I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor 1. Untar tar -zxvf R-2.3.0.tar.gz 2. changed the directory to the newly created directory R-2.3.0 3. Typed ./configure 4. Typed make 5. Copied the Script File R from directory R-2.3.0/bin/R to /usr/local/bin/R. 6. Typed R Fatal error: unable to open the base package I get the error message. Please advice [[alternative HTML version deleted]]
At step 5, don't copy the file. Instead, do: make install ---------------------------------------------------------------------- Andrew J Perrin - andrew_perrin (at) unc.edu - http://perrin.socsci.unc.edu Assistant Professor of Sociology; Book Review Editor, _Social Forces_ University of North Carolina - CB#3210, Chapel Hill, NC 27599-3210 USA New Book: http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/178592.ctl On Wed, 31 May 2006, Pramod Anugu wrote:> I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor > 1. Untar tar -zxvf R-2.3.0.tar.gz > 2. changed the directory to the newly created directory R-2.3.0 > 3. Typed ./configure > 4. Typed make > 5. Copied the Script File R from directory R-2.3.0/bin/R to > /usr/local/bin/R. > 6. Typed R > > Fatal error: unable to open the base package > I get the error message. Please advice > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >
On 05/31/06 09:25, Pramod Anugu wrote:> I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor > 1. Untar tar -zxvf R-2.3.0.tar.gz > 2. changed the directory to the newly created directory R-2.3.0 > 3. Typed ./configure > 4. Typed make > 5. Copied the Script File R from directory R-2.3.0/bin/R to > /usr/local/bin/R. > 6. Typed RThe instructions say that you should use make install unless you want to run R from the directory into which you unpacked it.> Fatal error: unable to open the base package > I get the error message. Please adviceIf you are using Fedora Core 5, the RPM works well. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron
It's always a good idea to do make check or even make check-all before make install. If the build does not pass the checks, there's no point in installing. (I've run into successful builds that failed the checks several times before.) Andy From: Pramod Anugu> > Still the same problem after changing the step 5 > I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor > 1. Untar tar -zxvf R-2.3.0.tar.gz > 2. changed the directory to the newly created directory R-2.3.0 > 3. Typed ./configure > 4. Typed make > 5. Typed make install > 6. Typed R > > Fatal error: unable to open the base package > I get the error message. Please advice > > -----Original Message----- > From: Andrew Perrin [mailto:clists at perrin.socsci.unc.edu] > Sent: Wednesday, May 31, 2006 9:33 AM > To: Pramod Anugu > Cc: r-help at stat.math.ethz.ch > Subject: Re: [R] Running R > > At step 5, don't copy the file. Instead, do: > > make install > > ---------------------------------------------------------------------- > Andrew J Perrin - andrew_perrin (at) unc.edu - > http://perrin.socsci.unc.edu > Assistant Professor of Sociology; Book Review Editor, _Social Forces_ > University of North Carolina - CB#3210, Chapel Hill, NC 27599-3210 USA > New Book: http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/178592.ctl > > > > On Wed, 31 May 2006, Pramod Anugu wrote: > > > I have downloaded R-2.3.0.tar.gz for Linux 64 bit processor > > 1. Untar tar -zxvf R-2.3.0.tar.gz > > 2. changed the directory to the newly created directory R-2.3.0 > > 3. Typed ./configure > > 4. Typed make > > 5. Copied the Script File R from directory R-2.3.0/bin/R to > > /usr/local/bin/R. > > 6. Typed R > > > > Fatal error: unable to open the base package > > I get the error message. Please advice > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help at stat.math.ethz.ch mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > >
Under the below seection it talks about X86_64 archetecture for Linux.
1. tar -zxvf R-2.3.0.tar.gz
2. changed the directory to the newly created directory R-2.3.0
3. Typed ./configure 'r_arch=name'
4. Typed make
5. Make check
6. make check-all
7. Typed make install
8. Typed R
I still get the same error message.
Fatal error: unable to open the base package
2.5 Sub-architectures
Some platforms can support closely related builds of R which can share all
but the executables and dynamic objects. Examples include builds under
Solaris for different chips (in particular, 32- and 64-bit builds), 64- and
32- bit builds on `x86_64' Linux and different CPUs (`ppc', `ppc64'
and
`i386') under MacOS 10.4.
R supports the idea of architecture-specific builds, specified by adding
`r_arch=name' to the configure line. Here name can be anything non-empty,
and is used to name subdirectories of lib, etc, include and libs. Example
names from other systems are the use of sparcv9 on Solaris and 32 by gcc on
`x86_64' Linux.
If you have two or more such builds you can install them over each other
(and one build can be done without `r_arch'). The space savings can be
considerable: on `x86_64' Linux a basic install (without debugging symbols)
took 63Mb, and adding a 32-bit build added 6Mb. If you have installed
multiple build you can select which build to run by
R --arch=name
and running `R' will run the last build that was installed.
R CMD INSTALL will detect if more that one build is installed and try to
install packages with the appropriate library objects for each. This will
not be done if the package has an executable configure script or a
src/Makefile file. In such cases you can install for extra builds by
R --arch=name CMD INSTALL --libs-only pkg(s)
-----------------------------------------------------
My Server Archeitecute is X86_64
-bash-2.05b# rpm -q --qf '%{ARCH}\n' zlib
x86_64
[[alternative HTML version deleted]]
1. tar -zxvf R-2.3.0.tar.gz 2. changed the directory to the newly created directory R-2.3.0 3. Typed ./configure 4. Typed make make: *** No targets specified and no makefile found. Stop. I cannot run make. Please let me know. #gcc -v Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.4/specs Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=x86_64-redhat-linux Thread model: posix gcc version 3.4.4 20050721 (Red Hat 3.4.4-2) *5. Make check *6. make check-all *7. Typed make install *8. Typed R [[alternative HTML version deleted]]
[root at genetics R-2.3.0]# ./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 working makeinfo... found
checking for gawk... gawk
checking for egrep... grep -E
checking whether ln -s works... yes
checking for ranlib... ranlib
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 less... /usr/bin/less
checking for perl... /usr/bin/perl
checking whether perl version is at least 5.004... yes
checking for dvips... /usr/bin/dvips
checking for tex... /usr/bin/tex
checking for latex... /usr/bin/latex
checking for makeindex... /usr/bin/makeindex
checking for pdftex... /usr/bin/pdftex
checking for pdflatex... /usr/bin/pdflatex
checking for makeinfo... /usr/bin/makeinfo
checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /bin/gzip
checking for firefox... /usr/bin/firefox
using default browser ... /usr/bin/firefox
checking for acroread... no
checking for acroread4... no
checking for xpdf... no
checking for gv... no
checking for gnome-gv... no
checking for ggv... /usr/bin/ggv
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 ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking whether gcc needs -traditional... no
checking how to run the C preprocessor... gcc -E
checking for g77... g77
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether g77 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 g77 accepts -fvisibility... yes
checking for a sed that does not truncate output... /bin/sed
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking how to recognise dependent libraries... pass_all
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 dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ranlib... (cached) ranlib
checking for strip... strip
checking if gcc static flag works... yes
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc supports -c -o file.o... 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
configure: creating libtool
appending configuration tag "CXX" to libtool
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
checking if g++ PIC flag -fPIC works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for g77 option to produce PIC... -fPIC
checking if g77 PIC flag -fPIC works... yes
checking if g77 supports -c -o file.o... yes
checking whether the g77 linker (/usr/bin/ld -m elf_x86_64) supports shared
libraries... yes
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 whether makeinfo version is at least 4.7... yes
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
--One suggestion was to install readline-devel. But according to the below I
already have readline-devel.
# find . -iname readline-devel\*
find -iname readline-devel\*
./os/4.1/x86_64/RedHat/RPMS/readline-devel-4.3-13.x86_64.rpm
#rpm -ivh readline*.rpm
Preparing... ###########################################
[100%]
package readline-4.3-13 is already installed
Once you've found an RPM, to install it on the frontend, just type
# rpm -ivh filename.rpm
-------------
1. tar -zxvf R-2.3.0.tar.gz
2. changed the directory to the newly created directory R-2.3.0
3. Typed ./configure
4. Typed make
make: *** No targets specified and no makefile found. Stop.
I cannot run make. Please let me know.
*5. Make check
*6. make check-all
*7. Typed make install
*8. Typed R
Thank you Andy for your suggestion. I used the method 2 and was able to go upto Step 8. But When I type R # R Fatal error: unable to open the base package ? 1.? Tell configure exactly where to find the readline header files (by something like --with-readline=/where/the/files/are, check configure --help). ? 2.? Compile R without readline; i.e., configure --with-readline=no. ? Andy ?? 1. gunzip R-patched.tar.gz 2. tar -xvf R-patched.tar ?? 3. changed the directory to the newly created directory R-patched ?? 4. Typed ./configure ? ?5. Typed make ?? 6. Make check ?? 7. make check-all ?? 8. Typed make install ?? *9. Typed R
Does any one have solution for R not running? I am getting the error message. Please Advice. Thanks ? ? 1. gunzip R-patched.tar.gz 2. tar -xvf R-patched.tar ?? 3. changed the directory to the newly created directory R-patched ?? 4. Typed ./configure ? ?5. Typed make ?? 6. Make check ?? 7. make check-all ?? 8. Typed make install ?? *9. Typed R # R Fatal error: unable to open the base package
Have you checked and see if there is any error in steps 5 through 8? If you can't start R, I doubt steps 6 and 7 ran fine. Andy From: Pramod Anugu> > Does any one have solution for R not running? I am getting > the error message. Please Advice. > Thanks > > ? > ? 1. gunzip R-patched.tar.gz > 2. tar -xvf R-patched.tar > ?? 3. changed the directory to the newly created directory R-patched > ?? 4. Typed ./configure > ? ?5. Typed make > ?? 6. Make check > ?? 7. make check-all > ?? 8. Typed make install > ?? *9. Typed R > # R > Fatal error: unable to open the base package > >
Just for the record. (One of the) problem was that configure picked up ATLAS, but had problem with it at link time for whatever reason. (This is on some version of Redhat, x86_64. I should think there are people who have similar setup and got both ATLAS and readline to work.) Andy> From: Pramod Anugu > > IT WORKS!!! > Thanks you very much for your help. So the below line fixed > my installation > > #./configure --with-blas=no --with-readline=no > >