My goal is to install R on a EC2 Amazon Linux AMI cluster that I have built.
I have logged into the master and:
When in the home directory:
$ sudo yum -y install make libX11-devel.* libICE-devel.* libSM-devel.* libdmx-devel.* libx* xorg-x11* libFS* libX* readline-devel gcc-gfortran gcc-c++ texinfo tetex
wget https://cran.r-project.org/src/base/R-3/R-3.2.2.tar.gz
tar zxf R-3.2.2.tar.gz && cd R-3.2.2
./configure
make
make install
I start to see somethings that look like errors after I run the ./configure. Then make: *** No targets specified and no makefile found. Stop.
[
ec2-user#ip-172-31-31-243 R-3.2.2]$ ./configure
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... found
checking for working autoconf... found
checking for working automake... found
checking for working autoheader... found
checking for gawk... gawk
checking whether ln -s works... yes
checking for bison... no
checking for byacc... no
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... /bin/gtar
checking for tex... no
checking for pdftex... no
configure: WARNING: you cannot build PDF versions of the R manuals
checking for pdflatex... no
configure: WARNING: you cannot build PDF versions of vignettes and help pages
checking for makeindex... no
checking for texi2any... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... no
checking for kpsewhich... no
checking for latex inconsolata package... checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /bin/gzip
checking for bzip2... /usr/bin/bzip2
checking for firefox... no
checking for mozilla... no
checking for galeon... no
checking for opera... no
checking for xdg-open... no
checking for kfmclient... no
checking for gnome-moz-remote... no
checking for open... /usr/bin/open
using default browser ... /usr/bin/open
checking for acroread... no
checking for acroread4... no
checking for xdg-open... no
checking for evince... no
checking for xpdf... no
checking for gv... no
checking for gnome-gv... no
checking for ggv... no
checking for okular... no
checking for kpdf... no
checking for open... /usr/bin/open
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc needs -traditional... no
checking how to run the C preprocessor... gcc -E
checking for gfortran... no
checking for f95... no
checking for fort... no
checking for xlf95... no
checking for ifort... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for gfortran... no
checking for ftn... no
checking for g95... no
checking for f90... no
checking for xlf90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for g77... no
checking for f77... no
checking for xlf... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for fc... no
configure: error: No F77 compiler found
[ec2-user#ip-172-31-31-243 R-3.2.2]$ make
make: *** No targets specified and no makefile found. Stop.
Related
I am trying to install and older version of R (3.2.1), and am following the instructions on this page: https://www.miskatonic.org/2015/06/23/installing-r-from-source/
As suggested by the webpage, I uninstalled R
usr#ubuntu:/usr/lib/R/R-3.2.1$ R
The program 'R' is currently not installed. You can install it by typing:
sudo apt install r-base-core
And I am fairly positive that "make" is installed:
usr#ubuntu:/usr/lib/R/R-3.2.1$ sudo apt-get install make
Reading package lists... Done
Building dependency tree
Reading state information... Done
make is already the newest version (4.1-6).
0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
When I run
$ ./configure
$ make
I get the following (I am not sure what is normal and what is an error message). In addition, the following files are created: Makeconf.in, Makefile.fw, Makefile.in
usr#ubuntu:/usr/lib/R/R-3.2.1$ sudo ./configure
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... found
checking for working autoconf... found
checking for working automake... found
checking for working autoheader... found
checking for gawk... gawk
checking whether ln -s works... yes
checking for bison... no
checking for byacc... no
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... no
checking for gnutar... no
checking for tar... /bin/tar
checking for tex... no
checking for pdftex... no
configure: WARNING: you cannot build PDF versions of the R manuals
checking for pdflatex... no
configure: WARNING: you cannot build PDF versions of vignettes and help pages
checking for makeindex... no
checking for texi2any... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... no
checking for kpsewhich... no
checking for latex inconsolata package... checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /bin/gzip
checking for bzip2... /bin/bzip2
checking for firefox... /usr/bin/firefox
using default browser ... /usr/bin/firefox
checking for acroread... no
checking for acroread4... no
checking for xdg-open... /usr/bin/xdg-open
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc needs -traditional... no
checking how to run the C preprocessor... gcc -E
checking for f95... f95
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether f95 accepts -g... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc accepts -fvisibility... yes
checking whether f95 accepts -fvisibility... yes
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking for Objective C++ compiler... trying some possibilities
checking whether g++ can compile ObjC++... no
checking whether can compile ObjC++... no
no working ObjC++ compiler found
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU Fortran 77 compiler... (cached) yes
checking whether f95 accepts -g... (cached) yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for f95 option to produce PIC... -fPIC
checking if f95 PIC flag -fPIC works... yes
checking if f95 static flag -static works... yes
checking if f95 supports -c -o file.o... yes
checking if f95 supports -c -o file.o... (cached) yes
checking whether the f95 linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... no
checking readline/history.h presence... no
checking for readline/history.h... no
checking readline/readline.h usability... no
checking readline/readline.h presence... no
checking for readline/readline.h... no
checking for rl_callback_read_char in -lreadline... no
checking for main in -lncurses... yes
checking for rl_callback_read_char in -lreadline... no
checking for history_truncate_file... no
configure: error: --with-readline=yes (default) and headers/libs are not available
usr#ubuntu:/usr/lib/R/R-3.2.1$ make
make: *** No targets specified and no makefile found. Stop.
I also tried following the instructions here: Installing older version of R, but the R version 3.2.1 is NOT listed in the directory (xenial).
Does anyone have any suggestions on how I can finish installing this version of R? I appreciate the help - ahhn
EDIT:
I am now receiving the following when I get to the "./configure" step:
usr#ubuntu:~/Downloads/R-3.2.1$ ./configure --prefix=/home/usr/Downloads/R3.2.1_VERSION --enable-R-shlib --with-blas --with-lapack
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... found
checking for working autoconf... found
checking for working automake... found
checking for working autoheader... found
checking for gawk... gawk
checking whether ln -s works... yes
checking for bison... no
checking for byacc... no
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... no
checking for gnutar... no
checking for tar... /bin/tar
checking for tex... no
checking for pdftex... no
configure: WARNING: you cannot build PDF versions of the R manuals
checking for pdflatex... no
configure: WARNING: you cannot build PDF versions of vignettes and help pages
checking for makeindex... no
checking for texi2any... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... no
checking for kpsewhich... no
checking for latex inconsolata package... checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /bin/gzip
checking for bzip2... /bin/bzip2
checking for firefox... /usr/bin/firefox
using default browser ... /usr/bin/firefox
checking for acroread... no
checking for acroread4... no
checking for xdg-open... /usr/bin/xdg-open
checking for notangle... false
checking for realpath... /usr/bin/realpath
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc needs -traditional... no
checking how to run the C preprocessor... gcc -E
checking for f95... f95
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether f95 accepts -g... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc accepts -fvisibility... yes
checking whether f95 accepts -fvisibility... yes
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking for Objective C++ compiler... trying some possibilities
checking whether g++ can compile ObjC++... no
checking whether can compile ObjC++... no
no working ObjC++ compiler found
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU Fortran 77 compiler... (cached) yes
checking whether f95 accepts -g... (cached) yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for f95 option to produce PIC... -fPIC
checking if f95 PIC flag -fPIC works... yes
checking if f95 static flag -static works... yes
checking if f95 supports -c -o file.o... yes
checking if f95 supports -c -o file.o... (cached) yes
checking whether the f95 linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... no
checking readline/history.h presence... no
checking for readline/history.h... no
checking readline/readline.h usability... no
checking readline/readline.h presence... no
checking for readline/readline.h... no
checking for rl_callback_read_char in -lreadline... no
checking for main in -lncurses... yes
checking for rl_callback_read_char in -lreadline... no
checking for history_truncate_file... no
configure: error: --with-readline=yes (default) and headers/libs are not available
usr#ubuntu:~/Downloads/R-3.2.1$ make
make: *** No targets specified and no makefile found. Stop.
EDIT 2:
I am running into errors when I try to install readline-devel and xorg-dev:
usr#ubuntu:~$ sudo apt-get install readline-devel
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package readline-devel
usr#ubuntu:~$ sudo apt-get install xorg-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
xorg-dev : Depends: libxaw7-dev but it is not going to be installed
Depends: libxcursor-dev but it is not going to be installed
Depends: libxfont-dev but it is not going to be installed
Depends: libxft-dev but it is not going to be installed
Depends: libxpm-dev but it is not going to be installed
Depends: xserver-xorg-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
Please try the following steps:
First make sure if you have libxt-dev and jdk.
dpkg -l <package name>
If not do these following commands:
sudo apt -f install && sudo apt update && sudo apt dist-upgrade
sudo apt-get install build-essential
sudo apt-get install fort77
sudo apt-get install xorg-dev
sudo apt-get install liblzma-dev libblas-dev gfortran
sudo apt-get install gcc-multilib
sudo apt-get install gobjc++
sudo apt-get install aptitude
sudo aptitude install libreadline-dev
sudo apt-get install libxt-dev
sudo apt-get install default-jdk
Then download your preferred R version and do as follows:
wget https://cran.r-project.org/src/base/R-3/R-3.2.1.tar.gz
mkdir R-3.2.1
mv R-3.2.1.tar.gz R-3.2.1/
cd R-3.2.1/
tar -xzvf R-3.2.1.tar.gz
Next, make another folder for R's binary version and use the to that folder here:
mkdir <full path>/R3.2.1_VERSION
Build R from source, please make sure to add the full path in prefix
./configure --prefix=<full path>/R3.2.1_OLDERVERSION --enable-R-shlib --with-blas --with-lapack
make
sudo make install
Once, you are finished, please set the environment variable to make sure the right version of R is called
export PATH=<full path>/R3.2.1_VERSION/bin:$PATH
If everything went smoothly then you can see your current R version as 3.2.1 when you run R.
If you want to switch to another version of R then change the environment variable to your preferred version of R package in your account as follows:
export PATH=<full path>/R<your preferred>_VERSION/bin:$PATH
I want to install R in Linux Server. I was going through the site: https://cran.r-project.org/doc/manuals/r-release/R-admin.html.
When I run the ./configure command I am getting the following:
[root#sd-cd1a-b9e0 R-devel]# ./configure
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking whether ln -s works... yes
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... /bin/gtar
checking for tex... no
checking for pdftex... no
configure: WARNING: you cannot build PDF versions of the R manuals
checking for pdflatex... no
configure: WARNING: you cannot build PDF versions of vignettes and help pages
checking for makeindex... no
checking for texi2any... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... no
checking for kpsewhich... no
checking for latex inconsolata package... checking for unzip...
/usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /bin/gzip
checking for bzip2... /usr/bin/bzip2
checking for firefox... no
checking for mozilla... no
checking for galeon... no
checking for opera... no
checking for xdg-open... no
checking for kfmclient... no
checking for gnome-moz-remote... no
checking for open... /usr/bin/open
using default browser ... /usr/bin/open
checking for acroread... no
checking for acroread4... no
checking for xdg-open... no
checking for evince... no
checking for xpdf... no
checking for gv... no
checking for gnome-gv... no
checking for ggv... no
checking for okular... no
checking for kpdf... no
checking for open... /usr/bin/open
checking for working aclocal... missing
checking for working autoconf... missing
checking for working autoheader... missing
checking for bison... no
checking for byacc... no
checking for yacc... no
checking for notangle... false
checking for realpath... false
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc needs -traditional... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking how to run the C preprocessor... gcc -E
checking for gfortran... gfortran
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether gfortran accepts -g... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether g++ -g -O2 can compile C++ code... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc accepts -fvisibility... yes
checking whether gfortran accepts -fvisibility... yes
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking whether g++ can compile ObjC++... no
checking whether can compile ObjC++... no
checking for Objective C++ compiler... no working ObjC++ compiler found
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1966080
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu
format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format...
func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver #FILE support... #
checking for strip... strip
checking for ranlib... ranlib
checking for gawk... gawk
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... no
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/bin/ld -m elf_x86_64) supports
shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... no
checking readline/history.h presence... no
checking for readline/history.h... no
checking readline/readline.h usability... no
checking readline/readline.h presence... no
checking for readline/readline.h... no
checking for rl_callback_read_char in -lreadline... no
checking for main in -lncurses... no
checking for main in -ltermcap... no
checking for main in -ltermlib... no
checking for rl_callback_read_char in -lreadline... no
configure: error: --with-readline=yes (default) and headers/libs are not
available
When I run the make command I am getting the following issue:
[root#sd-cd1a-b9e0 R-devel]# make
make: *** No targets specified and no makefile found. Stop.
Can anyone please help how to get rid of this issue?
Your ./configure command failed as you can see at the bottom of the log:
configure: error: --with-readline=yes (default) and headers/libs are not
available
Here's SO answer to the error above:
error: --with-readline=yes (default) and headers/libs are not available
Even though I am a bit late here but I think this is still a quite common problem. What you have seen is that R is complaining about missing dependencies. You need to install A LOT OF packages before you are able to compile it. Here is a full list of them:
https://github.com/Jiefei-Wang/Painless-R-compilation-and-installation-on-Ubuntu
If you are using Ubuntu this is just a matter of copy and paste. Otherwise, you may need to take some time and figure out how to install them on your machine.
Please could you help me, i try to install this packages in R and my OS is linux ubuntu 15.04
devtools
rjava
but i get some error, for example, when i install devtools
Warning in install.packages :
installation of package ‘git2r’ had non-zero exit status
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
and when i install rjava
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc -std=gnu99 supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver : '/usr/bin/jar'
compiler : '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-7-openjdk-i386/jre/../include'
java libs : '-L/usr/lib/jvm/java-7-openjdk-i386/jre/lib/i386/client -ljvm'
checking whether Java run-time works...
Picked up JAVA_TOOL_OPTIONS: -javaagent:/usr/share/java/jayatanaag.jar
yes
checking whether -Xrs is supported...
Picked up JAVA_TOOL_OPTIONS: -javaagent:/usr/share/java/jayatanaag.jar
yes
checking whether JNI programs can be compiled...
configure: error: Cannot compile a simple JNI program. See config.log for details.
Make sure you have Java Development Kit installed and correctly registered in R.
If in doubt, re-run "R CMD javareconf" as root.
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/dave/R/i686-pc-linux-gnu-library/3.1/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmp86RnJ1/downloaded_packages’
of course before ask this question i found similar questions on this site, but given advices didn't help me
i used this
sudo apt-get build-dep libxml2-dev
sudo apt-get install r-cran-rjava
what i should do to install needed packages. This problem concern and other packages like jgr,deducer,rweka
While installing R i am getting the following error...
[root#bivm R-2.15.2]# ./configure
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking for working aclocal... missing
checking for working autoconf... missing
checking for working automake... missing
checking for working autoheader... missing
checking for gawk... gawk
checking whether ln -s works... yes
checking for bison... no
checking for byacc... no
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... /bin/gtar
checking for tex... no
checking for pdftex... no
configure: WARNING: you cannot build PDF versions of the R manuals
checking for pdflatex... no
configure: WARNING: you cannot build PDF versions of vignettes and help pages
checking for makeindex... no
checking for makeinfo... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... no
checking for kpsewhich... no
checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /usr/bin/gzip
checking for bzip2... /usr/bin/bzip2
checking for firefox... /usr/bin/firefox
using default browser ... /usr/bin/firefox
checking for acroread... no
checking for acroread4... no
checking for xdg-open... no
checking for evince... /usr/bin/evince
checking for notangle... false
checking for pkg-config... /usr/bin/pkg-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc needs -traditional... no
checking how to run the C preprocessor... gcc -E
checking for gfortran... no
checking for f95... no
checking for fort... no
checking for xlf95... no
checking for ifort... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for gfortran... no
checking for ftn... no
checking for g95... no
checking for f90... no
checking for xlf90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for g77... no
checking for f77... no
checking for xlf... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for fc... no
configure: error: No F77 compiler found
I installed gcc compiler.But still showing the same.
[root#bivm R-2.15.2]# gcc --version
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Any help is appreciated.
Thanks in advance.
You need to install gfortran, which is probably by default not part of the gcc package. You can have a look at what packages are fortran related:
yum search "*fortran*"
And find the package that contains gfortran, something like gcc4-gfortran, and install it.
I'm trying to install NS2.35 on fedora 17 using allinone package.
I'm new to linux environment and have already spent many hours trying this. So far I've found out it is a problem with dependent packages. But I'm not able to figure out following error.
Please help.
===========================================================
* Build Tclcl-1.20
============================================================
No .configure file found in current directory
Continuing with default options...
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl.exe... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking for main in -lXbsd... no
checking for socket in -lsocket... no
checking for gethostbyname in -lnsl... yes
checking for dcgettext in -lintl... no
checking for getnodebyname in -ldnet_stub... no
checking that g++ can handle -O2... no
checking standard STL is available... no
checking for ranlib... ranlib
checking for snprintf... yes
checking for ANSI C header files... (cached) yes
checking for strtoq... yes
checking for strtoll... yes
checking size of long... 8
checking for strtol... yes
checking for __int64_t... no
checking for long long... yes
checking for int64_t... yes
checking which kind of 64-bit int to use... int64_t
checking for tcl.h... -I../include
checking for tclInt.h... -I../include
checking for libtcl8.5... -L../lib -ltcl8.5
checking for init.tcl... ../lib/tcl8.5
checking for http.tcl... ../lib/tcl8.5/http1.0
checking Tcl http.tcl library... yes
checking for tclsh8.5.10... no
checking for tclsh8.5... ../bin/tclsh8.5
checking for tk.h... -I../include
checking for libtk8.5... -L../lib -ltk8.5
checking for tk.tcl... ../lib/tk8.5
checking for otcl.h... -I../otcl-1.14
checking for libotcl1.14... -L../otcl-1.14 -lotcl
checking for X11 header files
checking for X11 library archive
checking for XOpenDisplay in -lX11... yes
checking for XShmAttach in -lXext... yes
checking for zlib.h... -I/usr/include
checking for libz1.1.3... no
No explicit static compilation flag; setting V_STATIC to ""
checking for dlopen in -ldl... yes
checking system version (for system-dependent libraries)... Linux-3.3.4-5.fc17.x86_64
checking for unistd.h... (cached) yes
checking for a BSD-compatible install... /usr/bin/install -c
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: config.h is unchanged
rm -f tcl2c++
g++ -o tcl2c++ tcl2c++.o
make: g++: Command not found
make: *** [tcl2c++] Error 127
tclcl-1.20 make failed! Exiting ...
See http://www.isi.edu/nsnam/ns/ns-problems.html for problems
Many many thanks
-Uday