory `/software/R-3.3.2/src/modules/X11'
make[2]: Leaving directory `/software/R-3.3.2/src/modules'
make[2]: Entering directory `/software/R-3.3.2/src/library'
mkdir -p -- /home/liyg/software/R/lib64/R/library
installing packages ...
  building HTML index ...
make[2]: Leaving directory `/software/R-3.3.2/src/library'
make[1]: Leaving directory `/software/R-3.3.2/src'
make[1]: Entering directory `/software/R-3.3.2/tests'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/software/R-3.3.2/tests'